From f334b6beb2e36d56b6074fe3b1130a1f0bc74e37 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 26 Feb 2025 17:21:50 +0100
Subject: [PATCH 01/72] Change 'var' for 'data' in VizEquiMap.R

---
 R/VizEquiMap.R | 164 ++++++++++++++++++++++++-------------------------
 1 file changed, 82 insertions(+), 82 deletions(-)

diff --git a/R/VizEquiMap.R b/R/VizEquiMap.R
index 2633ceb..e13211b 100644
--- a/R/VizEquiMap.R
+++ b/R/VizEquiMap.R
@@ -10,7 +10,7 @@
 #'include continents, oceans, and lakes. This plot function is compatible with
 #'figure layouts if colour bar is disabled.
 #'
-#'@param var Array with the values at each cell of a grid on a regular 
+#'@param data Array with the values at each cell of a grid on a regular 
 #'  rectangular or gaussian grid. The array is expected to have two 
 #'  dimensions: c(latitude, longitude). Longitudes can be in ascending or 
 #'  descending order and latitudes in any order. It can contain NA values 
@@ -20,37 +20,37 @@
 #'  the positions of the longitudinal and latitudinal coordinate dimensions 
 #'  are interchanged.
 #'@param lon Numeric vector of longitude locations of the cell centers of the 
-#'  grid of 'var', in ascending or descending order (same as 'var'). Expected 
+#'  grid of 'data', in ascending or descending order (same as 'data'). Expected 
 #'  to be regularly spaced, within either of the ranges [-180, 180] or 
 #'  [0, 360]. Data for two adjacent regions split by the limits of the 
 #'  longitude range can also be provided, e.g. \code{lon = c(0:50, 300:360)} 
-#'  ('var' must be provided consitently).
+#'  ('data' must be provided consitently).
 #'@param lat Numeric vector of latitude locations of the cell centers of the 
-#'  grid of 'var', in any order (same as 'var'). Expected to be from a regular 
+#'  grid of 'data', in any order (same as 'data'). Expected to be from a regular 
 #'  rectangular or gaussian grid, within the range [-90, 90].
 #'@param varu Array of the zonal component of wind/current/other field with 
-#'  the same dimensions as 'var'. It is allowed that the positions of the 
+#'  the same dimensions as 'data'. It is allowed that the positions of the 
 #'  longitudinal and latitudinal coordinate dimensions are interchanged.
 #'@param varv Array of the meridional component of wind/current/other field 
-#'  with the same dimensions as 'var'. It is allowed that the positions of the 
+#'  with the same dimensions as 'data'. It is allowed that the positions of the 
 #'  longitudinal and latitudinal coordinate dimensions are interchanged.
 #'@param toptitle Top title of the figure, scalable with parameter 
 #'  'title_scale'.
 #'@param sizetit Scale factor for the figure top title provided in parameter 
 #'  'toptitle'. Deprecated. Use 'title_scale' instead.
 #'@param units Title at the top of the colour bar, most commonly the units of 
-#'  the variable provided in parameter 'var'.
+#'  the variable provided in parameter 'data'.
 #'@param brks,cols,bar_limits,triangle_ends Usually only providing 'brks' is 
 #'  enough to generate the desired colour bar. These parameters allow to 
 #'  define n breaks that define n - 1 intervals to classify each of the values 
-#'  in 'var'. The corresponding grid cell of a given value in 'var' will be 
+#'  in 'data'. The corresponding grid cell of a given value in 'data' will be 
 #'  coloured in function of the interval it belongs to. These parameters are 
 #'  sent to \code{ColorBar()} to generate the breaks and colours. Additional 
 #'  colours for values beyond the limits of the colour bar are also generated 
 #'  and applied to the plot if 'bar_limits' or 'brks' and 'triangle_ends' are 
 #'  properly provided to do so. See ?ColorBar for a full explanation.
 #'@param col_inf,col_sup,colNA Colour identifiers to colour the values in 
-#'  'var' that go beyond the extremes of the colour bar and to colour NA 
+#'  'data' that go beyond the extremes of the colour bar and to colour NA 
 #'  values, respectively. 'colNA' takes attr(cols, 'na_color') if available by 
 #'  default, where cols is the parameter 'cols' if provided or the vector of 
 #'  colors returned by 'color_fun'. If not available, it takes 'pink' by 
@@ -66,7 +66,7 @@
 #'  parameters to control the visual aspect of the drawn colour bar (3/3). 
 #'  See ?ColorBar for a full explanation.
 #'@param square Logical value to choose either to draw a coloured square for 
-#'  each grid cell in 'var' (TRUE; default) or to draw contour lines and fill 
+#'  each grid cell in 'data' (TRUE; default) or to draw contour lines and fill 
 #'  the spaces in between with colours (FALSE). In the latter case, 
 #'  'filled.continents' will take the value FALSE if not specified.
 #'@param filled.continents Colour to fill in drawn projected continents. 
@@ -90,7 +90,7 @@
 #'  location of the shape. The default value is NULL.
 #'@param shapefile_color Line color of the shapefile.
 #'@param shapefile_lwd Line width of the shapefile. The default value is 1. 
-#'@param contours Array of same dimensions as 'var' to be added to the plot 
+#'@param contours Array of same dimensions as 'data' to be added to the plot 
 #'  and displayed with contours. Parameter 'brks2' is required to define the 
 #'  magnitude breaks for each contour curve. Disregarded if 'square = FALSE'.
 #'  It is allowed that the positions of the longitudinal and latitudinal 
@@ -107,8 +107,8 @@
 #'  contour labels or not. The default value is TRUE.
 #'@param contour_label_scale Scale factor for the superimposed labels when 
 #'  drawing contour levels.
-#'@param dots Array of same dimensions as 'var' or with dimensions 
-#'  c(n, dim(var)), where n is the number of dot/symbol layers to add to the 
+#'@param dots Array of same dimensions as 'data' or with dimensions 
+#'  c(n, dim(data)), where n is the number of dot/symbol layers to add to the 
 #'  plot. A value of TRUE at a grid cell will draw a dot/symbol on the 
 #'  corresponding square of the plot. By default all layers provided in 'dots' 
 #'  are plotted with dots, but a symbol can be specified for each of the 
@@ -122,7 +122,7 @@
 #'@param dot_size Scale factor for the dots/symbols to be plotted, specified 
 #'  in 'dots'. If a single value is specified, it will be applied to all 
 #'  layers in 'dots'. Takes 1 by default.
-#'@param mask An array with the same dimensions as 'var' of [0, 1] or logical
+#'@param mask An array with the same dimensions as 'data' of [0, 1] or logical
 #'  indicating the grids to not plot data. The value 0 or FALSE is the point not
 #'  to be plotted.
 #'@param mask_color Color of the mask. The default value is 'white'.
@@ -236,11 +236,11 @@
 #'  \dontrun{
 #'ano <- s2dv::Ano_CrossValid(map_temp$exp, map_temp$obs, memb = FALSE,
 #'                            dat_dim = c('dat', 'member'), memb_dim = 'member')
-#'var <- s2dv::MeanDims(ano$exp, "member")
+#'data <- s2dv::MeanDims(ano$exp, "member")
 #'lats <- attr(map_temp$exp, "Variables")$common$lat
 #'lons <- attr(map_temp$exp, "Variables")$common$lon
 #'
-#'VizEquiMap(var[1, 1, 1, 1, , ], lon = lons, lat = lats,
+#'VizEquiMap(data[1, 1, 1, 1, , ], lon = lons, lat = lats,
 #'           toptitle = 'Near-surface temperature anomaly, Nov. 2000',
 #'           filled.continents = FALSE, title_scale = 0.7)
 #'  }
@@ -249,7 +249,7 @@
 #'@importFrom stats cor
 #' @importFrom s2dv InsertDim
 #'@export
-VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
+VizEquiMap <- function(data, lon, lat, varu = NULL, varv = NULL,
                         toptitle = NULL, sizetit = NULL, units = NULL, 
                         brks = NULL, cols = NULL, bar_limits = NULL, 
                         triangle_ends = NULL, col_inf = NULL, col_sup = NULL, 
@@ -301,59 +301,59 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
     stop("Parameters 'lon' and 'lat' must be numeric vectors.")
   }
 
-  # Check var
-  if (is.null(var)) {
-    stop("Parameter 'var' cannot be NULL.")
+  # Check data
+  if (is.null(data)) {
+    stop("Parameter 'data' cannot be NULL.")
   }
-  if (!is.array(var)) {
-    stop("Parameter 'var' must be a numeric array.")
+  if (!is.array(data)) {
+    stop("Parameter 'data' must be a numeric array.")
   }
 
   transpose <- FALSE
-  if (!is.null(names(dim(var)))) {
-    if (any(names(dim(var)) %in% .KnownLonNames()) &&
-        any(names(dim(var)) %in% .KnownLatNames())) {
-      lon_dim <- names(dim(var))[names(dim(var)) %in% .KnownLonNames()]
-      lat_dim <- names(dim(var))[names(dim(var)) %in% .KnownLatNames()]
+  if (!is.null(names(dim(data)))) {
+    if (any(names(dim(data)) %in% .KnownLonNames()) &&
+        any(names(dim(data)) %in% .KnownLatNames())) {
+      lon_dim <- names(dim(data))[names(dim(data)) %in% .KnownLonNames()]
+      lat_dim <- names(dim(data))[names(dim(data)) %in% .KnownLatNames()]
     } else {
-      names(dim(var)) <- NULL
+      names(dim(data)) <- NULL
       lat_dim <- NULL
       lon_dim <- NULL
-      warning("Dimension names of 'var' doesn't correspond to any coordinates names supported by s2dv package.")
+      warning("Dimension names of 'data' doesn't correspond to any coordinates names supported by s2dv package.")
     }
   } else {
     lon_dim <- NULL
     lat_dim <- NULL
-    warning("Parameter 'var' should have dimension names. Coordinates 'lon' and 'lat' have been assigned into the corresponding coordinates dimensions.")
+    warning("Parameter 'data' should have dimension names. Coordinates 'lon' and 'lat' have been assigned into the corresponding coordinates dimensions.")
   }
 
-  if (length(dim(var)) > 2) {
+  if (length(dim(data)) > 2) {
     if (!is.null(lon_dim) & !is.null(lat_dim)) {
-      dimnames <- names(dim(var))
-      dim(var) <- dim(var)[which((dimnames == lon_dim | dimnames == lat_dim | dim(var) != 1))]
+      dimnames <- names(dim(data))
+      dim(data) <- dim(data)[which((dimnames == lon_dim | dimnames == lat_dim | dim(data) != 1))]
     } else {
-      if (all(dim(var) == 1)) {
-        dim(var) <- c(1, 1)
-      } else if (length(dim(var)[which(dim(var) > 1)]) == 2) {
-        var <- drop(var)
-      } else if (length(dim(var)[which(dim(var) > 1)]) == 1) {
-        dim(var) <- c(dim(var)[which(dim(var) > 1)], 1)
+      if (all(dim(data) == 1)) {
+        dim(data) <- c(1, 1)
+      } else if (length(dim(data)[which(dim(data) > 1)]) == 2) {
+        data <- drop(data)
+      } else if (length(dim(data)[which(dim(data) > 1)]) == 1) {
+        dim(data) <- c(dim(data)[which(dim(data) > 1)], 1)
       }
     }
   }
 
-  if (length(dim(var)) != 2) {
-    stop("Parameter 'var' must be a numeric array with two dimensions.")
+  if (length(dim(data)) != 2) {
+    stop("Parameter 'data' must be a numeric array with two dimensions.")
   }
 
-  if ((dim(var)[1] == length(lon) && dim(var)[2] == length(lat)) ||
-      (dim(var)[2] == length(lon) && dim(var)[1] == length(lat))) {
-    if (dim(var)[2] == length(lon) && dim(var)[1] == length(lat)) {
+  if ((dim(data)[1] == length(lon) && dim(data)[2] == length(lat)) ||
+      (dim(data)[2] == length(lon) && dim(data)[1] == length(lat))) {
+    if (dim(data)[2] == length(lon) && dim(data)[1] == length(lat)) {
       if (length(lon) == length(lat)) {
-        if (is.null(names(dim(var)))) {
-          warning("Parameter 'var' should have dimension names. Coordinates 'lon' and 'lat' have been assigned into the first and second dimensions.")
+        if (is.null(names(dim(data)))) {
+          warning("Parameter 'data' should have dimension names. Coordinates 'lon' and 'lat' have been assigned into the first and second dimensions.")
         } else {
-          if (names(dim(var)[1]) == lat_dim) {
+          if (names(dim(data)[1]) == lat_dim) {
             transpose <- TRUE
           }
         }
@@ -362,17 +362,17 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
       }   
     }
   } else {
-    stop("Parameters 'lon' and 'lat' must have as many elements as the number of cells along longitudes and latitudes in the input array 'var'.")
+    stop("Parameters 'lon' and 'lat' must have as many elements as the number of cells along longitudes and latitudes in the input array 'data'.")
   }
 
-  if (!is.null(names(dim(var)))) {
-    if (names(dim(var)[1]) == lon_dim) {
+  if (!is.null(names(dim(data)))) {
+    if (names(dim(data)[1]) == lon_dim) {
       if (transpose) {
-        stop("Coordinates dimensions of 'var' doesn't correspond to lat or lon.")
+        stop("Coordinates dimensions of 'data' doesn't correspond to lat or lon.")
       }
-    } else if (names(dim(var)[2]) == lon_dim) {
+    } else if (names(dim(data)[2]) == lon_dim) {
       if (!transpose) {
-        stop("Coordinates dimensions of 'var' doesn't correspond to lat or lon.")
+        stop("Coordinates dimensions of 'data' doesn't correspond to lat or lon.")
       }
     }
   }
@@ -381,13 +381,13 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
   # with dimensions c(lon, lat).
 
   if (transpose) {
-    var <- t(var)
+    data <- t(data)
   }
 
   transpose <- FALSE
 
-  names(dim(var)) <- c(lon_dim, lat_dim)
-  dims <- dim(var)
+  names(dim(data)) <- c(lon_dim, lat_dim)
+  dims <- dim(data)
 
   # Check varu and varv
   if (!is.null(varu) && !is.null(varv)) {
@@ -415,9 +415,9 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
     } else {
       if (!is.null(names(dim(varu)))) {
         if (!(lon_dim %in% names(dim(varu)) && lat_dim %in% names(dim(varu)))) {
-          stop("Parameters 'varu' and 'varv' must have same dimension names as 'var'.")
-        } else if (dim(varu)[lon_dim] != dim(var)[lon_dim] || dim(varu)[lat_dim] != dim(var)[lat_dim]) {
-          stop("Parameters 'varu' and 'varv' must have same dimensions as 'var'.")
+          stop("Parameters 'varu' and 'varv' must have same dimension names as 'data'.")
+        } else if (dim(varu)[lon_dim] != dim(data)[lon_dim] || dim(varu)[lat_dim] != dim(data)[lat_dim]) {
+          stop("Parameters 'varu' and 'varv' must have same dimensions as 'data'.")
         }
       } else {
         warning("Parameters 'varu' and 'varv' should have dimension names. Coordinates 'lon' and 'lat' have been assigned into the corresponding coordinates dimensions.")
@@ -468,9 +468,9 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
     } else {
       if (!is.null(names(dim(contours)))) {
         if (!(lon_dim %in% names(dim(contours)) && lat_dim %in% names(dim(contours)))) {
-          stop("Parameters 'contours' must have same dimension names as 'var'.")
-        } else if (dim(contours)[lon_dim] != dim(var)[lon_dim] || dim(contours)[lat_dim] != dim(var)[lat_dim]) {
-          stop("Parameters 'contours' must have same dimensions as 'var'.")
+          stop("Parameters 'contours' must have same dimension names as 'data'.")
+        } else if (dim(contours)[lon_dim] != dim(data)[lon_dim] || dim(contours)[lat_dim] != dim(data)[lat_dim]) {
+          stop("Parameters 'contours' must have same dimensions as 'data'.")
         }
       } else {
         warning("Parameters 'contours' should have dimension names. Coordinates 'lon' and 'lat' have been assigned into the corresponding coordinates dimensions.")
@@ -531,7 +531,7 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
     stop("Parameter 'include_upper_boundary' must be a logical element.")
   }    
 
-  tmp <- .create_var_limits(data = var, brks = brks, 
+  tmp <- .create_var_limits(data = data, brks = brks, 
                             bar_limits = bar_limits, drawleg = drawleg)
   var_limits <- tmp$var_limits
   drawleg <- tmp$drawleg
@@ -554,14 +554,14 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
   col_sup <- colorbar$col_sup
   bar_limits <- c(head(brks, 1), tail(brks, 1))
 
-  # Adjust 'var' values according to 'include_lower_boundary' and 'include_upper_boundary'.
+  # Adjust 'data' values according to 'include_lower_boundary' and 'include_upper_boundary'.
   # This adjustment ensures that, by default, values at the lower limit of the color bars ('brks[1]') are included. 
   # Refer to issue #15 in the esviz GitLab for more details.
   if (include_lower_boundary) {
-    var[var == head(brks, 1)] <- head(brks, 1) + head(diff(brks), 1)/10
+    data[data == head(brks, 1)] <- head(brks, 1) + head(diff(brks), 1)/10
   }
   if (!include_upper_boundary) {
-    var[var == tail(brks, 1)] <- tail(brks, 1) + tail(diff(brks), 1)/10
+    data[data == tail(brks, 1)] <- tail(brks, 1) + tail(diff(brks), 1)/10
   }  
 
   # Check colNA
@@ -690,7 +690,7 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
     if (is.null(contours)) { 
       if (!square) {
         brks2 <- brks
-        contours <- var 
+        contours <- data 
       }
     } else {
       ll <- signif(min(contours, na.rm = TRUE), 2)
@@ -738,9 +738,9 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
     } else {
       if (!is.null(names(dim(dots)))) {
         if (!(lon_dim %in% names(dim(dots)) && lat_dim %in% names(dim(dots)))) {
-          stop("Parameters 'dots' must have same dimension names as 'var'.")
-        } else if (dim(dots)[lon_dim] != dim(var)[lon_dim] || dim(dots)[lat_dim] != dim(var)[lat_dim]) {
-          stop("Parameters 'dots' must have same dimensions as 'var'.")
+          stop("Parameters 'dots' must have same dimension names as 'data'.")
+        } else if (dim(dots)[lon_dim] != dim(data)[lon_dim] || dim(dots)[lat_dim] != dim(data)[lat_dim]) {
+          stop("Parameters 'dots' must have same dimensions as 'data'.")
         }
       } else {
         warning("Parameters 'dots' should have dimension names. Coordinates 'lon' and 'lat' have been assigned into the corresponding coordinates dimensions.")
@@ -764,7 +764,7 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
         }
       }
     } else {
-      stop("Parameter 'dots' must have same number of longitudes and latitudes as 'var'.")
+      stop("Parameter 'dots' must have same number of longitudes and latitudes as 'data'.")
     }
 
     if (transpose) {
@@ -799,14 +799,14 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
   if (!is.null(mask)) {
     mask <- drop(mask)
     if (!is.array(mask) || any(!names(dim(mask)) %in% c(lon_dim, lat_dim))) {
-      stop("Parameter 'mask' must have two dimensions named as the longitude and latitude dimensions in 'var'.")
+      stop("Parameter 'mask' must have two dimensions named as the longitude and latitude dimensions in 'data'.")
     } else {
-      if (!identical(names(dim(mask)), names(dim(var)))) {
-        mask <- aperm(mask, match(names(dim(mask)), names(dim(var))))
+      if (!identical(names(dim(mask)), names(dim(data)))) {
+        mask <- aperm(mask, match(names(dim(mask)), names(dim(data))))
       }
     }
-    if (!identical(dim(mask), dim(var))) {
-      stop("Parameter 'mask' must have the same dimensions as 'var'.")
+    if (!identical(dim(mask), dim(data))) {
+      stop("Parameter 'mask' must have the same dimensions as 'data'.")
     } else if (is.numeric(mask)) {
       if (all(mask %in% c(0, 1))) {
         mask <- array(as.logical(mask), dim = dim(mask))
@@ -1124,18 +1124,18 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
     # If lat and lon are both regular-spaced, "useRaster = TRUE" can avoid
     # artifact white lines on the figure. If not, useRaster has to be FALSE (default)
     tryCatch({
-      image(lonb$x, latb$x, var[lonb$ix, latb$ix], 
+      image(lonb$x, latb$x, data[lonb$ix, latb$ix], 
             col = c(col_inf_image, cols, col_sup_image), 
             breaks = c(-.Machine$double.xmax, brks, .Machine$double.xmax),
             axes = FALSE, xlab = "", ylab = "", add = TRUE, useRaster = TRUE)
     }, error = function(x) {
-      image(lonb$x, latb$x, var[lonb$ix, latb$ix], 
+      image(lonb$x, latb$x, data[lonb$ix, latb$ix], 
             col = c(col_inf_image, cols, col_sup_image), 
             breaks = c(-.Machine$double.xmax, brks, .Machine$double.xmax),
             axes = FALSE, xlab = "", ylab = "", add = TRUE)
     })
   } else {
-    .filled.contour(lonb$x, latb$x, var[lonb$ix, latb$ix], 
+    .filled.contour(lonb$x, latb$x, data[lonb$ix, latb$ix], 
                     levels = c(.Machine$double.xmin, brks, .Machine$double.xmax), 
                     col = c(col_inf_image, cols, col_sup_image))
   }
@@ -1157,13 +1157,13 @@ VizEquiMap <- function(var, lon, lat, varu = NULL, varv = NULL,
   # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   #
   if (!is.null(dots)) {
-    data_avail <- !is.na(var)
+    data_avail <- !is.na(data)
     for (counter in 1:(dim(dots)[1])) {
       points <- which(dots[counter, , ] & data_avail, arr.ind = TRUE)
       points(lon[points[, 1]], lat[points[, 2]], 
              pch = dot_symbol[counter], 
-             cex = dot_size[counter] * 3 / sqrt(sqrt(length(var))),
-             lwd = dot_size[counter] * 3 / sqrt(sqrt(length(var))))
+             cex = dot_size[counter] * 3 / sqrt(sqrt(length(data))),
+             lwd = dot_size[counter] * 3 / sqrt(sqrt(length(data))))
     }
   }
   
-- 
GitLab


From 2bd969c5bc6ddd478a0e29f2798f5bbf9201e503 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 27 Feb 2025 10:10:54 +0100
Subject: [PATCH 02/72] Change 'var' for 'data' in VizStereoMap.R

---
 R/VizStereoMap.R | 76 ++++++++++++++++++++++++------------------------
 1 file changed, 38 insertions(+), 38 deletions(-)

diff --git a/R/VizStereoMap.R b/R/VizStereoMap.R
index 047c545..5b30fab 100644
--- a/R/VizStereoMap.R
+++ b/R/VizStereoMap.R
@@ -8,7 +8,7 @@
 #'adjust the position, size and colour of the components. This plot function is 
 #'compatible with figure layouts if colour bar is disabled.
 #'
-#'@param var Array with the values at each cell of a grid on a regular 
+#'@param data Array with the values at each cell of a grid on a regular 
 #'  rectangular or gaussian grid. The array is expected to have two dimensions: 
 #'  c(latitude, longitude). Longitudes can be in ascending or descending order 
 #'  and latitudes in any order. It can contain NA values (coloured with 
@@ -16,18 +16,18 @@
 #'  accepted but 'lon' and 'lat' will be used to disambiguate so this 
 #'  alternative is not appropriate for square arrays.
 #'@param lon Numeric vector of longitude locations of the cell centers of the 
-#'  grid of 'var', in ascending or descending order (same as 'var'). Expected 
+#'  grid of 'data', in ascending or descending order (same as 'data'). Expected 
 #'  to be regularly spaced, within either of the ranges [-180, 180] or 
 #'  [0, 360]. Data for two adjacent regions split by the limits of the 
 #'  longitude range can also be provided, e.g. \code{lon = c(0:50, 300:360)} 
-#'  ('var' must be provided consitently).
+#'  ('data' must be provided consitently).
 #'@param lat Numeric vector of latitude locations of the cell centers of the 
-#'  grid of 'var', in any order (same as 'var'). Expected to be from a regular 
+#'  grid of 'data', in any order (same as 'data'). Expected to be from a regular 
 #'  rectangular or gaussian grid, within the range [-90, 90].
 #'@param varu Array of the zonal component of wind/current/other field with 
-#'  the same dimensions as 'var'.
+#'  the same dimensions as 'data'.
 #'@param varv Array of the meridional component of wind/current/other field 
-#'  with the same dimensions as 'var'.
+#'  with the same dimensions as 'data'.
 #'@param latlims Latitudinal limits of the figure.\cr
 #'  Example : c(60, 90) for the North Pole\cr
 #'            c(-90,-60) for the South Pole
@@ -36,18 +36,18 @@
 #'@param sizetit Scale factor for the figure top title provided in parameter 
 #'  'toptitle'. Deprecated. Use 'title_scale' instead.
 #'@param units Title at the top of the colour bar, most commonly the units of 
-#'  the variable provided in parameter 'var'.
+#'  the variable provided in parameter 'data'.
 #'@param brks,cols,bar_limits,triangle_ends Usually only providing 'brks' is 
 #'  enough to generate the desired colour bar. These parameters allow to 
 #'  define n breaks that define n - 1 intervals to classify each of the values 
-#'  in 'var'. The corresponding grid cell of a given value in 'var' will be 
+#'  in 'data'. The corresponding grid cell of a given value in 'data' will be 
 #'  coloured in function of the interval it belongs to. These parameters are 
 #'  sent to \code{ColorBarContinuous()} to generate the breaks and colours. Additional 
 #'  colours for values beyond the limits of the colour bar are also generated 
 #'  and applied to the plot if 'bar_limits' or 'brks' and 'triangle_ends' are 
 #'  properly provided to do so. See ?ColorBarContinuous for a full explanation.
 #'@param col_inf,col_sup,colNA Colour identifiers to colour the values in 
-#'  'var' that go beyond the extremes of the colour bar and to colour NA 
+#'  'data' that go beyond the extremes of the colour bar and to colour NA 
 #'  values, respectively. 'colNA' takes attr(cols, 'na_color') if available by 
 #'  default, where cols is the parameter 'cols' if provided or the vector of 
 #'  colors returned by 'color_fun'. If not available, it takes 'pink' by 
@@ -62,7 +62,7 @@
 #'  continents. Takes the value gray(0.5) by default.
 #'@param coast_width Line width of the coast line of the drawn projected 
 #'  continents. Takes the value 1 by default.
-#'@param contours Array of same dimensions as 'var' to be added to the plot 
+#'@param contours Array of same dimensions as 'data' to be added to the plot 
 #'  and displayed with contours. Parameter 'brks2' is required to define the 
 #'  magnitude breaks for each contour curve.
 #'@param brks2 A numeric value or vector of magnitude breaks where to draw 
@@ -80,8 +80,8 @@
 #'  value is TRUE.
 #'@param contour_label_scale Scale factor for the superimposed labels when 
 #'  drawing contour levels. The default value is 0.6.
-#'@param dots Array of same dimensions as 'var' or with dimensions 
-#'  c(n, dim(var)), where n is the number of dot/symbol layers to add to the 
+#'@param dots Array of same dimensions as 'data' or with dimensions 
+#'  c(n, dim(data)), where n is the number of dot/symbol layers to add to the 
 #'  plot. A value of TRUE at a grid cell will draw a dot/symbol on the 
 #'  corresponding square of the plot. By default all layers provided in 'dots' 
 #'  are plotted with dots, but a symbol can be specified for each of the 
@@ -177,7 +177,7 @@
 #'@importFrom stats median
 #' @importFrom s2dv InsertDim
 #'@export
-VizStereoMap <- function(var, lon, lat, varu = NULL, varv = NULL, latlims = c(60, 90), 
+VizStereoMap <- function(data, lon, lat, varu = NULL, varv = NULL, latlims = c(60, 90), 
                           toptitle = NULL, sizetit = NULL, units = NULL, 
                           brks = NULL, cols = NULL, bar_limits = NULL, 
                           triangle_ends = NULL, col_inf = NULL, col_sup = NULL,
@@ -229,20 +229,20 @@ VizStereoMap <- function(var, lon, lat, varu = NULL, varv = NULL, latlims = c(60
     stop("Parameters 'lon' and 'lat' must be numeric vectors.")
   }
 
-  # Check var
-  if (!is.array(var)) {
-    stop("Parameter 'var' must be a numeric array.")
+  # Check data
+  if (!is.array(data)) {
+    stop("Parameter 'data' must be a numeric array.")
   }
-  if (length(dim(var)) > 2) {
-    var <- drop(var)
-    dim(var) <- head(c(dim(var), 1, 1), 2)
+  if (length(dim(data)) > 2) {
+    data <- drop(data)
+    dim(data) <- head(c(dim(data), 1, 1), 2)
   }
-  if (length(dim(var)) > 2) {
-    stop("Parameter 'var' must be a numeric array with two dimensions. See PlotMultiMap() for multi-pannel maps or AnimateMap() for animated maps.")
-  } else if (length(dim(var)) < 2) {
-    stop("Parameter 'var' must be a numeric array with two dimensions.")
+  if (length(dim(data)) > 2) {
+    stop("Parameter 'data' must be a numeric array with two dimensions. See PlotMultiMap() for multi-pannel maps or AnimateMap() for animated maps.")
+  } else if (length(dim(data)) < 2) {
+    stop("Parameter 'data' must be a numeric array with two dimensions.")
   }
-  dims <- dim(var)
+  dims <- dim(data)
 
   # Check varu and varv
   if (!is.null(varu) && !is.null(varv)) {
@@ -258,10 +258,10 @@ VizStereoMap <- function(var, lon, lat, varu = NULL, varv = NULL, latlims = c(60
 
   if (!is.null(varu) && !is.null(varv)) {
     if (dim(varu)[1] != dims[1] || dim(varu)[2] != dims[2]) {
-      stop("Parameter 'varu' must have same number of longitudes and latitudes as 'var'.")
+      stop("Parameter 'varu' must have same number of longitudes and latitudes as 'data'.")
     }
     if (dim(varv)[1] != dims[1] || dim(varv)[2] != dims[2]) {
-      stop("Parameter 'varv' must have same number of longitudes and latitudes as 'var'.")
+      stop("Parameter 'varv' must have same number of longitudes and latitudes as 'data'.")
     }
   }
 
@@ -269,22 +269,22 @@ VizStereoMap <- function(var, lon, lat, varu = NULL, varv = NULL, latlims = c(60
   # with dimensions c(lon, lat).
   if (dims[1] != length(lon) || dims[2] != length(lat)) {
     if (dims[1] == length(lat) && dims[2] == length(lon)) {
-      var <- t(var)
+      data <- t(data)
       if (!is.null(varu)) varu <- t(varu)
       if (!is.null(varv)) varv <- t(varv)
       if (!is.null(dots)) dots <- aperm(dots, c(1, 3, 2))
-      dims <- dim(var)
+      dims <- dim(data)
     }
   }
 
   # Check lon
   if (length(lon) != dims[1]) {
-    stop("Parameter 'lon' must have as many elements as the number of cells along longitudes in the input array 'var'.")
+    stop("Parameter 'lon' must have as many elements as the number of cells along longitudes in the input array 'data'.")
   }
 
   # Check lat
   if (length(lat) != dims[2]) {
-    stop("Parameter 'lat' must have as many elements as the number of cells along longitudes in the input array 'var'.")
+    stop("Parameter 'lat' must have as many elements as the number of cells along longitudes in the input array 'data'.")
   }
 
   # Prepare sorted lon/lat and other arguments
@@ -331,7 +331,7 @@ VizStereoMap <- function(var, lon, lat, varu = NULL, varv = NULL, latlims = c(60
     title_scale <- sizetit
   }
 
-  tmp <- .create_var_limits(data = var, brks = brks, 
+  tmp <- .create_var_limits(data = data, brks = brks, 
                             bar_limits = bar_limits, drawleg = drawleg)
   var_limits <- tmp$var_limits
   drawleg <- tmp$drawleg
@@ -413,7 +413,7 @@ VizStereoMap <- function(var, lon, lat, varu = NULL, varv = NULL, latlims = c(60
     if (dim(contours)[1] == dims[2] & dim(contours)[2] == dims[1]) {
       contours <- t(contours)
     } else {
-      stop("Parameter 'contours' must have the same number of longitudes and latitudes as 'var'.")
+      stop("Parameter 'contours' must have the same number of longitudes and latitudes as 'data'.")
     }
   }
 
@@ -461,7 +461,7 @@ VizStereoMap <- function(var, lon, lat, varu = NULL, varv = NULL, latlims = c(60
   # Check dots, dot_symbol and dot_size
   if (!is.null(dots)) {
     if (dim(dots)[2] != dims[1] || dim(dots)[3] != dims[2]) {
-      stop("Parameter 'dots' must have the same number of longitudes and latitudes as 'var'.")
+      stop("Parameter 'dots' must have the same number of longitudes and latitudes as 'data'.")
     }
     if (!is.numeric(dot_symbol) && !is.character(dot_symbol)) {
       stop("Parameter 'dot_symbol' must be a numeric or character string vector.")
@@ -642,14 +642,14 @@ VizStereoMap <- function(var, lon, lat, varu = NULL, varv = NULL, latlims = c(60
                                      lon[jx] + dlon, lon[jx] - dlon),
                                    c(lat[lat_plot_ind][jy] - dlat, lat[lat_plot_ind][jy] - dlat,
                                      lat[lat_plot_ind][jy] + dlat, lat[lat_plot_ind][jy] + dlat))
-      if (is.na(var[jx, lat_plot_ind[jy]] > 0)) {
+      if (is.na(data[jx, lat_plot_ind[jy]] > 0)) {
         col <- colNA
-      } else if (var[jx, lat_plot_ind[jy]] <= brks[1]) {
+      } else if (data[jx, lat_plot_ind[jy]] <= brks[1]) {
         col <- col_inf_image
-      } else if (var[jx, lat_plot_ind[jy]] >= tail(brks, 1)) {
+      } else if (data[jx, lat_plot_ind[jy]] >= tail(brks, 1)) {
         col <- col_sup_image
       } else {
-        ind <- which(brks[-1] >= var[jx, lat_plot_ind[jy]] & var[jx, lat_plot_ind[jy]] > brks[-length(brks)])
+        ind <- which(brks[-1] >= data[jx, lat_plot_ind[jy]] & data[jx, lat_plot_ind[jy]] > brks[-length(brks)])
         col <- cols[ind]
       }
       polygon(coord, col = col, border = NA)
@@ -719,7 +719,7 @@ VizStereoMap <- function(var, lon, lat, varu = NULL, varv = NULL, latlims = c(60
   if (!is.null(dots)) {
     numbfig <- 1  # for compatibility with PlotEquiMap code
     dots <- dots[, , lat_plot_ind, drop = FALSE]
-    data_avail <- !is.na(var[, lat_plot_ind, drop = FALSE])
+    data_avail <- !is.na(data[, lat_plot_ind, drop = FALSE])
     for (counter in 1:(dim(dots)[1])) {
       points <- which(dots[counter, , ] & data_avail, arr.ind = TRUE)
       points_proj <- mapproj::mapproject(lon[points[, 1]], lat[lat_plot_ind][points[, 2]])
-- 
GitLab


From 39cfe3c89ae1be4578453d369e8e393a0afe6d78 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 27 Feb 2025 10:28:26 +0100
Subject: [PATCH 03/72] Change 'contour_label_draw' for 'contour_draw_label' in
 VizStereoMap.R

---
 R/VizStereoMap.R | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/VizStereoMap.R b/R/VizStereoMap.R
index 5b30fab..e28e0fb 100644
--- a/R/VizStereoMap.R
+++ b/R/VizStereoMap.R
@@ -75,7 +75,7 @@
 #'  and 'brks2'.
 #'@param contour_lty Line type of the contour curves. Takes 1 (solid) by 
 #'  default. See help on 'lty' in par() for other accepted values.
-#'@param contour_label_draw A logical value indicating whether to draw the 
+#'@param contour_draw_label A logical value indicating whether to draw the 
 #'  contour labels (TRUE) or not (FALSE) when 'contours' is used. The default
 #'  value is TRUE.
 #'@param contour_label_scale Scale factor for the superimposed labels when 
@@ -186,7 +186,7 @@ VizStereoMap <- function(data, lon, lat, varu = NULL, varv = NULL, latlims = c(6
                           coast_width = 1,
                           contours = NULL, brks2 = NULL, contour_lwd = 0.5,
                           contour_color = 'black', contour_lty = 1,
-                          contour_label_draw = TRUE, contour_label_scale = 0.6,
+                          contour_draw_label = TRUE, contour_label_scale = 0.6,
                           dots = NULL, dot_symbol = 4, dot_size = 0.8,
                           intlat = 10,
                           arr_subsamp = floor(length(lon) / 30), arr_scale = 1,
@@ -448,9 +448,9 @@ VizStereoMap <- function(data, lon, lat, varu = NULL, varv = NULL, latlims = c(6
     stop("Parameter 'contour_lty' must be either a number or a character string.")
   }
 
-  # Check contour_label_draw
-  if (!is.logical(contour_label_draw)) {
-    stop("Parameter 'contour_label_draw' must be a logical value.")
+  # Check contour_draw_label
+  if (!is.logical(contour_draw_label)) {
+    stop("Parameter 'contour_draw_label' must be a logical value.")
   }
 
   # Check contour_label_scale
@@ -672,7 +672,7 @@ VizStereoMap <- function(data, lon, lat, varu = NULL, varv = NULL, latlims = c(6
           lines(xc, yc, col = contour_color, lwd = contour_lwd, lty = contour_lty)
 
           # draw label
-          if (contour_label_draw) {
+          if (contour_draw_label) {
             label_char <- as.character(signif(brks2[n_brks2], 2))
             ## Check if the label has enough space to draw first.
             last_slope <- Inf
-- 
GitLab


From d6ee6f9c00e51e67d5b8ca41662387164b27e8f4 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 27 Feb 2025 10:31:09 +0100
Subject: [PATCH 04/72] Change 'title_size' for 'title_scale' in VizRobinson.R

---
 R/VizRobinson.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/VizRobinson.R b/R/VizRobinson.R
index 63f5c7f..4596f99 100644
--- a/R/VizRobinson.R
+++ b/R/VizRobinson.R
@@ -65,7 +65,7 @@
 #'@param vertical A logical value indicating the direction of colorbar if 
 #' parameter 'drawleg' is 'bar'. The default value is TRUE.
 #'@param toptitle A character string of the top title of the figure, scalable 
-#'  with parameter 'title_size'.
+#'  with parameter 'title_scale'.
 #'@param caption A character string of the caption located at left-bottom of the
 #'  plot.
 #'@param units A character string of the data units, which is the title of the 
@@ -75,7 +75,7 @@
 #'  cannot exceed 180 degrees.
 #'@param point_size A number of the size of the data points if "style = 'point'".
 #'  The default is 'auto' and the function tries to find the appropriate size.
-#'@param title_size A number of the size of the top title. The default is 16.
+#'@param title_scale A number of the size of the top title. The default is 16.
 #'@param dots_size A number of the size of the dots. The default is 0.5.
 #'@param dots_shape A number indicating the dot shape recognized by parameter 
 #'  'shape' in \code{geom_point()}.
@@ -126,7 +126,7 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
                         triangle_ends = NULL, col_inf = NULL, col_sup = NULL, colNA = NULL, 
                         color_fun = ClimPalette(), bar_extra_margin = rep(0, 4), vertical = TRUE,
                         toptitle = NULL, caption = NULL, units = NULL, crop_coastlines = NULL,
-                        point_size = "auto", title_size = 16, dots_size = 0.5,
+                        point_size = "auto", title_scale = 16, dots_size = 0.5,
                         dots_shape = 47, coastlines_width = 0.3,
                         fileout = NULL, width = 8, height = 4, size_units = "in", 
                         res = 300) {
@@ -522,7 +522,7 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
 
   if (!is.null(toptitle)) {
     res_p <- res_p + ggtitle(toptitle) +
-      theme(plot.title = element_text(size = title_size, hjust = 0.5, vjust = 3))
+      theme(plot.title = element_text(size = title_scale, hjust = 0.5, vjust = 3))
   }
   if (!is.null(caption)) {
     res_p <- res_p + labs(caption = caption) +
-- 
GitLab


From af8ef318691c0019e63680bafd94f8f4cc276b0e Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 27 Feb 2025 10:39:34 +0100
Subject: [PATCH 05/72] Update unit tests

---
 tests/testthat/test-VizEquiMap.R  | 124 +++++++++++++++---------------
 tests/testthat/test-VizRobinson.R |   4 +-
 2 files changed, 64 insertions(+), 64 deletions(-)

diff --git a/tests/testthat/test-VizEquiMap.R b/tests/testthat/test-VizEquiMap.R
index 8ae3f21..38673db 100644
--- a/tests/testthat/test-VizEquiMap.R
+++ b/tests/testthat/test-VizEquiMap.R
@@ -30,259 +30,259 @@ test_that("1. Input checks", {
     "Parameters 'lon' and 'lat' must be numeric vectors."
   )
   
-  # Check var
+  # Check data
   expect_error(
-    VizEquiMap(var = NULL, lon = lons1, lat = lats1), 
-    "Parameter 'var' cannot be NULL."
+    VizEquiMap(data = NULL, lon = lons1, lat = lats1), 
+    "Parameter 'data' cannot be NULL."
   )
   
   # Check varu and varv
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, varu = "test1"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, varu = "test1"), 
     "Only one of the components 'varu' or 'varv' has been provided. Both must be provided."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, varu = "test1", varv = "test2"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, varu = "test1", varv = "test2"), 
     "Parameter 'varu' must be a numerical array with two dimensions."
   )
   
   # Check contours
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, contours = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, contours = "test"), 
     "Parameter 'contours' must be a numerical array with two dimensions."
   )
   
   # Check toptitle
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, toptitle = 1), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, toptitle = 1), 
     "Parameter 'toptitle' must be a character string."
   )
   
   # Check include_lower_boundary and include_upper_boundary
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, include_lower_boundary = 1), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, include_lower_boundary = 1), 
     "Parameter 'include_lower_boundary' must be a logical element."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, include_upper_boundary = 1), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, include_upper_boundary = 1), 
     "Parameter 'include_upper_boundary' must be a logical element."
   )
   
   # Check colNA
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, colNA = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, colNA = "test"), 
     "Parameter 'colNA' must be a valid colour identifier."
   )
   
   # Check square
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, square = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, square = "test"), 
     "Parameter 'square' must be logical."
   )
   
   # Check filled.continents
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, filled.continents = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, filled.continents = "test"), 
     "Parameter 'filled.continents' must be logical or a colour identifier."
   )
   
   # Check filled.oceans
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, filled.oceans = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, filled.oceans = "test"), 
     "Parameter 'filled.oceans' must be logical or a colour identifier."
   )
   
   # Check country.borders
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, country.borders = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, country.borders = "test"), 
     "Parameter 'country.borders' must be logical."
   )
   
   # Check coast_color
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, coast_color = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, coast_color = "test"), 
     "Parameter 'coast_color' must be a valid colour identifier."
   )
   
   # Check coast_width
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, coast_width = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, coast_width = "test"), 
     "Parameter 'coast_width' must be numeric."
   )
   
   # Check lake_color
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, lake_color = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, lake_color = "test"), 
     "Parameter 'lake_color' must be a valid colour identifier."
   )
   
   # Check shapefile
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, shapefile = list()), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, shapefile = list()), 
     "The list names of the object in 'shapefile' .rds file should have at least 'x' and 'y'."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, shapefile = 1), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, shapefile = 1), 
     "Parameter 'shapefile' must be a .rds file or a list."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, shapefile = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, shapefile = "test"), 
     "Parameter 'shapefile' is not a valid file."
   )
   
   # Check shapefile_col
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, shapefile_color = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, shapefile_color = "test"), 
     "Parameter 'shapefile_color' must be a valid colour identifier."
   )
   
   # Check contour_lwd
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, contour_lwd = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, contour_lwd = "test"), 
     "Parameter 'contour_lwd' must be numeric."
   )
   
   # Check contour_color
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, contour_color = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, contour_color = "test"), 
     "Parameter 'contour_color' must be a valid colour identifier."
   )
   
   # Check contour_lty
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, contour_lty = c()), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, contour_lty = c()), 
     "Parameter 'contour_lty' must be either a number or a character string."
   )
   
   # Check contour_draw_label
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, contour_draw_label = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, contour_draw_label = "test"), 
     "Parameter 'contour_draw_label' must be logical."
   )
   
   # Check contour_label_scale
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, contour_label_scale = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, contour_label_scale = "test"), 
     "Parameter 'contour_label_scale' must be numeric."
   )
   
   # Check dots
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, dots = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, dots = "test"), 
     "Parameter 'dots' must be a logical array with two or three dimensions."
   )
   
   # Check mask
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, mask = "test"), 
-    "Parameter 'mask' must have two dimensions named as the longitude and latitude dimensions in 'var'."
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, mask = "test"), 
+    "Parameter 'mask' must have two dimensions named as the longitude and latitude dimensions in 'data'."
   )
   
   # Check arrow parameters
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, arr_subsamp = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, arr_subsamp = "test"), 
     "Parameter 'arr_subsamp' must be numeric."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, arr_scale = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, arr_scale = "test"), 
     "Parameter 'arr_scale' must be numeric."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, arr_ref_len = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, arr_ref_len = "test"), 
     "Parameter 'arr_ref_len' must be numeric."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, arr_units = 1), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, arr_units = 1), 
     "Parameter 'arr_units' must be character."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, arr_scale_shaft = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, arr_scale_shaft = "test"), 
     "Parameter 'arr_scale_shaft' must be numeric."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, arr_scale_shaft_angle = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, arr_scale_shaft_angle = "test"), 
     "Parameter 'arr_scale_shaft_angle' must be numeric."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, arr_scale_shaft_angle = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, arr_scale_shaft_angle = "test"), 
     "Parameter 'arr_scale_shaft_angle' must be numeric."
   )
   
   # Check axis parameters
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, axelab = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, axelab = "test"), 
     "Parameter 'axelab' must be logical."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, labW = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, labW = "test"), 
     "Parameter 'labW' must be logical."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, lab_dist_x = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, lab_dist_x = "test"), 
     "Parameter 'lab_dist_x' must be numeric."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, lab_dist_y = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, lab_dist_y = "test"), 
     "Parameter 'lab_dist_y' must be numeric."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, intylat = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, intylat = "test"), 
     "Parameter 'intylat' must be numeric."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, intxlon = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, intxlon = "test"), 
     "Parameter 'intxlon' must be numeric."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, xlonshft = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, xlonshft = "test"), 
     "Parameter 'xlonshft' must be a number."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, ylatshft = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, ylatshft = "test"), 
     "Parameter 'ylatshft' must be a number."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, xlabels = 1), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, xlabels = 1), 
     "Parameter 'xlabels' must be a vector of character string."
   )
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, ylabels = 1), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, ylabels = 1), 
     "Parameter 'ylabels' must be a vector of character string."
   )
   
   # Check legend parameters
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, drawleg = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, drawleg = "test"), 
     "Parameter 'drawleg' must be logical."
   )
   
   # Check margin_scale
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, margin_scale = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, margin_scale = "test"), 
     "Parameter 'margin_scale' must be a numeric vector of length 4."
   )
   
   # Check title_scale
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, title_scale = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, title_scale = "test"), 
     "Parameter 'title_scale' must be numeric."
   )
   
   # Check axes_tick_scale
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, axes_tick_scale = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, axes_tick_scale = "test"), 
     "Parameter 'axes_tick_scale' must be numeric."
   )
   
   # Check axes_label_scale
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, axes_label_scale = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, axes_label_scale = "test"), 
     "Parameter 'axes_label_scale' must be numeric."
   )
   
   # Check numbfig
   expect_error(
-    VizEquiMap(var = data1, lon = lons1, lat = lats1, numbfig = "test"), 
+    VizEquiMap(data = data1, lon = lons1, lat = lats1, numbfig = "test"), 
     "Parameter 'numbfig' must be numeric."
   )
   
@@ -302,7 +302,7 @@ save_fun <- function(...) {
 test_that("2. Output checks", {
 
   expect_snapshot_file(
-    save_fun(var = data1, lon = lons1, lat = lats1, filled.continents = F,
+    save_fun(data = data1, lon = lons1, lat = lats1, filled.continents = F,
              bar_limits = c(0, 10), toptitle = "plot 1",
              cols = cols_white_red1, colNA = "grey", triangle_ends = c(F, F)),
     name = 'VizEquiMap_1a.png'
@@ -310,21 +310,21 @@ test_that("2. Output checks", {
   
   # check include_lower_boundary and include_upper_boundary
   expect_snapshot_file(
-    save_fun(var = data1, lon = lons1, lat = lats1, filled.continents = F,
+    save_fun(data = data1, lon = lons1, lat = lats1, filled.continents = F,
              bar_limits = c(0, 10), toptitle = "plot 1",
              cols = cols_white_red1, colNA = "grey", triangle_ends = c(F, F),
              include_lower_boundary = FALSE),
     name = 'VizEquiMap_1b.png'
   )
   expect_snapshot_file(
-    save_fun(var = data1, lon = lons1, lat = lats1, filled.continents = F,
+    save_fun(data = data1, lon = lons1, lat = lats1, filled.continents = F,
              bar_limits = c(0, 10), toptitle = "plot 1",
              cols = cols_white_red1, colNA = "grey", triangle_ends = c(F, F),
              include_upper_boundary = FALSE),
     name = 'VizEquiMap_1c.png'
   )
   expect_snapshot_file(
-    save_fun(var = data1, lon = lons1, lat = lats1, filled.continents = F,
+    save_fun(data = data1, lon = lons1, lat = lats1, filled.continents = F,
              bar_limits = c(0, 10), toptitle = "plot 1",
              cols = cols_white_red1, colNA = "grey", triangle_ends = c(F, F),
              include_lower_boundary = FALSE, include_upper_boundary = FALSE),
@@ -333,7 +333,7 @@ test_that("2. Output checks", {
   
   # check triangle_ends
   expect_snapshot_file(
-    save_fun(var = data1, lon = lons1, lat = lats1, filled.continents = F,
+    save_fun(data = data1, lon = lons1, lat = lats1, filled.continents = F,
              bar_limits = c(1, 9), toptitle = "plot 1",
              cols = cols_white_red1, colNA = "grey", triangle_ends = c(T, T),
              col_inf = "lightblue", col_sup = "lightblue"),
@@ -342,7 +342,7 @@ test_that("2. Output checks", {
   
   # check filled.continents
   expect_snapshot_file(
-    save_fun(var = data1, lon = lons1, lat = lats1, filled.continents = T,
+    save_fun(data = data1, lon = lons1, lat = lats1, filled.continents = T,
              bar_limits = c(0, 10), toptitle = "plot 1",
              cols = cols_white_red1, colNA = "grey", triangle_ends = c(F, F)),
     name = 'VizEquiMap_filled.continents.png'
@@ -351,7 +351,7 @@ test_that("2. Output checks", {
   # check mask
   mask <- array(rep(c(rep(0, 60), rep(1, 60)), 10), dim = c(lat = 30, lon = 44))
   expect_snapshot_file(
-    save_fun(var = data1, lon = lons1, lat = lats1, filled.continents = F,
+    save_fun(data = data1, lon = lons1, lat = lats1, filled.continents = F,
              bar_limits = c(0, 10), toptitle = "plot 1",
              cols = cols_white_red1, colNA = "grey", triangle_ends = c(F, F),
              mask = mask),
@@ -360,7 +360,7 @@ test_that("2. Output checks", {
   
   # check title_scale
   expect_snapshot_file(
-    save_fun(var = data1, lon = lons1, lat = lats1, filled.continents = F,
+    save_fun(data = data1, lon = lons1, lat = lats1, filled.continents = F,
              bar_limits = c(0, 10), toptitle = "plot 1",
              cols = cols_white_red1, colNA = "grey", triangle_ends = c(F, F), 
              title_scale = 0.5),
@@ -369,7 +369,7 @@ test_that("2. Output checks", {
   
   # check bar_label_scale
   expect_snapshot_file(
-    save_fun(var = data1, lon = lons1, lat = lats1, filled.continents = F,
+    save_fun(data = data1, lon = lons1, lat = lats1, filled.continents = F,
              bar_limits = c(0, 10), toptitle = "plot 1",
              cols = cols_white_red1, colNA = "grey", triangle_ends = c(F, F), 
              bar_label_scale = 0.5),
@@ -378,7 +378,7 @@ test_that("2. Output checks", {
   
   # check margin_scale
   expect_snapshot_file(
-    save_fun(var = data1, lon = lons1, lat = lats1, filled.continents = F,
+    save_fun(data = data1, lon = lons1, lat = lats1, filled.continents = F,
              bar_limits = c(0, 10), toptitle = "plot 1",
              cols = cols_white_red1, colNA = "grey", triangle_ends = c(F, F), 
              margin_scale = rep(10, 4)),
diff --git a/tests/testthat/test-VizRobinson.R b/tests/testthat/test-VizRobinson.R
index fd2463e..d460aa2 100644
--- a/tests/testthat/test-VizRobinson.R
+++ b/tests/testthat/test-VizRobinson.R
@@ -126,7 +126,7 @@ test_that("3. data2: Europe", {
   expect_snapshot_file(
     save_VizRobinson(data2, lon = lon2, lat = lat2, dots = dots2, target_proj = 102014,
       brks = seq(-10, 0, 2), cols = c("#FDD49E", "#FDBB84", "#FC8D59", "#E34A33", "#B30000"), col_inf = "#FEF0D9",
-      toptitle = 'VizRobinson', caption = 'unit test: 1a\n projection: Lambert Europe (ESRI:102014)', point_size = 1.1, title_size = 12,
+      toptitle = 'VizRobinson', caption = 'unit test: 1a\n projection: Lambert Europe (ESRI:102014)', point_size = 1.1, title_scale = 12,
       width = 6, vertical = F, bar_extra_margin = c(0.5, 4, 0.5, 4), crop_coastlines = c(latmin = 27, latmax = 70, lonmin = -20, lonmax = 40)),
     name = 'VizRobinson_2a.png'
   )
@@ -136,7 +136,7 @@ test_that("3. data2: Europe", {
   # expect_snapshot_file(
   # save_VizRobinson(data2, lon = lon2, lat = lat2, dots = dots2, target_proj = 102014,
   #   brks = seq(-10, 0, 2), cols = c("#FDD49E", "#FDBB84", "#FC8D59", "#E34A33", "#B30000"), col_inf = "#FEF0D9",
-  #   toptitle = 'VizRobinson', caption = 'unit test: 1a\n projection: Lambert Europe (ESRI:102014)', point_size = 1.1, title_size = 12,
+  #   toptitle = 'VizRobinson', caption = 'unit test: 1a\n projection: Lambert Europe (ESRI:102014)', point_size = 1.1, title_scale = 12,
   #   width = 6, vertical = F, bar_extra_margin = c(0.5, 4, 0.5, 4), crop_coastlines = c(latmin = 27, latmax = 70, lonmin = -20, lonmax = 40), style = 'polygon'),
   # name = 'VizRobinson_2b.png'
   # )
-- 
GitLab


From 39a2a7297c8d5cdd479eab02dfad9bacbd9f6d09 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 27 Feb 2025 10:54:06 +0100
Subject: [PATCH 06/72] Update man .Rd files

---
 man/VizEquiMap.Rd   | 40 ++++++++++++++++++++--------------------
 man/VizRobinson.Rd  | 16 +++++++++-------
 man/VizStereoMap.Rd | 30 +++++++++++++++---------------
 3 files changed, 44 insertions(+), 42 deletions(-)

diff --git a/man/VizEquiMap.Rd b/man/VizEquiMap.Rd
index 7fadb87..d2d9e4d 100644
--- a/man/VizEquiMap.Rd
+++ b/man/VizEquiMap.Rd
@@ -5,7 +5,7 @@
 \title{Maps A Two-Dimensional Variable On A Cylindrical Equidistant Projection}
 \usage{
 VizEquiMap(
-  var,
+  data,
   lon,
   lat,
   varu = NULL,
@@ -42,7 +42,7 @@ VizEquiMap(
   dot_symbol = 4,
   dot_size = 1,
   mask = NULL,
-  mask_color = "white"
+  mask_color = "white",
   arr_subsamp = floor(length(lon)/30),
   arr_scale = 1,
   arr_ref_len = 15,
@@ -90,7 +90,7 @@ VizEquiMap(
 )
 }
 \arguments{
-\item{var}{Array with the values at each cell of a grid on a regular 
+\item{data}{Array with the values at each cell of a grid on a regular 
 rectangular or gaussian grid. The array is expected to have two 
 dimensions: c(latitude, longitude). Longitudes can be in ascending or 
 descending order and latitudes in any order. It can contain NA values 
@@ -101,22 +101,22 @@ the positions of the longitudinal and latitudinal coordinate dimensions
 are interchanged.}
 
 \item{lon}{Numeric vector of longitude locations of the cell centers of the 
-grid of 'var', in ascending or descending order (same as 'var'). Expected 
+grid of 'data', in ascending or descending order (same as 'data'). Expected 
 to be regularly spaced, within either of the ranges [-180, 180] or 
 [0, 360]. Data for two adjacent regions split by the limits of the 
 longitude range can also be provided, e.g. \code{lon = c(0:50, 300:360)} 
-('var' must be provided consitently).}
+('data' must be provided consitently).}
 
 \item{lat}{Numeric vector of latitude locations of the cell centers of the 
-grid of 'var', in any order (same as 'var'). Expected to be from a regular 
+grid of 'data', in any order (same as 'data'). Expected to be from a regular 
 rectangular or gaussian grid, within the range [-90, 90].}
 
 \item{varu}{Array of the zonal component of wind/current/other field with 
-the same dimensions as 'var'. It is allowed that the positions of the 
+the same dimensions as 'data'. It is allowed that the positions of the 
 longitudinal and latitudinal coordinate dimensions are interchanged.}
 
 \item{varv}{Array of the meridional component of wind/current/other field 
-with the same dimensions as 'var'. It is allowed that the positions of the 
+with the same dimensions as 'data'. It is allowed that the positions of the 
 longitudinal and latitudinal coordinate dimensions are interchanged.}
 
 \item{toptitle}{Top title of the figure, scalable with parameter 
@@ -126,12 +126,12 @@ longitudinal and latitudinal coordinate dimensions are interchanged.}
 'toptitle'. Deprecated. Use 'title_scale' instead.}
 
 \item{units}{Title at the top of the colour bar, most commonly the units of 
-the variable provided in parameter 'var'.}
+the variable provided in parameter 'data'.}
 
 \item{brks, cols, bar_limits, triangle_ends}{Usually only providing 'brks' is 
 enough to generate the desired colour bar. These parameters allow to 
 define n breaks that define n - 1 intervals to classify each of the values 
-in 'var'. The corresponding grid cell of a given value in 'var' will be 
+in 'data'. The corresponding grid cell of a given value in 'data' will be 
 coloured in function of the interval it belongs to. These parameters are 
 sent to \code{ColorBar()} to generate the breaks and colours. Additional 
 colours for values beyond the limits of the colour bar are also generated 
@@ -139,7 +139,7 @@ and applied to the plot if 'bar_limits' or 'brks' and 'triangle_ends' are
 properly provided to do so. See ?ColorBar for a full explanation.}
 
 \item{col_inf, col_sup, colNA}{Colour identifiers to colour the values in 
-'var' that go beyond the extremes of the colour bar and to colour NA 
+'data' that go beyond the extremes of the colour bar and to colour NA 
 values, respectively. 'colNA' takes attr(cols, 'na_color') if available by 
 default, where cols is the parameter 'cols' if provided or the vector of 
 colors returned by 'color_fun'. If not available, it takes 'pink' by 
@@ -151,7 +151,7 @@ parameters to control the visual aspect of the drawn colour bar
 (1/3). See ?ColorBar for a full explanation.}
 
 \item{square}{Logical value to choose either to draw a coloured square for 
-each grid cell in 'var' (TRUE; default) or to draw contour lines and fill 
+each grid cell in 'data' (TRUE; default) or to draw contour lines and fill 
 the spaces in between with colours (FALSE). In the latter case, 
 'filled.continents' will take the value FALSE if not specified.}
 
@@ -185,7 +185,7 @@ location of the shape. The default value is NULL.}
 
 \item{shapefile_lwd}{Line width of the shapefile. The default value is 1.}
 
-\item{contours}{Array of same dimensions as 'var' to be added to the plot 
+\item{contours}{Array of same dimensions as 'data' to be added to the plot 
 and displayed with contours. Parameter 'brks2' is required to define the 
 magnitude breaks for each contour curve. Disregarded if 'square = FALSE'.
 It is allowed that the positions of the longitudinal and latitudinal 
@@ -209,8 +209,8 @@ contour labels or not. The default value is TRUE.}
 \item{contour_label_scale}{Scale factor for the superimposed labels when 
 drawing contour levels.}
 
-\item{dots}{Array of same dimensions as 'var' or with dimensions 
-c(n, dim(var)), where n is the number of dot/symbol layers to add to the 
+\item{dots}{Array of same dimensions as 'data' or with dimensions 
+c(n, dim(data)), where n is the number of dot/symbol layers to add to the 
 plot. A value of TRUE at a grid cell will draw a dot/symbol on the 
 corresponding square of the plot. By default all layers provided in 'dots' 
 are plotted with dots, but a symbol can be specified for each of the 
@@ -227,7 +227,7 @@ additional accepted options.}
 in 'dots'. If a single value is specified, it will be applied to all 
 layers in 'dots'. Takes 1 by default.}
 
-\item{mask}{An array with the same dimensions as 'var' of [0, 1] or logical
+\item{mask}{An array with the same dimensions as 'data' of [0, 1] or logical
 indicating the grids to not plot data. The value 0 or FALSE is the point not
 to be plotted.}
 
@@ -349,10 +349,10 @@ the corresponding device.}
 \item{res}{Resolution of the device (file or window) to plot in. See 
 ?Devices and the creator function of the corresponding device.}
 
-\item{include_lower_boundary}{Logical value indicating whether to include 
+\item{include_lower_boundary}{Logical value indicating whether to include
 the minimum value of the field. Takes TRUE by default.}
 
-\item{include_upper_boundary}{Logical value indicating whether to include 
+\item{include_upper_boundary}{Logical value indicating whether to include
 the maximum value of the field. Takes TRUE by default.}
 
 \item{\dots}{Arguments to be passed to the method. Only accepts the following 
@@ -395,11 +395,11 @@ figure layouts if colour bar is disabled.
  \dontrun{
 ano <- s2dv::Ano_CrossValid(map_temp$exp, map_temp$obs, memb = FALSE,
                            dat_dim = c('dat', 'member'), memb_dim = 'member')
-var <- s2dv::MeanDims(ano$exp, "member")
+data <- s2dv::MeanDims(ano$exp, "member")
 lats <- attr(map_temp$exp, "Variables")$common$lat
 lons <- attr(map_temp$exp, "Variables")$common$lon
 
-VizEquiMap(var[1, 1, 1, 1, , ], lon = lons, lat = lats,
+VizEquiMap(data[1, 1, 1, 1, , ], lon = lons, lat = lats,
           toptitle = 'Near-surface temperature anomaly, Nov. 2000',
           filled.continents = FALSE, title_scale = 0.7)
  }
diff --git a/man/VizRobinson.Rd b/man/VizRobinson.Rd
index 48687f1..fda10df 100644
--- a/man/VizRobinson.Rd
+++ b/man/VizRobinson.Rd
@@ -10,7 +10,7 @@ VizRobinson(
   lat,
   lon_dim = NULL,
   lat_dim = NULL,
-  target_proj = "ESRI:54030",
+  target_proj = NULL,
   drawleg = "bar",
   style = "point",
   dots = NULL,
@@ -30,7 +30,7 @@ VizRobinson(
   units = NULL,
   crop_coastlines = NULL,
   point_size = "auto",
-  title_size = 16,
+  title_scale = 16,
   dots_size = 0.5,
   dots_shape = 47,
   coastlines_width = 0.3,
@@ -62,9 +62,11 @@ of ascending or descending order.}
 \code{esviz:::.KnownLatNames}. The default value is NULL.}
 
 \item{target_proj}{A character string indicating the target projection. It 
-should be a valid crs string. The default projection is Robinson 
-(ESRI:54030). Note that the character string may work differently depending
-on PROJ and GDAL module version.}
+should be a valid crs string. The default projection is Robinson: 
+"ESRI:54030". Note that the character string may work differently depending
+on PROJ and GDAL module version. If package version 'sf' is lower than 
+"1.0.10" and an error appears regarding the target crs, you can try with 
+numeric crs (e.g. target_proj = 54030).}
 
 \item{drawleg}{A character string indicating the legend style. It can be 
 'bar' (color bar by \code{ColorBarContinuous()}), 'ggplot2' (discrete legend 
@@ -108,7 +110,7 @@ parameters to control the visual aspect of the drawn colour bar
 parameter 'drawleg' is 'bar'. The default value is TRUE.}
 
 \item{toptitle}{A character string of the top title of the figure, scalable 
-with parameter 'title_size'.}
+with parameter 'title_scale'.}
 
 \item{caption}{A character string of the caption located at left-bottom of the
 plot.}
@@ -123,7 +125,7 @@ cannot exceed 180 degrees.}
 \item{point_size}{A number of the size of the data points if "style = 'point'".
 The default is 'auto' and the function tries to find the appropriate size.}
 
-\item{title_size}{A number of the size of the top title. The default is 16.}
+\item{title_scale}{A number of the size of the top title. The default is 16.}
 
 \item{dots_size}{A number of the size of the dots. The default is 0.5.}
 
diff --git a/man/VizStereoMap.Rd b/man/VizStereoMap.Rd
index 0bd6fd2..b7eeddc 100644
--- a/man/VizStereoMap.Rd
+++ b/man/VizStereoMap.Rd
@@ -5,7 +5,7 @@
 \title{Maps A Two-Dimensional Variable On A Polar Stereographic Projection}
 \usage{
 VizStereoMap(
-  var,
+  data,
   lon,
   lat,
   varu = NULL,
@@ -30,7 +30,7 @@ VizStereoMap(
   contour_lwd = 0.5,
   contour_color = "black",
   contour_lty = 1,
-  contour_label_draw = TRUE,
+  contour_draw_label = TRUE,
   contour_label_scale = 0.6,
   dots = NULL,
   dot_symbol = 4,
@@ -68,7 +68,7 @@ VizStereoMap(
 )
 }
 \arguments{
-\item{var}{Array with the values at each cell of a grid on a regular 
+\item{data}{Array with the values at each cell of a grid on a regular 
 rectangular or gaussian grid. The array is expected to have two dimensions: 
 c(latitude, longitude). Longitudes can be in ascending or descending order 
 and latitudes in any order. It can contain NA values (coloured with 
@@ -77,21 +77,21 @@ accepted but 'lon' and 'lat' will be used to disambiguate so this
 alternative is not appropriate for square arrays.}
 
 \item{lon}{Numeric vector of longitude locations of the cell centers of the 
-grid of 'var', in ascending or descending order (same as 'var'). Expected 
+grid of 'data', in ascending or descending order (same as 'data'). Expected 
 to be regularly spaced, within either of the ranges [-180, 180] or 
 [0, 360]. Data for two adjacent regions split by the limits of the 
 longitude range can also be provided, e.g. \code{lon = c(0:50, 300:360)} 
-('var' must be provided consitently).}
+('data' must be provided consitently).}
 
 \item{lat}{Numeric vector of latitude locations of the cell centers of the 
-grid of 'var', in any order (same as 'var'). Expected to be from a regular 
+grid of 'data', in any order (same as 'data'). Expected to be from a regular 
 rectangular or gaussian grid, within the range [-90, 90].}
 
 \item{varu}{Array of the zonal component of wind/current/other field with 
-the same dimensions as 'var'.}
+the same dimensions as 'data'.}
 
 \item{varv}{Array of the meridional component of wind/current/other field 
-with the same dimensions as 'var'.}
+with the same dimensions as 'data'.}
 
 \item{latlims}{Latitudinal limits of the figure.\cr
 Example : c(60, 90) for the North Pole\cr
@@ -104,12 +104,12 @@ Example : c(60, 90) for the North Pole\cr
 'toptitle'. Deprecated. Use 'title_scale' instead.}
 
 \item{units}{Title at the top of the colour bar, most commonly the units of 
-the variable provided in parameter 'var'.}
+the variable provided in parameter 'data'.}
 
 \item{brks, cols, bar_limits, triangle_ends}{Usually only providing 'brks' is 
 enough to generate the desired colour bar. These parameters allow to 
 define n breaks that define n - 1 intervals to classify each of the values 
-in 'var'. The corresponding grid cell of a given value in 'var' will be 
+in 'data'. The corresponding grid cell of a given value in 'data' will be 
 coloured in function of the interval it belongs to. These parameters are 
 sent to \code{ColorBarContinuous()} to generate the breaks and colours. Additional 
 colours for values beyond the limits of the colour bar are also generated 
@@ -117,7 +117,7 @@ and applied to the plot if 'bar_limits' or 'brks' and 'triangle_ends' are
 properly provided to do so. See ?ColorBarContinuous for a full explanation.}
 
 \item{col_inf, col_sup, colNA}{Colour identifiers to colour the values in 
-'var' that go beyond the extremes of the colour bar and to colour NA 
+'data' that go beyond the extremes of the colour bar and to colour NA 
 values, respectively. 'colNA' takes attr(cols, 'na_color') if available by 
 default, where cols is the parameter 'cols' if provided or the vector of 
 colors returned by 'color_fun'. If not available, it takes 'pink' by 
@@ -137,7 +137,7 @@ continents. Takes the value gray(0.5) by default.}
 \item{coast_width}{Line width of the coast line of the drawn projected 
 continents. Takes the value 1 by default.}
 
-\item{contours}{Array of same dimensions as 'var' to be added to the plot 
+\item{contours}{Array of same dimensions as 'data' to be added to the plot 
 and displayed with contours. Parameter 'brks2' is required to define the 
 magnitude breaks for each contour curve.}
 
@@ -155,15 +155,15 @@ and 'brks2'.}
 \item{contour_lty}{Line type of the contour curves. Takes 1 (solid) by 
 default. See help on 'lty' in par() for other accepted values.}
 
-\item{contour_label_draw}{A logical value indicating whether to draw the 
+\item{contour_draw_label}{A logical value indicating whether to draw the 
 contour labels (TRUE) or not (FALSE) when 'contours' is used. The default
 value is TRUE.}
 
 \item{contour_label_scale}{Scale factor for the superimposed labels when 
 drawing contour levels. The default value is 0.6.}
 
-\item{dots}{Array of same dimensions as 'var' or with dimensions 
-c(n, dim(var)), where n is the number of dot/symbol layers to add to the 
+\item{dots}{Array of same dimensions as 'data' or with dimensions 
+c(n, dim(data)), where n is the number of dot/symbol layers to add to the 
 plot. A value of TRUE at a grid cell will draw a dot/symbol on the 
 corresponding square of the plot. By default all layers provided in 'dots' 
 are plotted with dots, but a symbol can be specified for each of the 
-- 
GitLab


From de7b56551aaa899b356533e187063342d4f4e513 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 27 Feb 2025 15:25:45 +0100
Subject: [PATCH 07/72] Add warning to deprecated parameters

---
 R/VizEquiMap.R      | 80 +++++++++++++++++++++++++--------------------
 R/VizRobinson.R     | 23 ++++++++-----
 R/VizStereoMap.R    | 69 +++++++++++++++++++++++---------------
 man/VizEquiMap.Rd   |  5 ++-
 man/VizRobinson.Rd  |  3 ++
 man/VizStereoMap.Rd |  8 ++++-
 6 files changed, 117 insertions(+), 71 deletions(-)

diff --git a/R/VizEquiMap.R b/R/VizEquiMap.R
index e13211b..1994507 100644
--- a/R/VizEquiMap.R
+++ b/R/VizEquiMap.R
@@ -19,6 +19,7 @@
 #'  this alternative is not appropriate for square arrays. It is allowed that
 #'  the positions of the longitudinal and latitudinal coordinate dimensions 
 #'  are interchanged.
+#'@param var Deprecated. Use 'data' instead.
 #'@param lon Numeric vector of longitude locations of the cell centers of the 
 #'  grid of 'data', in ascending or descending order (same as 'data'). Expected 
 #'  to be regularly spaced, within either of the ranges [-180, 180] or 
@@ -249,40 +250,40 @@
 #'@importFrom stats cor
 #' @importFrom s2dv InsertDim
 #'@export
-VizEquiMap <- function(data, lon, lat, varu = NULL, varv = NULL,
-                        toptitle = NULL, sizetit = NULL, units = NULL, 
-                        brks = NULL, cols = NULL, bar_limits = NULL, 
-                        triangle_ends = NULL, col_inf = NULL, col_sup = NULL, 
-                        colNA = NULL, color_fun = ClimPalette(),
-                        square = TRUE, filled.continents = FALSE,
-                        filled.oceans = FALSE, country.borders = FALSE,
-                        coast_color = NULL, coast_width = 1, lake_color = NULL,
-                        shapefile = NULL, shapefile_color = NULL, shapefile_lwd = 1,
-                        contours = NULL, brks2 = NULL, contour_lwd = 0.5,
-                        contour_color = 'black', contour_lty = 1,
-                        contour_draw_label = TRUE, contour_label_scale = 1,
-                        dots = NULL, dot_symbol = 4, dot_size = 1,
-                        mask = NULL, mask_color = 'white',
-                        arr_subsamp = floor(length(lon) / 30), arr_scale = 1, 
-                        arr_ref_len = 15, arr_units = "m/s", 
-                        arr_scale_shaft = 1, arr_scale_shaft_angle = 1,
-                        axelab = TRUE, labW = FALSE, 
-                        lab_dist_x = NULL, lab_dist_y = NULL, degree_sym = FALSE,
-                        intylat = 20, intxlon = 20,
-                        xlonshft = 0, ylatshft = 0, xlabels = NULL, ylabels = NULL,
-                        axes_tick_scale = 1, axes_label_scale = 1,
-                        drawleg = TRUE, subsampleg = NULL, 
-                        bar_extra_labels = NULL, draw_bar_ticks = TRUE, 
-                        draw_separators = FALSE, triangle_ends_scale = 1, 
-                        bar_label_digits = 4, bar_label_scale = 1, 
-                        units_scale = 1, bar_tick_scale = 1, 
-                        bar_extra_margin = rep(0, 4),
-                        boxlim = NULL, boxcol = 'purple2', boxlwd = 5, 
-                        margin_scale = rep(1, 4), title_scale = 1, 
-                        numbfig = NULL, fileout = NULL, 
-                        width = 8, height = 5, size_units = 'in', 
-                        res = 100, include_lower_boundary = TRUE,
-                        include_upper_boundary = TRUE, ...) {
+VizEquiMap <- function(data = NULL, var = NULL, lon, lat, varu = NULL, varv = NULL,
+                       toptitle = NULL, sizetit = NULL, units = NULL, 
+                       brks = NULL, cols = NULL, bar_limits = NULL, 
+                       triangle_ends = NULL, col_inf = NULL, col_sup = NULL, 
+                       colNA = NULL, color_fun = ClimPalette(),
+                       square = TRUE, filled.continents = FALSE,
+                       filled.oceans = FALSE, country.borders = FALSE,
+                       coast_color = NULL, coast_width = 1, lake_color = NULL,
+                       shapefile = NULL, shapefile_color = NULL, shapefile_lwd = 1,
+                       contours = NULL, brks2 = NULL, contour_lwd = 0.5,
+                       contour_color = 'black', contour_lty = 1,
+                       contour_draw_label = TRUE, contour_label_scale = 1,
+                       dots = NULL, dot_symbol = 4, dot_size = 1,
+                       mask = NULL, mask_color = 'white',
+                       arr_subsamp = floor(length(lon) / 30), arr_scale = 1, 
+                       arr_ref_len = 15, arr_units = "m/s", 
+                       arr_scale_shaft = 1, arr_scale_shaft_angle = 1,
+                       axelab = TRUE, labW = FALSE, 
+                       lab_dist_x = NULL, lab_dist_y = NULL, degree_sym = FALSE,
+                       intylat = 20, intxlon = 20,
+                       xlonshft = 0, ylatshft = 0, xlabels = NULL, ylabels = NULL,
+                       axes_tick_scale = 1, axes_label_scale = 1,
+                       drawleg = TRUE, subsampleg = NULL, 
+                       bar_extra_labels = NULL, draw_bar_ticks = TRUE, 
+                       draw_separators = FALSE, triangle_ends_scale = 1, 
+                       bar_label_digits = 4, bar_label_scale = 1, 
+                       units_scale = 1, bar_tick_scale = 1, 
+                       bar_extra_margin = rep(0, 4),
+                       boxlim = NULL, boxcol = 'purple2', boxlwd = 5, 
+                       margin_scale = rep(1, 4), title_scale = 1, 
+                       numbfig = NULL, fileout = NULL, 
+                       width = 8, height = 5, size_units = 'in', 
+                       res = 100, include_lower_boundary = TRUE,
+                       include_upper_boundary = TRUE, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("cex", "cex.axis", "cex.lab", "cex.main", "col", "din", "fig", "fin", "lab", "las", "lty", "lwd", "mai", "mar", "mgp", "new", "oma", "ps", "tck")
@@ -303,7 +304,16 @@ VizEquiMap <- function(data, lon, lat, varu = NULL, varv = NULL,
 
   # Check data
   if (is.null(data)) {
-    stop("Parameter 'data' cannot be NULL.")
+    if (!is.null(var)) {
+      data <- var
+      warning("The parameter 'var' is deprecated. Use 'data' instead.")
+    } else {
+      stop("Parameter 'data' cannot be NULL.")
+    }
+  } else {
+    if (!is.null(var)) {
+      warning("The parameter 'var' is deprecated. 'data' will be used instead.")
+    }
   }
   if (!is.array(data)) {
     stop("Parameter 'data' must be a numeric array.")
diff --git a/R/VizRobinson.R b/R/VizRobinson.R
index 4596f99..301ddf7 100644
--- a/R/VizRobinson.R
+++ b/R/VizRobinson.R
@@ -76,6 +76,7 @@
 #'@param point_size A number of the size of the data points if "style = 'point'".
 #'  The default is 'auto' and the function tries to find the appropriate size.
 #'@param title_scale A number of the size of the top title. The default is 16.
+#'@param title_size Deprecated. Use 'title_scale' instead.
 #'@param dots_size A number of the size of the dots. The default is 0.5.
 #'@param dots_shape A number indicating the dot shape recognized by parameter 
 #'  'shape' in \code{geom_point()}.
@@ -122,14 +123,15 @@
 #'@export
 VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
                         target_proj = NULL, drawleg = 'bar', style = 'point', 
-                        dots = NULL, mask = NULL, brks = NULL, cols = NULL, bar_limits = NULL,
-                        triangle_ends = NULL, col_inf = NULL, col_sup = NULL, colNA = NULL, 
-                        color_fun = ClimPalette(), bar_extra_margin = rep(0, 4), vertical = TRUE,
-                        toptitle = NULL, caption = NULL, units = NULL, crop_coastlines = NULL,
-                        point_size = "auto", title_scale = 16, dots_size = 0.5,
-                        dots_shape = 47, coastlines_width = 0.3,
-                        fileout = NULL, width = 8, height = 4, size_units = "in", 
-                        res = 300) {
+                        dots = NULL, mask = NULL, brks = NULL, cols = NULL,
+                        bar_limits = NULL, triangle_ends = NULL, col_inf = NULL,
+                        col_sup = NULL, colNA = NULL, color_fun = ClimPalette(),
+                        bar_extra_margin = rep(0, 4), vertical = TRUE,
+                        toptitle = NULL, caption = NULL, units = NULL,
+                        crop_coastlines = NULL, point_size = "auto",
+                        title_scale = 16, title_size = NULL, dots_size = 0.5,
+                        dots_shape = 47, coastlines_width = 0.3, fileout = NULL,
+                        width = 8, height = 4, size_units = "in", res = 300) {
 
   # Sanity check
   # data
@@ -261,6 +263,11 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
       stop("Parameter 'mask' must be a logical or numerical array.")
     }
   }
+  # title_scale
+  if (missing(title_scale) && !is.null(title_size)) {
+    title_scale <- title_size
+    warning("The parameter 'title_size' is deprecated. Use 'title_scale' instead.")
+  }
 
   tmp <- .create_var_limits(data = data, brks = brks, 
                             bar_limits = bar_limits, drawleg = drawleg)
diff --git a/R/VizStereoMap.R b/R/VizStereoMap.R
index e28e0fb..4773cd0 100644
--- a/R/VizStereoMap.R
+++ b/R/VizStereoMap.R
@@ -15,6 +15,7 @@
 #'  'colNA'). Arrays with dimensions c(longitude, latitude) will also be 
 #'  accepted but 'lon' and 'lat' will be used to disambiguate so this 
 #'  alternative is not appropriate for square arrays.
+#'@param var Deprecated. Use 'data' instead.
 #'@param lon Numeric vector of longitude locations of the cell centers of the 
 #'  grid of 'data', in ascending or descending order (same as 'data'). Expected 
 #'  to be regularly spaced, within either of the ranges [-180, 180] or 
@@ -78,6 +79,7 @@
 #'@param contour_draw_label A logical value indicating whether to draw the 
 #'  contour labels (TRUE) or not (FALSE) when 'contours' is used. The default
 #'  value is TRUE.
+#'@param contour_label_draw Deprecated. Use 'contour_draw_label' instead.
 #'@param contour_label_scale Scale factor for the superimposed labels when 
 #'  drawing contour levels. The default value is 0.6.
 #'@param dots Array of same dimensions as 'data' or with dimensions 
@@ -177,32 +179,31 @@
 #'@importFrom stats median
 #' @importFrom s2dv InsertDim
 #'@export
-VizStereoMap <- function(data, lon, lat, varu = NULL, varv = NULL, latlims = c(60, 90), 
-                          toptitle = NULL, sizetit = NULL, units = NULL, 
-                          brks = NULL, cols = NULL, bar_limits = NULL, 
-                          triangle_ends = NULL, col_inf = NULL, col_sup = NULL,
-                          colNA = NULL, color_fun = ClimPalette(),
-                          filled.continents = FALSE, coast_color = NULL, 
-                          coast_width = 1,
-                          contours = NULL, brks2 = NULL, contour_lwd = 0.5,
-                          contour_color = 'black', contour_lty = 1,
-                          contour_draw_label = TRUE, contour_label_scale = 0.6,
-                          dots = NULL, dot_symbol = 4, dot_size = 0.8,
-                          intlat = 10,
-                          arr_subsamp = floor(length(lon) / 30), arr_scale = 1,
-                          arr_ref_len = 15, arr_units = "m/s",
-                          arr_scale_shaft = 1, arr_scale_shaft_angle = 1, 
-                          drawleg = TRUE, subsampleg = NULL, 
-                          bar_extra_labels = NULL, draw_bar_ticks = TRUE, 
-                          draw_separators = FALSE, triangle_ends_scale = 1,
-                          bar_label_digits = 4, bar_label_scale = 1, 
-                          units_scale = 1, bar_tick_scale = 1,
-                          bar_extra_margin = rep(0, 4), 
-                          boxlim = NULL, boxcol = "purple2", boxlwd = 5, 
-                          margin_scale = rep(1, 4), title_scale = 1,
-                          numbfig = NULL, fileout = NULL, 
-                          width = 6, height = 5, size_units = 'in', 
-                          res = 100, ...) {
+VizStereoMap <- function(data = NULL, var = NULL, lon, lat, varu = NULL,
+                         varv = NULL, latlims = c(60, 90), toptitle = NULL,
+                         sizetit = NULL, units = NULL, brks = NULL, cols = NULL,
+                         bar_limits = NULL, triangle_ends = NULL,
+                         col_inf = NULL, col_sup = NULL, colNA = NULL,
+                         color_fun = ClimPalette(), filled.continents = FALSE,
+                         coast_color = NULL, coast_width = 1,
+                         contours = NULL, brks2 = NULL, contour_lwd = 0.5,
+                         contour_color = 'black', contour_lty = 1,
+                         contour_draw_label = TRUE, contour_label_draw = NULL,
+                         contour_label_scale = 0.6, dots = NULL, dot_symbol = 4,
+                         dot_size = 0.8, intlat = 10,
+                         arr_subsamp = floor(length(lon) / 30), arr_scale = 1,
+                         arr_ref_len = 15, arr_units = "m/s",
+                         arr_scale_shaft = 1, arr_scale_shaft_angle = 1, 
+                         drawleg = TRUE, subsampleg = NULL, 
+                         bar_extra_labels = NULL, draw_bar_ticks = TRUE, 
+                         draw_separators = FALSE, triangle_ends_scale = 1,
+                         bar_label_digits = 4, bar_label_scale = 1, 
+                         units_scale = 1, bar_tick_scale = 1,
+                         bar_extra_margin = rep(0, 4), boxlim = NULL,
+                         boxcol = "purple2", boxlwd = 5, 
+                         margin_scale = rep(1, 4), title_scale = 1,
+                         numbfig = NULL, fileout = NULL, width = 6, height = 5,
+                         size_units = 'in', res = 100, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("cex", "cex.main", "col", "fin", "lab", "las", "lwd", "mai", "mar", "mgp", "new", "pch", "ps")
@@ -230,6 +231,18 @@ VizStereoMap <- function(data, lon, lat, varu = NULL, varv = NULL, latlims = c(6
   }
 
   # Check data
+  if (is.null(data)) {
+    if (!is.null(var)) {
+      data <- var
+      warning("The parameter 'var' is deprecated. Use 'data' instead.")
+    } else {
+      stop("Parameter 'data' cannot be NULL.")
+    }
+  } else {
+    if (!is.null(var)) {
+      warning("The parameter 'var' is deprecated. 'data' will be used instead.")
+    }
+  }
   if (!is.array(data)) {
     stop("Parameter 'data' must be a numeric array.")
   }
@@ -449,6 +462,10 @@ VizStereoMap <- function(data, lon, lat, varu = NULL, varv = NULL, latlims = c(6
   }
 
   # Check contour_draw_label
+  if (missing(contour_draw_label) && !is.null(contour_label_draw)) {
+    contour_draw_label <- contour_label_draw
+    warning("The parameter 'contour_label_draw' is deprecated. Use 'contour_draw_label' instead.")
+  }
   if (!is.logical(contour_draw_label)) {
     stop("Parameter 'contour_draw_label' must be a logical value.")
   }
diff --git a/man/VizEquiMap.Rd b/man/VizEquiMap.Rd
index d2d9e4d..2128f3e 100644
--- a/man/VizEquiMap.Rd
+++ b/man/VizEquiMap.Rd
@@ -5,7 +5,8 @@
 \title{Maps A Two-Dimensional Variable On A Cylindrical Equidistant Projection}
 \usage{
 VizEquiMap(
-  data,
+  data = NULL,
+  var = NULL,
   lon,
   lat,
   varu = NULL,
@@ -100,6 +101,8 @@ this alternative is not appropriate for square arrays. It is allowed that
 the positions of the longitudinal and latitudinal coordinate dimensions 
 are interchanged.}
 
+\item{var}{Deprecated. Use 'data' instead.}
+
 \item{lon}{Numeric vector of longitude locations of the cell centers of the 
 grid of 'data', in ascending or descending order (same as 'data'). Expected 
 to be regularly spaced, within either of the ranges [-180, 180] or 
diff --git a/man/VizRobinson.Rd b/man/VizRobinson.Rd
index fda10df..bb0ba94 100644
--- a/man/VizRobinson.Rd
+++ b/man/VizRobinson.Rd
@@ -31,6 +31,7 @@ VizRobinson(
   crop_coastlines = NULL,
   point_size = "auto",
   title_scale = 16,
+  title_size = NULL,
   dots_size = 0.5,
   dots_shape = 47,
   coastlines_width = 0.3,
@@ -127,6 +128,8 @@ The default is 'auto' and the function tries to find the appropriate size.}
 
 \item{title_scale}{A number of the size of the top title. The default is 16.}
 
+\item{title_size}{Deprecated. Use 'title_scale' instead.}
+
 \item{dots_size}{A number of the size of the dots. The default is 0.5.}
 
 \item{dots_shape}{A number indicating the dot shape recognized by parameter 
diff --git a/man/VizStereoMap.Rd b/man/VizStereoMap.Rd
index b7eeddc..6e09d21 100644
--- a/man/VizStereoMap.Rd
+++ b/man/VizStereoMap.Rd
@@ -5,7 +5,8 @@
 \title{Maps A Two-Dimensional Variable On A Polar Stereographic Projection}
 \usage{
 VizStereoMap(
-  data,
+  data = NULL,
+  var = NULL,
   lon,
   lat,
   varu = NULL,
@@ -31,6 +32,7 @@ VizStereoMap(
   contour_color = "black",
   contour_lty = 1,
   contour_draw_label = TRUE,
+  contour_label_draw = NULL,
   contour_label_scale = 0.6,
   dots = NULL,
   dot_symbol = 4,
@@ -76,6 +78,8 @@ and latitudes in any order. It can contain NA values (coloured with
 accepted but 'lon' and 'lat' will be used to disambiguate so this 
 alternative is not appropriate for square arrays.}
 
+\item{var}{Deprecated. Use 'data' instead.}
+
 \item{lon}{Numeric vector of longitude locations of the cell centers of the 
 grid of 'data', in ascending or descending order (same as 'data'). Expected 
 to be regularly spaced, within either of the ranges [-180, 180] or 
@@ -159,6 +163,8 @@ default. See help on 'lty' in par() for other accepted values.}
 contour labels (TRUE) or not (FALSE) when 'contours' is used. The default
 value is TRUE.}
 
+\item{contour_label_draw}{Deprecated. Use 'contour_draw_label' instead.}
+
 \item{contour_label_scale}{Scale factor for the superimposed labels when 
 drawing contour levels. The default value is 0.6.}
 
-- 
GitLab


From 9fc2902d0ea26350df2ddfebb6c575ee8abf8ffa Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 27 Feb 2025 15:53:27 +0100
Subject: [PATCH 08/72] Define lat and lon in R/VizStereoMap.R documentation
 example

---
 R/VizStereoMap.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/VizStereoMap.R b/R/VizStereoMap.R
index 4773cd0..e67792c 100644
--- a/R/VizStereoMap.R
+++ b/R/VizStereoMap.R
@@ -172,7 +172,7 @@
 #'data <- matrix(rnorm(100 * 50), 100, 50)
 #'x <- seq(from = 0, to = 360, length.out = 100)
 #'y <- seq(from = -90, to = 90, length.out = 50)
-#'VizStereoMap(data, x, y, latlims = c(60, 90), brks = 50,
+#'VizStereoMap(data, lon = x, lat = y, latlims = c(60, 90), brks = 50,
 #'             toptitle = "This is the title")
 #'@import mapproj utils
 #'@importFrom grDevices dev.cur dev.new dev.off gray
-- 
GitLab


From 29618e53258238b2dd9983fa46e5e2b80d796420 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 27 Feb 2025 16:12:44 +0100
Subject: [PATCH 09/72] Update 'title_scale' parameter name in
 vignettes/map_proj_stereo.Rmd

---
 vignettes/map_proj_stereo.Rmd | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/vignettes/map_proj_stereo.Rmd b/vignettes/map_proj_stereo.Rmd
index 66d5a3a..5100da4 100644
--- a/vignettes/map_proj_stereo.Rmd
+++ b/vignettes/map_proj_stereo.Rmd
@@ -143,7 +143,7 @@ VizRobinson(exp1_clim[1, lats_np_ind, ],  target_proj = 3995,
             legend = 's2dv', style = 'polygon',
             toptitle = "SEAS5 tas climatology (Nov. 2011-2016), ftime = 1, North Pole",
             caption = paste0("plotted by esviz::VizRobinson"),
-            units = "K", title_size = 14,
+            units = "K", title_scale = 14,
             width = 8, height = 8,
             fileout = "map_stereo_clim_exp1_np_robin.png")
 ```
-- 
GitLab


From 1a7d3c05ec7a3d5478ad6cd79d2a122cbbb45f73 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 27 Feb 2025 16:46:14 +0100
Subject: [PATCH 10/72] Update VizStereoMap documentation

---
 R/VizStereoMap.R    | 2 +-
 man/VizStereoMap.Rd | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/VizStereoMap.R b/R/VizStereoMap.R
index e67792c..0c6aa0b 100644
--- a/R/VizStereoMap.R
+++ b/R/VizStereoMap.R
@@ -172,7 +172,7 @@
 #'data <- matrix(rnorm(100 * 50), 100, 50)
 #'x <- seq(from = 0, to = 360, length.out = 100)
 #'y <- seq(from = -90, to = 90, length.out = 50)
-#'VizStereoMap(data, lon = x, lat = y, latlims = c(60, 90), brks = 50,
+#'VizStereoMap(data = data, lon = x, lat = y, latlims = c(60, 90), brks = 50,
 #'             toptitle = "This is the title")
 #'@import mapproj utils
 #'@importFrom grDevices dev.cur dev.new dev.off gray
diff --git a/man/VizStereoMap.Rd b/man/VizStereoMap.Rd
index 6e09d21..0630135 100644
--- a/man/VizStereoMap.Rd
+++ b/man/VizStereoMap.Rd
@@ -289,6 +289,6 @@ compatible with figure layouts if colour bar is disabled.
 data <- matrix(rnorm(100 * 50), 100, 50)
 x <- seq(from = 0, to = 360, length.out = 100)
 y <- seq(from = -90, to = 90, length.out = 50)
-VizStereoMap(data, x, y, latlims = c(60, 90), brks = 50,
+VizStereoMap(data = data, lon = x, lat = y, latlims = c(60, 90), brks = 50,
             toptitle = "This is the title")
 }
-- 
GitLab


From 8126db225180ba2fb432942adda21f9569a35f35 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 28 Feb 2025 12:08:08 +0100
Subject: [PATCH 11/72] Move 'var' argument to end of function definition and
 some format fixes

---
 R/VizEquiMap.R   | 70 ++++++++++++++++++++++++------------------------
 R/VizRobinson.R  | 12 ++++-----
 R/VizStereoMap.R | 10 +++----
 3 files changed, 46 insertions(+), 46 deletions(-)

diff --git a/R/VizEquiMap.R b/R/VizEquiMap.R
index 69be8c2..a51c872 100644
--- a/R/VizEquiMap.R
+++ b/R/VizEquiMap.R
@@ -259,42 +259,42 @@
 #'@import graphics maps utils
 #'@importFrom grDevices dev.cur dev.new dev.off gray
 #'@importFrom stats cor
-#' @importFrom s2dv InsertDim
+#'@importFrom s2dv InsertDim
 #'@export
-VizEquiMap <- function(data = NULL, var = NULL, lon, lat, varu = NULL, varv = NULL,
-                        toptitle = NULL, sizetit = NULL, caption = NULL,
-                        units = NULL, brks = NULL, cols = NULL, bar_limits = NULL, 
-                        triangle_ends = NULL, col_inf = NULL, col_sup = NULL, 
-                        colNA = NULL, color_fun = ClimPalette(),
-                        square = TRUE, filled.continents = FALSE,
-                        filled.oceans = FALSE, country.borders = FALSE,
-                        coast_color = NULL, coast_width = 1, lake_color = NULL,
-                        shapefile = NULL, shapefile_color = NULL, shapefile_lwd = 1,
-                        contours = NULL, brks2 = NULL, contour_lwd = 0.5,
-                        contour_color = 'black', contour_lty = 1,
-                        contour_draw_label = TRUE, contour_label_scale = 1,
-                        dots = NULL, dot_symbol = 4, dot_size = 1,
-                        mask = NULL, mask_color = 'white',
-                        arr_subsamp = floor(length(lon) / 30), arr_scale = 1, 
-                        arr_ref_len = 15, arr_units = "m/s", 
-                        arr_scale_shaft = 1, arr_scale_shaft_angle = 1,
-                        axelab = TRUE, labW = FALSE, 
-                        lab_dist_x = NULL, lab_dist_y = NULL, degree_sym = FALSE,
-                        intylat = 20, intxlon = 20,
-                        xlonshft = 0, ylatshft = 0, xlabels = NULL, ylabels = NULL,
-                        axes_tick_scale = 1, axes_label_scale = 1,
-                        drawleg = TRUE, vertical = FALSE, subsampleg = NULL, 
-                        bar_extra_labels = NULL, draw_bar_ticks = TRUE, 
-                        draw_separators = FALSE, triangle_ends_scale = 1, 
-                        bar_label_digits = 4, bar_label_scale = 1, 
-                        units_scale = 1, bar_tick_scale = 1, 
-                        bar_extra_margin = rep(0, 4),
-                        boxlim = NULL, boxcol = 'purple2', boxlwd = 5, 
-                        margin_scale = rep(1, 4), title_scale = 1, 
-                        caption_size = 0.8, numbfig = NULL, fileout = NULL, 
-                        width = 8, height = 5, size_units = 'in', 
-                        res = 100, include_lower_boundary = TRUE,
-                        include_upper_boundary = TRUE, ...) {
+VizEquiMap <- function(data = NULL, lon, lat, varu = NULL, varv = NULL,
+                       toptitle = NULL, sizetit = NULL, caption = NULL,
+                       units = NULL, brks = NULL, cols = NULL, bar_limits = NULL, 
+                       triangle_ends = NULL, col_inf = NULL, col_sup = NULL, 
+                       colNA = NULL, color_fun = ClimPalette(),
+                       square = TRUE, filled.continents = FALSE,
+                       filled.oceans = FALSE, country.borders = FALSE,
+                       coast_color = NULL, coast_width = 1, lake_color = NULL,
+                       shapefile = NULL, shapefile_color = NULL, shapefile_lwd = 1,
+                       contours = NULL, brks2 = NULL, contour_lwd = 0.5,
+                       contour_color = 'black', contour_lty = 1,
+                       contour_draw_label = TRUE, contour_label_scale = 1,
+                       dots = NULL, dot_symbol = 4, dot_size = 1,
+                       mask = NULL, mask_color = 'white',
+                       arr_subsamp = floor(length(lon) / 30), arr_scale = 1, 
+                       arr_ref_len = 15, arr_units = "m/s", 
+                       arr_scale_shaft = 1, arr_scale_shaft_angle = 1,
+                       axelab = TRUE, labW = FALSE, 
+                       lab_dist_x = NULL, lab_dist_y = NULL, degree_sym = FALSE,
+                       intylat = 20, intxlon = 20,
+                       xlonshft = 0, ylatshft = 0, xlabels = NULL, ylabels = NULL,
+                       axes_tick_scale = 1, axes_label_scale = 1,
+                       drawleg = TRUE, vertical = FALSE, subsampleg = NULL, 
+                       bar_extra_labels = NULL, draw_bar_ticks = TRUE, 
+                       draw_separators = FALSE, triangle_ends_scale = 1, 
+                       bar_label_digits = 4, bar_label_scale = 1, 
+                       units_scale = 1, bar_tick_scale = 1, 
+                       bar_extra_margin = rep(0, 4),
+                       boxlim = NULL, boxcol = 'purple2', boxlwd = 5, 
+                       margin_scale = rep(1, 4), title_scale = 1, 
+                       caption_size = 0.8, numbfig = NULL, fileout = NULL, 
+                       width = 8, height = 5, size_units = 'in', 
+                       res = 100, include_lower_boundary = TRUE,
+                       include_upper_boundary = TRUE, var = NULL, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("cex", "cex.axis", "cex.lab", "cex.main", "col", "din", "fig", "fin", "lab", "las", "lty", "lwd", "mai", "mar", "mgp", "new", "oma", "ps", "tck")
diff --git a/R/VizRobinson.R b/R/VizRobinson.R
index 301ddf7..f77db5f 100644
--- a/R/VizRobinson.R
+++ b/R/VizRobinson.R
@@ -111,15 +111,15 @@
 #'            caption = 'Robinson Projection',
 #'            bar_extra_margin = c(0, 1, 0, 1), width = 8, height = 6)
 #'VizRobinson(data, lon = 0:359, lat = -90:90, mask = dots, drawleg = 'ggplot2',
-#'           target_proj = "+proj=moll", brks = seq(-10, 10, length.out = 11),
-#'           color_fun = ClimPalette("purpleorange"), colNA = 'green',
-#'           toptitle = 'synthetic example', caption = 'Mollweide Projection',
-#'           width = 8, height = 6)
+#'            target_proj = "+proj=moll", brks = seq(-10, 10, length.out = 11),
+#'            color_fun = ClimPalette("purpleorange"), colNA = 'green',
+#'            toptitle = 'synthetic example', caption = 'Mollweide Projection',
+#'            width = 8, height = 6)
 #'  }
 #'@import sf ggplot2 rnaturalearth cowplot utils
 #'@importFrom dplyr mutate group_by summarise
 #'@importFrom ClimProjDiags Subset
-#' @importFrom rlang .data
+#'@importFrom rlang .data
 #'@export
 VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
                         target_proj = NULL, drawleg = 'bar', style = 'point', 
@@ -283,7 +283,7 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
                        plot = FALSE, draw_ticks = TRUE, draw_separators = FALSE,
                        triangle_ends_scale = 1, extra_labels = NULL,
                        title = units, title_scale = 1, # units_scale
-                       label_scale = 1, tick_scale = 1, #bar_tick_scale
+                       label_scale = 1, tick_scale = 1, # bar_tick_scale
                        extra_margin = bar_extra_margin, label_digits = 4)
   brks <- colorbar$brks
   cols <- colorbar$cols
diff --git a/R/VizStereoMap.R b/R/VizStereoMap.R
index 0c6aa0b..d1d1dd5 100644
--- a/R/VizStereoMap.R
+++ b/R/VizStereoMap.R
@@ -177,11 +177,11 @@
 #'@import mapproj utils
 #'@importFrom grDevices dev.cur dev.new dev.off gray
 #'@importFrom stats median
-#' @importFrom s2dv InsertDim
+#'@importFrom s2dv InsertDim
 #'@export
-VizStereoMap <- function(data = NULL, var = NULL, lon, lat, varu = NULL,
-                         varv = NULL, latlims = c(60, 90), toptitle = NULL,
-                         sizetit = NULL, units = NULL, brks = NULL, cols = NULL,
+VizStereoMap <- function(data = NULL, lon, lat, varu = NULL, varv = NULL,
+                         latlims = c(60, 90), toptitle = NULL, sizetit = NULL,
+                         units = NULL, brks = NULL, cols = NULL,
                          bar_limits = NULL, triangle_ends = NULL,
                          col_inf = NULL, col_sup = NULL, colNA = NULL,
                          color_fun = ClimPalette(), filled.continents = FALSE,
@@ -203,7 +203,7 @@ VizStereoMap <- function(data = NULL, var = NULL, lon, lat, varu = NULL,
                          boxcol = "purple2", boxlwd = 5, 
                          margin_scale = rep(1, 4), title_scale = 1,
                          numbfig = NULL, fileout = NULL, width = 6, height = 5,
-                         size_units = 'in', res = 100, ...) {
+                         size_units = 'in', res = 100, var = NULL, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("cex", "cex.main", "col", "fin", "lab", "las", "lwd", "mai", "mar", "mgp", "new", "pch", "ps")
-- 
GitLab


From 20192b1a421d6663fb4496096b6528a48b216415 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 28 Feb 2025 12:21:49 +0100
Subject: [PATCH 12/72] Update man Rd files

---
 man/VizEquiMap.Rd   | 18 +++++++++---------
 man/VizRobinson.Rd  |  8 ++++----
 man/VizStereoMap.Rd |  6 +++---
 3 files changed, 16 insertions(+), 16 deletions(-)

diff --git a/man/VizEquiMap.Rd b/man/VizEquiMap.Rd
index 35f70ae..dc24552 100644
--- a/man/VizEquiMap.Rd
+++ b/man/VizEquiMap.Rd
@@ -6,7 +6,6 @@
 \usage{
 VizEquiMap(
   data = NULL,
-  var = NULL,
   lon,
   lat,
   varu = NULL,
@@ -90,6 +89,7 @@ VizEquiMap(
   res = 100,
   include_lower_boundary = TRUE,
   include_upper_boundary = TRUE,
+  var = NULL,
   ...
 )
 }
@@ -104,8 +104,6 @@ this alternative is not appropriate for square arrays. It is allowed that
 the positions of the longitudinal and latitudinal coordinate dimensions 
 are interchanged.}
 
-\item{var}{Deprecated. Use 'data' instead.}
-
 \item{lon}{Numeric vector of longitude locations of the cell centers of the 
 grid of 'data', in ascending or descending order (same as 'data'). Expected 
 to be regularly spaced, within either of the ranges [-180, 180] or 
@@ -131,10 +129,10 @@ longitudinal and latitudinal coordinate dimensions are interchanged.}
 \item{sizetit}{Scale factor for the figure top title provided in parameter 
 'toptitle'. Deprecated. Use 'title_scale' instead.}
 
-\item{caption}{A character string of the caption located at the left-bottom of 
+\item{caption}{A character string of the caption located at the left-bottom of
 the plot. Captions with multiple lines can be constructed using string 
-manipulation functions like \code{paste()} or \code{paste0()}, using \code{"\n"}
-to indicate line breaks.}
+manipulation functions like \code{paste()} or \code{paste0()}, using 
+\code{"\n"} to indicate line breaks.}
 
 \item{units}{Title at the top of the colour bar, most commonly the units of 
 the variable provided in parameter 'data'.}
@@ -315,9 +313,9 @@ and latitude axes.}
 TRUE. It is not possible to plot the colour bar if 'add = TRUE'. Use 
 ColorBar() and the return values of PlotEquiMap() instead.}
 
-\item{vertical}{TRUE/FALSE for vertical/horizontal colour bar. Default is FALSE.
-Parameters 'width' and 'height' might need to be modified to accommodate the 
-vertical colour bar.}
+\item{vertical}{TRUE/FALSE for vertical/horizontal colour bar. Default is 
+FALSE. Parameters 'width' and 'height' might need to be modified to
+accommodate the vertical colour bar.}
 
 \item{draw_separators, triangle_ends_scale, bar_label_digits}{Set of 
 parameters to control the visual aspect of the drawn colour bar 
@@ -373,6 +371,8 @@ the minimum value of the field. Takes TRUE by default.}
 \item{include_upper_boundary}{Logical value indicating whether to include
 the maximum value of the field. Takes TRUE by default.}
 
+\item{var}{Deprecated. Use 'data' instead.}
+
 \item{\dots}{Arguments to be passed to the method. Only accepts the following 
 graphical parameters:\cr
 adj ann ask bg bty cex.sub cin col.axis col.lab col.main col.sub cra crt 
diff --git a/man/VizRobinson.Rd b/man/VizRobinson.Rd
index bb0ba94..3c7fd57 100644
--- a/man/VizRobinson.Rd
+++ b/man/VizRobinson.Rd
@@ -184,9 +184,9 @@ VizRobinson(data, lon = 0:359, lat = -90:90, dots = dots,
            caption = 'Robinson Projection',
            bar_extra_margin = c(0, 1, 0, 1), width = 8, height = 6)
 VizRobinson(data, lon = 0:359, lat = -90:90, mask = dots, drawleg = 'ggplot2',
-          target_proj = "+proj=moll", brks = seq(-10, 10, length.out = 11),
-          color_fun = ClimPalette("purpleorange"), colNA = 'green',
-          toptitle = 'synthetic example', caption = 'Mollweide Projection',
-          width = 8, height = 6)
+           target_proj = "+proj=moll", brks = seq(-10, 10, length.out = 11),
+           color_fun = ClimPalette("purpleorange"), colNA = 'green',
+           toptitle = 'synthetic example', caption = 'Mollweide Projection',
+           width = 8, height = 6)
  }
 }
diff --git a/man/VizStereoMap.Rd b/man/VizStereoMap.Rd
index 0630135..7431beb 100644
--- a/man/VizStereoMap.Rd
+++ b/man/VizStereoMap.Rd
@@ -6,7 +6,6 @@
 \usage{
 VizStereoMap(
   data = NULL,
-  var = NULL,
   lon,
   lat,
   varu = NULL,
@@ -66,6 +65,7 @@ VizStereoMap(
   height = 5,
   size_units = "in",
   res = 100,
+  var = NULL,
   ...
 )
 }
@@ -78,8 +78,6 @@ and latitudes in any order. It can contain NA values (coloured with
 accepted but 'lon' and 'lat' will be used to disambiguate so this 
 alternative is not appropriate for square arrays.}
 
-\item{var}{Deprecated. Use 'data' instead.}
-
 \item{lon}{Numeric vector of longitude locations of the cell centers of the 
 grid of 'data', in ascending or descending order (same as 'data'). Expected 
 to be regularly spaced, within either of the ranges [-180, 180] or 
@@ -251,6 +249,8 @@ the corresponding device.}
 \item{res}{Resolution of the device (file or window) to plot in. See 
 ?Devices and the creator function of the corresponding device.}
 
+\item{var}{Deprecated. Use 'data' instead.}
+
 \item{\dots}{Arguments to be passed to the method. Only accepts the 
 following graphical parameters:\cr
 adj ann ask bg bty cex.sub cin col.axis col.lab col.main col.sub cra crt 
-- 
GitLab


From 71846196dd8a5d649cda965eef75f5391c36b43d Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 28 Feb 2025 15:52:57 +0100
Subject: [PATCH 13/72] Change 'var' for 'data' in R/VizAnimateMap.R

---
 R/VizAnimateMap.R | 93 +++++++++++++++++++++++++++--------------------
 1 file changed, 53 insertions(+), 40 deletions(-)

diff --git a/R/VizAnimateMap.R b/R/VizAnimateMap.R
index 061ca1e..0515e0d 100644
--- a/R/VizAnimateMap.R
+++ b/R/VizAnimateMap.R
@@ -7,9 +7,10 @@
 #'observed data along the forecast time (lead-time) for all input experiments 
 #'and input observational datasets.
 #'
-#'@param var Matrix of dimensions (nltime, nlat, nlon) or 
+#'@param data Matrix of dimensions (nltime, nlat, nlon) or 
 #'  (nexp/nmod, nltime, nlat, nlon) or (nexp/nmod, 3/4, nltime, nlat, nlon) or 
 #'  (nexp/nmod, nobs, 3/4, nltime, nlat, nlon).
+#'@param var Deprecated. Use 'data' instead.
 #'@param lon Vector containing longtitudes (degrees).
 #'@param lat Vector containing latitudes (degrees).
 #'@param toptitle c('','', \dots) array of main title for each animation, 
@@ -22,7 +23,7 @@
 #'@param msk95lev TRUE/FALSE grid points with dots if 95\% significance level 
 #'  reached. Default = FALSE.
 #'@param brks Limits of colour levels, optional. For example: 
-#'  seq(min(var), max(var), (max(var) - min(var)) / 10).
+#'  seq(min(data), max(data), (max(data) - min(data)) / 10).
 #'@param cols Vector of colours of length(brks) - 1, optional.
 #'@param filled.continents Continents filled in grey (TRUE) or represented by 
 #'  a black line (FALSE). Default = TRUE. Filling unavailable if crossing 
@@ -68,9 +69,9 @@
 #'  \item{
 #'  Model output from load/ano/smoothing:
 #'           (nmod, nmemb, sdate, nltime, nlat, nlon)
-#'  then passed through spread(var, posdim = 2, narm = TRUE)
-#'                    & mean1dim(var, posdim = 3, narm = TRUE)
-#'  or through trend(mean1dim(var, 2), posTR = 2):
+#'  then passed through spread(data, posdim = 2, narm = TRUE)
+#'                    & mean1dim(data, posdim = 3, narm = TRUE)
+#'  or through trend(mean1dim(data, 2), posTR = 2):
 #'           (nmod, 3, nltime, nlat, nlon)
 #'  animates average along start dates of IQR/MaxMin/SD/MAD across members 
 #'  or trends of the ensemble-mean computed accross the start dates.
@@ -102,15 +103,16 @@
 #'  }
 #'@importFrom grDevices postscript dev.off
 #'@importFrom s2dv InsertDim
-VizAnimateMap <- function(var, lon, lat, toptitle = rep("", 11), sizetit = 1, 
-                       units = "", monini = 1, freq = 12, msk95lev = FALSE, 
-                       brks = NULL, cols = NULL, filled.continents = FALSE, 
-                       lonmin = 0, lonmax = 360, latmin = -90, latmax = 90, 
-                       intlon = 20, intlat = 30, drawleg = TRUE, 
-                       subsampleg = 1, colNA = "white", equi = TRUE, 
-                       fileout = c("output1_animvsltime.gif", 
-                                   "output2_animvsltime.gif", 
-                                   "output3_animvsltime.gif"), ...) {
+VizAnimateMap <- function(data = NULL, lon, lat, toptitle = rep("", 11),
+                          sizetit = 1, units = "", monini = 1, freq = 12,
+                          msk95lev = FALSE, brks = NULL, cols = NULL,
+                          filled.continents = FALSE, lonmin = 0, lonmax = 360,
+                          latmin = -90, latmax = 90, intlon = 20, intlat = 30,
+                          drawleg = TRUE, subsampleg = 1, colNA = "white",
+                          equi = TRUE, fileout = c("output1_animvsltime.gif",
+                                                   "output2_animvsltime.gif",
+                                                   "output3_animvsltime.gif"),
+                          var = NULL, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("bg", "col", "fin", "lab", "lend", "new", "pin", "ps")
@@ -124,37 +126,48 @@ VizAnimateMap <- function(var, lon, lat, toptitle = rep("", 11), sizetit = 1,
   }
   fileout <- sub("\\.[a-zA-Z0-9]*$", "", fileout)
 
-  #
-
-  # Check var
-  if (!is.numeric(var) || !is.array(var)) {
-    stop("Parameter 'var' must be a numeric array.")
+  # Check data
+  if (is.null(data)) {
+    if (!is.null(var)) {
+      data <- var
+      warning("The parameter 'var' is deprecated. Use 'data' instead.")
+    } else {
+      stop("Parameter 'data' cannot be NULL.")
+    }
+  } else {
+    if (!is.null(var)) {
+      warning("The parameter 'var' is deprecated. 'data' will be used instead.")
+    }
+  }
+  
+  if (!is.numeric(data) || !is.array(data)) {
+    stop("Parameter 'data' must be a numeric array.")
   }
-  if (length(dim(var)) < 3 || length(dim(var)) > 6) {
-    stop("Parameter 'var' must be an array with 3 to 6 dimensions.")
+  if (length(dim(data)) < 3 || length(dim(data)) > 6) {
+    stop("Parameter 'data' must be an array with 3 to 6 dimensions.")
   }
-  if (length(dim(var)) == 3) {
-    var <- InsertDim(var, posdim = 1, lendim = 1, name = 'new')
+  if (length(dim(data)) == 3) {
+    data <- InsertDim(data, posdim = 1, lendim = 1, name = 'new')
   }
-  if (length(dim(var)) == 4) {
-    var <- InsertDim(var, posdim = 2, lendim = 3, name = 'new')
+  if (length(dim(data)) == 4) {
+    data <- InsertDim(data, posdim = 2, lendim = 3, name = 'new')
   }
-  if (length(dim(var)) == 5) {
-    var <- InsertDim(var, posdim = 2, lendim = 1, name = 'new')
+  if (length(dim(data)) == 5) {
+    data <- InsertDim(data, posdim = 2, lendim = 1, name = 'new')
   }
 
-  nleadtime <- dim(var)[4]
-  nexp <- dim(var)[1]
-  nobs <- dim(var)[2]
-  nlat <- dim(var)[5]
-  nlon <- dim(var)[6]
+  nleadtime <- dim(data)[4]
+  nexp <- dim(data)[1]
+  nobs <- dim(data)[2]
+  nlat <- dim(data)[5]
+  nlon <- dim(data)[6]
   if (length(lon) != nlon | length(lat) != nlat) {
-    stop("Inconsistent var dimensions / longitudes +  latitudes")
+    stop("Inconsistent data dimensions / longitudes +  latitudes")
   }
   colorbar <- ClimPalette()
   if (is.null(brks) == TRUE) {
-    ll <- signif(min(var[, , 2, , , ], na.rm = TRUE), 4)
-    ul <- signif(max(var[, , 2, , , ], na.rm = TRUE), 4)
+    ll <- signif(min(data[, , 2, , , ], na.rm = TRUE), 4)
+    ul <- signif(max(data[, , 2, , , ], na.rm = TRUE), 4)
     if (is.null(cols) == TRUE) {
       cols <- colorbar(10)
     }
@@ -198,17 +211,17 @@ VizAnimateMap <- function(var, lon, lat, toptitle = rep("", 11), sizetit = 1,
       for (jt in 1:nleadtime) {
         title <- paste(toptitle[(jexp - 1) * nobs + jobs], 
           " Time=", suffixtit[jt], sep = "")
-        varbis <- var[jexp, jobs, 2, jt, which(lat >= 
+        varbis <- data[jexp, jobs, 2, jt, which(lat >= 
           latmin & lat <= latmax), which(lon >= lonmin & 
           lon <= lonmax)]
         varbis <- varbis[latb$ix, lonb$ix]
         flag <- array(FALSE, dim(varbis))
         if (msk95lev) {
-          flag[which(var[jexp, jobs, 1, jt, latb$ix, 
-          lonb$ix] > 0 & var[jexp, jobs, 3, jt, latb$ix, 
+          flag[which(data[jexp, jobs, 1, jt, latb$ix, 
+          lonb$ix] > 0 & data[jexp, jobs, 3, jt, latb$ix, 
           lonb$ix] > 0)] <- TRUE
-          flag[which(var[jexp, jobs, 1, jt, latb$ix, 
-          lonb$ix] < 0 & var[jexp, jobs, 3, jt, latb$ix, 
+          flag[which(data[jexp, jobs, 1, jt, latb$ix, 
+          lonb$ix] < 0 & data[jexp, jobs, 3, jt, latb$ix, 
           lonb$ix] < 0)] <- TRUE
         }
         varbis[which(varbis <= min(brks))] <- min(brks) + 
-- 
GitLab


From 996344eca460c10f69320f263f54298659861cb9 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 28 Feb 2025 16:19:08 +0100
Subject: [PATCH 14/72] Change 'var' for 'data' in R/VizStereoMap.R and
 refactoring warning check

---
 R/VizAnimateMap.R |   7 +--
 R/VizEquiMap.R    |   6 +-
 R/VizLayout.R     | 147 +++++++++++++++++++++++++---------------------
 R/VizStereoMap.R  |   6 +-
 4 files changed, 85 insertions(+), 81 deletions(-)

diff --git a/R/VizAnimateMap.R b/R/VizAnimateMap.R
index 0515e0d..30cf632 100644
--- a/R/VizAnimateMap.R
+++ b/R/VizAnimateMap.R
@@ -134,12 +134,9 @@ VizAnimateMap <- function(data = NULL, lon, lat, toptitle = rep("", 11),
     } else {
       stop("Parameter 'data' cannot be NULL.")
     }
-  } else {
-    if (!is.null(var)) {
-      warning("The parameter 'var' is deprecated. 'data' will be used instead.")
-    }
+  } else if (!is.null(var)) {
+    warning("The parameter 'var' is deprecated. 'data' will be used instead.")
   }
-  
   if (!is.numeric(data) || !is.array(data)) {
     stop("Parameter 'data' must be a numeric array.")
   }
diff --git a/R/VizEquiMap.R b/R/VizEquiMap.R
index a51c872..bae6999 100644
--- a/R/VizEquiMap.R
+++ b/R/VizEquiMap.R
@@ -321,10 +321,8 @@ VizEquiMap <- function(data = NULL, lon, lat, varu = NULL, varv = NULL,
     } else {
       stop("Parameter 'data' cannot be NULL.")
     }
-  } else {
-    if (!is.null(var)) {
-      warning("The parameter 'var' is deprecated. 'data' will be used instead.")
-    }
+  } else if (!is.null(var)) {
+    warning("The parameter 'var' is deprecated. 'data' will be used instead.")
   }
   if (!is.array(data)) {
     stop("Parameter 'data' must be a numeric array.")
diff --git a/R/VizLayout.R b/R/VizLayout.R
index a115879..11f094e 100644
--- a/R/VizLayout.R
+++ b/R/VizLayout.R
@@ -8,7 +8,7 @@
 #'names or the indices of the corresponding input dimensions. It is possible 
 #'to draw a common colour bar at any of the sides of the multi-pannel for all 
 #'the s2dv plots that use a colour bar. Common plotting arguments 
-#'for all the arrays in 'var' can be specified via the '...' parameter, and 
+#'for all the arrays in 'data' can be specified via the '...' parameter, and 
 #'specific plotting arguments for each array can be fully adjusted via 
 #''special_args'. It is possible to draw titles for each of the figures, 
 #'layout rows, layout columns and for the whole figure. A number of parameters 
@@ -19,18 +19,18 @@
 #'nested in complex layouts.
 #'
 #'@param fun Plot function (or name of the function) to be called on the 
-#'  arrays provided in 'var'. If multiple arrays are provided in 'var', a 
+#'  arrays provided in 'data'. If multiple arrays are provided in 'data', a 
 #'  vector of as many function names (character strings!) can be provided in 
-#'  'fun', one for each array in 'var'.
+#'  'fun', one for each array in 'data'.
 #'@param plot_dims Numeric or character string vector with identifiers of the 
 #'  input plot dimensions of the plot function specified in 'fun'. If 
-#'  character labels are provided, names(dim(var)) or attr('dimensions', var) 
+#'  character labels are provided, names(dim(data)) or attr('dimensions', data) 
 #'  will be checked to locate the dimensions. As many plots as 
-#'  prod(dim(var)[-plot_dims]) will be generated. If multiple arrays are 
-#'  provided in 'var', 'plot_dims' can be sent a list with a vector of plot 
+#'  prod(dim(data)[-plot_dims]) will be generated. If multiple arrays are 
+#'  provided in 'data', 'plot_dims' can be sent a list with a vector of plot 
 #'  dimensions for each. If a single vector is provided, it will be used for 
-#'  all the arrays in 'var'.
-#'@param var Multi-dimensional array with at least the dimensions expected by 
+#'  all the arrays in 'data'.
+#'@param data Multi-dimensional array with at least the dimensions expected by 
 #'  the specified plot function in 'fun'. The dimensions reqired by the 
 #'  function must be specified in 'plot_dims'. The dimensions can be 
 #'  disordered and will be reordered automatically. Dimensions can optionally 
@@ -43,8 +43,9 @@
 #'  applied to each of them. NAs can be passed to the list: a NA will yield a 
 #'  blank cell in the layout, which can be populated after 
 #'  (see .SwitchToFigure).
+#'@param var Deprecated. Use 'data' instead.
 #'@param \dots Parameters to be sent to the plotting function 'fun'. If 
-#'  multiple arrays are provided in 'var' and multiple functions are provided 
+#'  multiple arrays are provided in 'data' and multiple functions are provided 
 #'  in 'fun', the parameters provided through \dots will be sent to all the 
 #'  plot functions, as common parameters. To specify concrete arguments for 
 #'  each of the plot functions see parameter 'special_args'.
@@ -52,13 +53,13 @@
 #'  arguments for each of the plot functions provided in 'fun'. If you want to 
 #'  fix a different value for each plot in the layout you can do so by 
 #'  a) splitting your array into a list of sub-arrays (each with the data for 
-#'  one plot) and providing it as parameter 'var', 
+#'  one plot) and providing it as parameter 'data', 
 #'  b) providing a list of named sub-lists in 'special_args', where the names 
 #'  of each sub-list match the names of the parameters to be adjusted, and 
 #'  each value in a sub-list contains the value of the corresponding parameter.
 #'  For example, if the plots are two maps with different arguments, the 
 #'  structure would be like:\cr
-#'  var:\cr
+#'  data:\cr
 #'   List of 2\cr
 #'    $ : num [1:360, 1:181] 1 3.82 5.02 6.63 8.72 ...\cr
 #'    $ : num [1:360, 1:181] 2.27 2.82 4.82 7.7 10.32 ...\cr
@@ -104,17 +105,17 @@
 #'@param subplot_titles_scale Scale factor for the subplots top titles. Takes 
 #'  1 by default.
 #'@param units Title at the top of the colour bar, most commonly the units of 
-#'  the variable provided in parameter 'var'.
+#'  the variable provided in parameter 'data'.
 #'@param brks,cols,bar_limits,triangle_ends Usually only providing 'brks' is 
 #'  enough to generate the desired colour bar. These parameters allow to 
 #'  define n breaks that define n - 1 intervals to classify each of the values 
-#'  in 'var'. The corresponding grid cell of a given value in 'var' will be 
+#'  in 'data'. The corresponding grid cell of a given value in 'data' will be 
 #'  coloured in function of the interval it belongs to. These parameters are 
 #'  sent to \code{ColorBarContinuous()} to generate the breaks and colours. Additional 
 #'  colours for values beyond the limits of the colour bar are also generated 
 #'  and applied to the plot if 'bar_limits' or 'brks' and 'triangle_ends' are 
 #'  properly provided to do so. See ?ColorBarContinuous for a full explanation.
-#'@param col_inf,col_sup Colour identifiers to colour the values in 'var' that 
+#'@param col_inf,col_sup Colour identifiers to colour the values in 'data' that 
 #'  go beyond the extremes of the colour bar and to colour NA values, 
 #'  respectively. 'colNA' takes 'white' by default. 'col_inf' and 'col_sup' 
 #'  will take the value of 'colNA' if not specified. See ?ColorBarContinuous for a full 
@@ -182,12 +183,12 @@
 #'  \dontrun{
 #'ano <- s2dv::Ano_CrossValid(map_temp$exp, map_temp$obs, memb = FALSE,
 #'                            dat_dim = c('dat', 'member'), memb_dim = 'member')
-#'var <- s2dv::MeanDims(ano$exp, "member")
-#'lats <- attr(map_temp$exp, "Variables")$common$lat
+#'data <- s2dv::MeanDims(ano$exp, "member")
+#'lats <- attr(map_temp$exp, "dataiables")$common$lat
 #'lons <- attr(map_temp$exp, "Variables")$common$lon
 #'
 #'VizLayout(fun = VizEquiMap, plot_dims = c('lat', 'lon'),
-#'          var = var[, 1, 1, 1, , ], lon = lons, lat = lats,
+#'          data = data[, 1, 1, 1, , ], lon = lons, lat = lats,
 #'          filled.continents = FALSE, 
 #'          toptitle = 'Near-surface temperature Nov.',
 #'          titles = paste(2000:2005))
@@ -196,25 +197,24 @@
 #'@importFrom grDevices dev.cur dev.new dev.off
 #'@importFrom s2dv Reorder
 #'@export
-VizLayout <- function(fun, plot_dims, var, ..., special_args = NULL, 
-                       nrow = NULL, ncol = NULL, toptitle = NULL,
-                       row_titles = NULL, col_titles = NULL, bar_scale = 1, 
-                       title_scale = 1, title_margin_scale = 1,
-                       title_left_shift_scale = 1,
-                       subtitle_scale = 1, subtitle_margin_scale = 1,
-                       subplot_titles_scale = 1,
-                       brks = NULL, cols = NULL, drawleg = 'S', titles = NULL, 
-                       subsampleg = NULL, bar_limits = NULL, 
-                       triangle_ends = NULL, col_inf = NULL, col_sup = NULL,
-                       color_fun = ClimColors, 
-                       draw_bar_ticks = TRUE, draw_separators = FALSE, 
-                       triangle_ends_scale = 1, bar_extra_labels = NULL, 
-                       units = NULL, units_scale = 1, bar_label_scale = 1, 
-                       bar_tick_scale = 1, bar_extra_margin = rep(0, 4), 
-                       bar_left_shift_scale = 1, bar_label_digits = 4, 
-                       extra_margin = rep(0, 4), layout_by_rows = TRUE,
-                       fileout = NULL, width = NULL, height = NULL, 
-                       size_units = 'in', res = 100, close_device = TRUE) {
+VizLayout <- function(fun, plot_dims, data = NULL, ..., special_args = NULL,
+                      nrow = NULL, ncol = NULL, toptitle = NULL,
+                      row_titles = NULL, col_titles = NULL, bar_scale = 1, 
+                      title_scale = 1, title_margin_scale = 1,
+                      title_left_shift_scale = 1, subtitle_scale = 1,
+                      subtitle_margin_scale = 1, subplot_titles_scale = 1,
+                      brks = NULL, cols = NULL, drawleg = 'S', titles = NULL, 
+                      subsampleg = NULL, bar_limits = NULL, 
+                      triangle_ends = NULL, col_inf = NULL, col_sup = NULL,
+                      color_fun = ClimColors, draw_bar_ticks = TRUE, 
+                      draw_separators = FALSE, triangle_ends_scale = 1,
+                      bar_extra_labels = NULL,units = NULL, units_scale = 1,
+                      bar_label_scale = 1,bar_tick_scale = 1,
+                      bar_extra_margin = rep(0, 4), bar_left_shift_scale = 1,
+                      bar_label_digits = 4, extra_margin = rep(0, 4),
+                      layout_by_rows = TRUE, fileout = NULL, width = NULL,
+                      height = NULL, size_units = 'in', res = 100,
+                      close_device = TRUE, var = NULL) {
   # If there is any filenames to store the graphics, process them
   # to select the right device
   if (!is.null(fileout)) {
@@ -224,15 +224,26 @@ VizLayout <- function(fun, plot_dims, var, ..., special_args = NULL,
   }
 
   is_single_na <- function(x) ifelse(length(x) > 1, FALSE, is.na(x))
-  # Check var
-  if (!is.list(var) & (is.array(var) || (is_single_na(var)))) {
-    var <- list(var)
-  } else if (is.list(var)) {
-    if (!all(sapply(var, is.array) | sapply(var, is_single_na))) {
-      stop("Parameter 'var' must be an array or a list of arrays (or NA values).")
+  
+  # Check data
+  if (is.null(data)) {
+    if (!is.null(var)) {
+      data <- var
+      warning("The parameter 'var' is deprecated. Use 'data' instead.")
+    } else {
+      stop("Parameter 'data' cannot be NULL.")
+    }
+  } else if (!is.null(var)) {
+    warning("The parameter 'var' is deprecated. 'data' will be used instead.")
+  }
+  if (!is.list(data) & (is.array(data) || (is_single_na(data)))) {
+    data <- list(data)
+  } else if (is.list(data)) {
+    if (!all(sapply(data, is.array) | sapply(data, is_single_na))) {
+      stop("Parameter 'data' must be an array or a list of arrays (or NA values).")
     }
   } else {
-    stop("Parameter 'var' must be an array or a list of arrays.")
+    stop("Parameter 'data' must be an array or a list of arrays.")
   }
 
   # Check fun
@@ -241,29 +252,29 @@ VizLayout <- function(fun, plot_dims, var, ..., special_args = NULL,
       fun <- as.character(substitute(fun))
     }
     if (is.character(fun)) {
-      fun <- rep(fun, length(var))
+      fun <- rep(fun, length(data))
     }
   }
-  if (!is.character(fun) || (length(fun) != length(var))) {
-    stop("Parameter 'fun' must be a single function or a vector of function names, one for each array provided in parameter 'var'.")
+  if (!is.character(fun) || (length(fun) != length(data))) {
+    stop("Parameter 'fun' must be a single function or a vector of function names, one for each array provided in parameter 'data'.")
   }
 
   # Check special_args
   if (!is.null(special_args)) {
     if (!is.list(special_args) || any(!sapply(special_args, is.list))) {
       stop("Parameter 'special_args' must be a list of lists.")
-    } else if (length(special_args) != length(var)) {
-      stop("Parameter 'special_args' must contain a list of special arguments for each array provided in 'var'.")
+    } else if (length(special_args) != length(data)) {
+      stop("Parameter 'special_args' must contain a list of special arguments for each array provided in 'data'.")
     }
   }
 
   # Check plot_dims
   if (is.character(plot_dims) || is.numeric(plot_dims)) {
-    plot_dims <- replicate(length(var), plot_dims, simplify = FALSE)
+    plot_dims <- replicate(length(data), plot_dims, simplify = FALSE)
   }
   if (!is.list(plot_dims) || !all(sapply(plot_dims, is.character) | sapply(plot_dims, is.numeric)) ||
-      (length(plot_dims) != length(var))) {
-    stop("Parameter 'plot_dims' must contain a single numeric or character vector with dimension identifiers or a vector for each array provided in parameter 'var'.")
+      (length(plot_dims) != length(data))) {
+    stop("Parameter 'plot_dims' must contain a single numeric or character vector with dimension identifiers or a vector for each array provided in parameter 'data'.")
   }
 
   # Check nrow
@@ -324,14 +335,14 @@ VizLayout <- function(fun, plot_dims, var, ..., special_args = NULL,
   } else if (!is.logical(drawleg)) {
     stop("Parameter 'drawleg' must be either TRUE, FALSE or a valid identifier of a position (see ?PlotMultiMap).")
   }
-  if (drawleg != FALSE && all(sapply(var, is_single_na)) && 
+  if (drawleg != FALSE && all(sapply(data, is_single_na)) && 
       (is.null(brks) || length(brks) < 2)) {
-    stop("Either data arrays in 'var' or breaks in 'brks' must be provided if 'drawleg' is requested.")
+    stop("Either data arrays in 'data' or breaks in 'brks' must be provided if 'drawleg' is requested.")
   }
 
   # Check the rest of parameters (unless the user simply wants to build an empty layout)
-  if (!all(sapply(var, is_single_na))) {
-    tmp <- .create_var_limits(data = unlist(var), brks = brks, 
+  if (!all(sapply(data, is_single_na))) {
+    tmp <- .create_var_limits(data = unlist(data), brks = brks, 
                               bar_limits = bar_limits, drawleg = drawleg)
     var_limits <- tmp$var_limits
     drawleg <- tmp$drawleg
@@ -426,7 +437,7 @@ VizLayout <- function(fun, plot_dims, var, ..., special_args = NULL,
   # Count the total number of maps and reorder each array of maps to have the lat and lon dimensions at the end.
   n_plots <- 0
   plot_array_i <- 1
-  for (plot_array in var) {
+  for (plot_array in data) {
     if (is_single_na(plot_array)) {
       n_plots <- n_plots + 1
     } else {
@@ -440,16 +451,16 @@ VizLayout <- function(fun, plot_dims, var, ..., special_args = NULL,
         }
         if (!is.null(dimnames)) {
           if (any(!sapply(dim_ids, `%in%`, dimnames))) {
-            stop("All arrays provided in parameter 'var' must have all the dimensions in 'plot_dims'.")
+            stop("All arrays provided in parameter 'data' must have all the dimensions in 'plot_dims'.")
           }
           dim_ids <- sapply(dim_ids, function(x) which(dimnames == x)[1])
-          var[[plot_array_i]] <- Reorder(var[[plot_array_i]], c((1:length(dim(plot_array)))[-dim_ids], dim_ids))
+          data[[plot_array_i]] <- Reorder(data[[plot_array_i]], c((1:length(dim(plot_array)))[-dim_ids], dim_ids))
         } else {
-          warning(paste0("Assuming the ", plot_array_i, "th array provided in 'var' has 'plot_dims' as last dimensions (right-most)."))
+          warning(paste0("Assuming the ", plot_array_i, "th array provided in 'data' has 'plot_dims' as last dimensions (right-most)."))
           dims <- tail(c(rep(1, length(dim_ids)), dim(plot_array)), length(dim_ids))
           dim_ids <- tail(1:length(dim(plot_array)), length(dim_ids))
-          if (length(dim(var[[plot_array_i]])) < length(dims)) {
-            dim(var[[plot_array_i]]) <- dims
+          if (length(dim(data[[plot_array_i]])) < length(dims)) {
+            dim(data[[plot_array_i]]) <- dims
           }
         }
       } else if (any(dim_ids > length(dim(plot_array)))) {
@@ -457,8 +468,8 @@ VizLayout <- function(fun, plot_dims, var, ..., special_args = NULL,
       }
       n_plots <- n_plots + prod(dim(plot_array)[-dim_ids])
       #n_plots <- n_plots + prod(head(c(rep(1, length(dim_ids)), dim(plot_array)), length(dim(plot_array))))
-      if (length(dim(var[[plot_array_i]])) == length(dim_ids)) {
-        dim(var[[plot_array_i]]) <- c(1, dim(var[[plot_array_i]]))
+      if (length(dim(data[[plot_array_i]])) == length(dim_ids)) {
+        dim(data[[plot_array_i]]) <- c(1, dim(data[[plot_array_i]]))
         dim_ids <- dim_ids + 1
       }
       plot_dims[[plot_array_i]] <- dim_ids
@@ -473,7 +484,7 @@ VizLayout <- function(fun, plot_dims, var, ..., special_args = NULL,
   } else if (is.null(nrow)) {
     nrow <- ceiling(n_plots/ncol)
   } else if (nrow * ncol < n_plots) {
-    stop("There are more arrays to plot in 'var' than cells defined by 'nrow' x 'ncol'.")
+    stop("There are more arrays to plot in 'data' than cells defined by 'nrow' x 'ncol'.")
   }
 
   if (is.logical(drawleg) && drawleg) {
@@ -538,7 +549,7 @@ VizLayout <- function(fun, plot_dims, var, ..., special_args = NULL,
       multi_colorbar <- TRUE
       cat_dim <- list(...)$cat_dim
       if (is.null(cat_dim)) cat_dim <- 'bin'  # default
-      nmap <- as.numeric(dim(var[[1]])[cat_dim])
+      nmap <- as.numeric(dim(data[[1]])[cat_dim])
       minimum_value <- ceiling(1 / nmap * 10 * 1.1) * 10
       display_range = c(minimum_value, 100)
       mat_layout <- mat_layout + nmap
@@ -682,10 +693,10 @@ VizLayout <- function(fun, plot_dims, var, ..., special_args = NULL,
 
   array_number <- 1
   plot_number <- 1
-  # For each array provided in var
-  lapply(var, function(x) {
+  # For each array provided in data
+  lapply(data, function(x) {
     if (is_single_na(x)) {
-      if (!all(sapply(var[array_number:length(var)], is_single_na))) {
+      if (!all(sapply(data[array_number:length(data)], is_single_na))) {
         plot.new()
         par(new = FALSE)
       }
diff --git a/R/VizStereoMap.R b/R/VizStereoMap.R
index d1d1dd5..49235ec 100644
--- a/R/VizStereoMap.R
+++ b/R/VizStereoMap.R
@@ -238,10 +238,8 @@ VizStereoMap <- function(data = NULL, lon, lat, varu = NULL, varv = NULL,
     } else {
       stop("Parameter 'data' cannot be NULL.")
     }
-  } else {
-    if (!is.null(var)) {
-      warning("The parameter 'var' is deprecated. 'data' will be used instead.")
-    }
+  } else if (!is.null(var)) {
+    warning("The parameter 'var' is deprecated. 'data' will be used instead.")
   }
   if (!is.array(data)) {
     stop("Parameter 'data' must be a numeric array.")
-- 
GitLab


From 7ea6cf6a9cc28cff074e68dd5b3b05fe4ffbd557 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 28 Feb 2025 16:32:37 +0100
Subject: [PATCH 15/72] change 'var' for 'data' in R/VizMatrix.R

---
 R/VizMatrix.R | 55 +++++++++++++++++++++++++++++++--------------------
 1 file changed, 34 insertions(+), 21 deletions(-)

diff --git a/R/VizMatrix.R b/R/VizMatrix.R
index 1fd9ac0..9043a6b 100644
--- a/R/VizMatrix.R
+++ b/R/VizMatrix.R
@@ -4,8 +4,9 @@
 #'grid. It is useful for a slide or article to present tabular results as 
 #'colors instead of numbers.
 #'
-#'@param var A numerical matrix containing the values to be displayed in a 
+#'@param data A numerical matrix containing the values to be displayed in a 
 #'  colored image.
+#'@param var Deprecated. Use 'data' instead.
 #'@param brks A vector of the color bar intervals. The length must be one more 
 #'  than the parameter 'cols'. Use ColorBarContinuous() to generate default
 #'  values.
@@ -18,13 +19,13 @@
 #'@param xtitle A string of title of the x-axis. Set NULL as default.
 #'@param ytitle A string of title of the y-axis. Set NULL as default.
 #'@param xlabels A vector of labels of the x-axis. The length must be 
-#'  length of the column of parameter 'var'. Set the sequence from 1 to the 
-#'  length of the column of parameter 'var' as default.
+#'  length of the column of parameter 'data'. Set the sequence from 1 to the 
+#'  length of the column of parameter 'data' as default.
 #'@param xvert A logical value to decide whether to place x-axis labels 
 #'  vertically. Set FALSE as default, which keeps the labels horizontally. 
 #'@param ylabels A vector of labels of the y-axis The length must be 
-#'  length of the row of parameter 'var'. Set the sequence from 1 to the 
-#'  length of the row of parameter 'var' as default.
+#'  length of the row of parameter 'data'. Set the sequence from 1 to the 
+#'  length of the row of parameter 'data' as default.
 #'@param line An integer specifying the distance between the title of the 
 #'  x-axis and the x-axis. Set 3 as default. Adjust if the x-axis labels 
 #'  are long.
@@ -35,9 +36,9 @@
 #'@param legend.width A number between 0 and 0.5 to adjust the legend width.
 #'  Set 0.15 as default.
 #'@param xlab_dist A number specifying the distance between the x labels and 
-#'  the x axis. If not specified, it equals to -1 - (nrow(var) / 10 - 1).
+#'  the x axis. If not specified, it equals to -1 - (nrow(data) / 10 - 1).
 #'@param ylab_dist A number specifying the distance between the y labels and 
-#'  the y axis. If not specified, it equals to 0.5 - ncol(var) / 10.
+#'  the y axis. If not specified, it equals to 0.5 - ncol(data) / 10.
 #'@param fileout A string of full directory path and file name indicating where 
 #'  to save the plot. If not specified (default), a graphics device will pop up. 
 #'@param size_units A string indicating the units of the size of the device 
@@ -52,7 +53,7 @@
 #'@examples
 #'#Example with random data
 #'  \dontrun{
-#' esviz:::VizMatrix(var = matrix(rnorm(n = 120, mean = 0.3), 10, 12),
+#' esviz:::VizMatrix(data = matrix(rnorm(n = 120, mean = 0.3), 10, 12),
 #'            cols = c('white','#fef0d9','#fdd49e','#fdbb84','#fc8d59',
 #'                      '#e34a33','#b30000', '#7f0000'),
 #'            brks = c(-1, 0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 1),
@@ -63,18 +64,30 @@
 #'  }
 #'
 #'@importFrom grDevices dev.new dev.off dev.cur 
-VizMatrix <- function(var, brks = NULL, cols = NULL, 
-                       toptitle = NULL, title.color = "royalblue4", 
-                       xtitle = NULL, ytitle = NULL, xlabels = NULL, xvert = FALSE, 
-                       ylabels = NULL, line = 3, figure.width = 1, legend = TRUE, 
-                       legend.width = 0.15, xlab_dist = NULL, ylab_dist = NULL, 
-                       fileout = NULL, size_units = 'px', res = 100, ...) {
-
-  # Check variables:  
-  if (!is.matrix(var))
+VizMatrix <- function(data = NULL, brks = NULL, cols = NULL, toptitle = NULL,
+                      title.color = "royalblue4", xtitle = NULL, ytitle = NULL,
+                      xlabels = NULL, xvert = FALSE, ylabels = NULL, line = 3,
+                      figure.width = 1, legend = TRUE, legend.width = 0.15,
+                      xlab_dist = NULL, ylab_dist = NULL, fileout = NULL,
+                      size_units = 'px', res = 100, var = NULL, ...) {
+
+  # Check data:
+  if (is.null(data)) {
+    if (!is.null(var)) {
+      data <- var
+      warning("The parameter 'var' is deprecated. Use 'data' instead.")
+    } else {
+      stop("Parameter 'data' cannot be NULL.")
+    }
+  } else if (!is.null(var)) {
+    warning("The parameter 'var' is deprecated. 'data' will be used instead.")
+  }
+  if (!is.matrix(data)) {
     stop("Input values are not a matrix")
-  if (!is.numeric(var))
+  }
+  if (!is.numeric(data)){
     stop("Input values are not always numbers")
+  }
 
   # Build: brks, cols 
   colorbar <- ColorBarContinuous(brks = brks, cols = cols, vertical = FALSE, 
@@ -87,8 +100,8 @@ VizMatrix <- function(var, brks = NULL, cols = NULL,
 
   if (n.brks != n.cols + 1)
     stop("There must be one break more than the number of colors")
-  ncols <- ncol(var) ## number of columns of the image
-  nrows <- nrow(var) ## number of rows of the image
+  ncols <- ncol(data) ## number of columns of the image
+  nrows <- nrow(data) ## number of rows of the image
   if (ncols < 2)
     stop("Matrix must have at least two columns")
   if (nrows < 2)
@@ -202,7 +215,7 @@ VizMatrix <- function(var, brks = NULL, cols = NULL,
 
   # Create an array of colors instead of numbers (it starts all gray):                
   array.colors <- array("gray", c(nrows, ncols))
-  for (int in n.cols:1) array.colors[var <= brks[int + 1]] <- cols[int]
+  for (int in n.cols:1) array.colors[data <= brks[int + 1]] <- cols[int]
 
   # fill with colors the cells in the figure:
   for (p in 1:nrows) {
-- 
GitLab


From 05b7927895050eba1796342203e63be45b83afda Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 28 Feb 2025 16:51:01 +0100
Subject: [PATCH 16/72] Change 'var' for 'data' in R/VizSection.R

---
 R/VizSection.R | 39 +++++++++++++++++++++++++--------------
 1 file changed, 25 insertions(+), 14 deletions(-)

diff --git a/R/VizSection.R b/R/VizSection.R
index f772333..4a4e373 100644
--- a/R/VizSection.R
+++ b/R/VizSection.R
@@ -2,7 +2,8 @@
 #'
 #'Plot a (longitude,depth) or (latitude,depth) section.
 #'
-#'@param var Matrix to plot with (longitude/latitude, depth) dimensions.
+#'@param data Matrix to plot with (longitude/latitude, depth) dimensions.
+#'@param var Deprecated. Use 'data' instead.
 #'@param horiz Array of longitudes or latitudes.
 #'@param depth Array of depths.
 #'@param toptitle Title, optional.
@@ -43,11 +44,11 @@
 #'esviz:::VizSection(data, horiz = 0:20, depth = seq(0, 300, length.out = 7),
 #'           toptitle = 'Temperature cross-section', units = "degC")
 #'@importFrom grDevices dev.cur dev.new dev.off rainbow
-VizSection <- function(var, horiz, depth, toptitle = '', sizetit = 1,
-                        units = '', brks = NULL, cols = NULL, axelab = TRUE,
-                        intydep = 200, intxhoriz = 20, drawleg = TRUE,
-                        fileout = NULL, width = 10, height = 8,
-                        size_units = 'in', res = 100, ...) {
+VizSection <- function(data = NULL, horiz, depth, toptitle = '', sizetit = 1,
+                       units = '', brks = NULL, cols = NULL, axelab = TRUE,
+                       intydep = 200, intxhoriz = 20, drawleg = TRUE,
+                       fileout = NULL, width = 10, height = 8,
+                       size_units = 'in', res = 100, data = NULL, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("cex", "cex.axis", "cex.main", "col", "lab", "las", "mai", "mar", "mgp", "new", "ps", "tck")
@@ -65,16 +66,26 @@ VizSection <- function(var, horiz, depth, toptitle = '', sizetit = 1,
   #  Input arguments 
   # ~~~~~~~~~~~~~~~~~
   #
-  dims <- dim(var)
+  if (is.null(data)) {
+    if (!is.null(var)) {
+      data <- var
+      warning("The parameter 'var' is deprecated. Use 'data' instead.")
+    } else {
+      stop("Parameter 'data' cannot be NULL.")
+    }
+  } else if (!is.null(var)) {
+    warning("The parameter 'var' is deprecated. 'data' will be used instead.")
+  }
+  dims <- dim(data)
   if (length(dims) > 2) {
-    stop("Only 2 dimensions expected for var : (lon,depth) or (lat,depth)")
+    stop("Only 2 dimensions expected for data : (lon,depth) or (lat,depth)")
   }
   if (dims[1] != length(horiz) | dims[2] != length(depth)) {
     if (dims[1] == length(depth) & dims[2] == length(horiz)) {
-      var <- t(var)
-      dims <- dim(var)
+      data <- t(data)
+      dims <- dim(data)
     } else {
-      stop("Inconsistent var dimensions and longitudes/latitudes + depth")
+      stop("Inconsistent data dimensions and longitudes/latitudes + depth")
     }
   }
   dhoriz <- horiz[2:dims[1]] - horiz[1:(dims[1] - 1)]
@@ -89,8 +100,8 @@ VizSection <- function(var, horiz, depth, toptitle = '', sizetit = 1,
   depmin <- min(depth)
   depmax <- max(depth)
   if (is.null(brks) == TRUE) {
-    ll <- signif(min(var, na.rm = TRUE), 4)
-    ul <- signif(max(var, na.rm = TRUE), 4)
+    ll <- signif(min(data, na.rm = TRUE), 4)
+    ul <- signif(max(data, na.rm = TRUE), 4)
     if (is.null(cols) == TRUE) {
       cols <- c("dodgerblue4", "dodgerblue1", "forestgreen", "yellowgreen",
                 "white", "white", "yellow", "orange", "red", "saddlebrown")
@@ -141,7 +152,7 @@ VizSection <- function(var, horiz, depth, toptitle = '', sizetit = 1,
   image(horizb$x, depthb$x, array(0, dims), col = 'grey', breaks = c(-1, 1),
         axes = FALSE, xlab = "", ylab = "", main = toptitle, 
         cex.main = 1.5 * sizetit)
-  image(horizb$x, depthb$x, var[horizb$ix, depthb$ix], col = cols, 
+  image(horizb$x, depthb$x, data[horizb$ix, depthb$ix], col = cols, 
         breaks = brks, axes = FALSE, xlab = "", ylab = "", add = TRUE)
   if (axelab) {
     minhoriz <- ceiling(round(min(horizb$x), 0) / 10) * 10
-- 
GitLab


From f2cd4aa0049b50b0b2eb619463e6d9ca38cd7513 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 28 Feb 2025 17:01:58 +0100
Subject: [PATCH 17/72] Change 'var' for 'data' in R/VizVsLTime.R

---
 R/VizVsLTime.R | 52 +++++++++++++++++++++++++++++++-------------------
 1 file changed, 32 insertions(+), 20 deletions(-)

diff --git a/R/VizVsLTime.R b/R/VizVsLTime.R
index 7fde226..941bc3d 100644
--- a/R/VizVsLTime.R
+++ b/R/VizVsLTime.R
@@ -9,9 +9,10 @@
 #'along the forecast time for all the input experiments on the same figure 
 #'with their confidence intervals.
 #'
-#'@param var Matrix containing any Prediction Score with dimensions:\cr
+#'@param data Matrix containing any Prediction Score with dimensions:\cr
 #'  (nexp/nmod, 3/4 ,nltime)\cr
 #'  or (nexp/nmod, nobs, 3/4 ,nltime).
+#'@param var Deprecated. Use 'data' instead.
 #'@param toptitle Main title, optional.
 #'@param ytitle Title of Y-axis, optional.
 #'@param monini Starting month between 1 and 12. Default = 1.
@@ -84,13 +85,14 @@
 #'@importFrom grDevices dev.cur dev.new dev.off
 #'@importFrom stats ts
 #'@importFrom s2dv InsertDim
-VizVsLTime <- function(var, toptitle = '', ytitle = '', monini = 1, freq = 12,
-               nticks = NULL, limits = NULL,
-               listexp = c('exp1', 'exp2', 'exp3'),
-               listobs = c('obs1', 'obs2', 'obs3'), biglab = FALSE, hlines = NULL,
-               leg = TRUE, siglev = FALSE, sizetit = 1, show_conf = TRUE,
-               fileout = NULL,
-               width = 8, height = 5, size_units = 'in', res = 100, ...) {
+VizVsLTime <- function(data = NULL, toptitle = '', ytitle = '', monini = 1,
+                       freq = 12, nticks = NULL, limits = NULL,
+                       listexp = c('exp1', 'exp2', 'exp3'),
+                       listobs = c('obs1', 'obs2', 'obs3'),
+                       biglab = FALSE, hlines = NULL, leg = TRUE,
+                       siglev = FALSE, sizetit = 1, show_conf = TRUE,
+                       fileout = NULL, width = 8, height = 5, size_units = 'in',
+                       res = 100, var = NULL, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("cex", "cex.axis", "cex.lab", "cex.main", "col", "fin", "lab", "las", "lend", "lty", "lwd", "mai", "mgp", "new", "pin", "ps", "pty")
@@ -108,20 +110,30 @@ VizVsLTime <- function(var, toptitle = '', ytitle = '', monini = 1, freq = 12,
   #  Get some arguments
   # ~~~~~~~~~~~~~~~~~~~~
   #
-  if (length(dim(var)) == 3) {
-    var <- s2dv::InsertDim(var, posdim = 2, lendim = 1, name = 'stats')
-  } else if (length(dim(var)) != 4) {
-    stop("Parameter 'var' should have 3 or 4 dimensions: c(n. exp[, n. obs], 3/4, n. lead-times)")
+  if (is.null(data)) {
+    if (!is.null(var)) {
+      data <- var
+      warning("The parameter 'var' is deprecated. Use 'data' instead.")
+    } else {
+      stop("Parameter 'data' cannot be NULL.")
+    }
+  } else if (!is.null(var)) {
+    warning("The parameter 'var' is deprecated. 'data' will be used instead.")
+  }
+  if (length(dim(data)) == 3) {
+    data <- s2dv::InsertDim(data, posdim = 2, lendim = 1, name = 'stats')
+  } else if (length(dim(data)) != 4) {
+    stop("Parameter 'data' should have 3 or 4 dimensions: c(n. exp[, n. obs], 3/4, n. lead-times)")
   }
-  nleadtime <- dim(var)[4]
-  nexp <- dim(var)[1]
-  nobs <- dim(var)[2]
+  nleadtime <- dim(data)[4]
+  nexp <- dim(data)[1]
+  nobs <- dim(data)[2]
   if (is.null(limits) == TRUE) {
-	if (all(is.na(var > 0))) {
+	if (all(is.na(data > 0))) {
       ll <- ul <- 0
 	} else {
-      ll <- min(var, na.rm = TRUE)
-      ul <- max(var, na.rm = TRUE)
+      ll <- min(data, na.rm = TRUE)
+      ul <- max(data, na.rm = TRUE)
     }
     if (biglab) {
       ul <- ul + 0.4 * (ul - ll)
@@ -220,7 +232,7 @@ VizVsLTime <- function(var, toptitle = '', ytitle = '', monini = 1, freq = 12,
   legendcol <- array(dim = nobs * nexp)
   ind <- 1
   if (show_conf == TRUE) {
-    start_line <- dim(var)[3]
+    start_line <- dim(data)[3]
     end_line <- 1
   } else {
     start_line <- 2
@@ -231,7 +243,7 @@ VizVsLTime <- function(var, toptitle = '', ytitle = '', monini = 1, freq = 12,
     for (jexp in 1:nexp) {
       for (jobs in 1:nobs) {
         par(new = TRUE)
-        plot(var[jexp, jobs, jt, ], type = lines[jt], ylim = c(ll, ul), 
+        plot(data[jexp, jobs, jt, ], type = lines[jt], ylim = c(ll, ul), 
              col = color[jexp], lty = type[jobs], lwd = thickness[jobs, jt], 
              ylab = "", xlab = "", axes = FALSE)
         legendnames[ind] <- paste(listexp[jexp], 'vs', listobs[jobs])
-- 
GitLab


From 47cde9cc2bd775885af06adcda4e8585fa1927c2 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 28 Feb 2025 17:05:10 +0100
Subject: [PATCH 18/72] bugfix

---
 R/VizSection.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/VizSection.R b/R/VizSection.R
index 4a4e373..14ed580 100644
--- a/R/VizSection.R
+++ b/R/VizSection.R
@@ -48,7 +48,7 @@ VizSection <- function(data = NULL, horiz, depth, toptitle = '', sizetit = 1,
                        units = '', brks = NULL, cols = NULL, axelab = TRUE,
                        intydep = 200, intxhoriz = 20, drawleg = TRUE,
                        fileout = NULL, width = 10, height = 8,
-                       size_units = 'in', res = 100, data = NULL, ...) {
+                       size_units = 'in', res = 100, var = NULL, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("cex", "cex.axis", "cex.main", "col", "lab", "las", "mai", "mar", "mgp", "new", "ps", "tck")
-- 
GitLab


From 2398df025a644f70edc48a440be54cc6c6c86e62 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 28 Feb 2025 17:21:07 +0100
Subject: [PATCH 19/72] Update Rd files

---
 man/VizAnimateMap.Rd | 15 +++++++++------
 man/VizLayout.Rd     | 41 ++++++++++++++++++++++-------------------
 man/VizMatrix.Rd     | 21 ++++++++++++---------
 man/VizSection.Rd    |  7 +++++--
 man/VizVsLTime.Rd    |  7 +++++--
 5 files changed, 53 insertions(+), 38 deletions(-)

diff --git a/man/VizAnimateMap.Rd b/man/VizAnimateMap.Rd
index 29b8eff..236a327 100644
--- a/man/VizAnimateMap.Rd
+++ b/man/VizAnimateMap.Rd
@@ -5,7 +5,7 @@
 \title{Animate Maps of Forecast/Observed Values or Scores Over Forecast Time}
 \usage{
 VizAnimateMap(
-  var,
+  data = NULL,
   lon,
   lat,
   toptitle = rep("", 11),
@@ -29,11 +29,12 @@ VizAnimateMap(
   equi = TRUE,
   fileout = c("output1_animvsltime.gif", "output2_animvsltime.gif",
     "output3_animvsltime.gif"),
+  var = NULL,
   ...
 )
 }
 \arguments{
-\item{var}{Matrix of dimensions (nltime, nlat, nlon) or 
+\item{data}{Matrix of dimensions (nltime, nlat, nlon) or 
 (nexp/nmod, nltime, nlat, nlon) or (nexp/nmod, 3/4, nltime, nlat, nlon) or 
 (nexp/nmod, nobs, 3/4, nltime, nlat, nlon).}
 
@@ -57,7 +58,7 @@ second exp with successive obs, etc ...}
 reached. Default = FALSE.}
 
 \item{brks}{Limits of colour levels, optional. For example: 
-seq(min(var), max(var), (max(var) - min(var)) / 10).}
+seq(min(data), max(data), (max(data) - min(data)) / 10).}
 
 \item{cols}{Vector of colours of length(brks) - 1, optional.}
 
@@ -97,6 +98,8 @@ Default: TRUE.}
  If RMS, RMSSS, correlations : first exp with successive obs, then second 
 exp with successive obs, etc ...}
 
+\item{var}{Deprecated. Use 'data' instead.}
+
 \item{...}{Arguments to be passed to the method. Only accepts the following 
 graphical parameters:\cr
 adj ann ask bty cex cex.axis cex.lab cex.main cex.sub
@@ -125,9 +128,9 @@ Examples of input:
  \item{
  Model output from load/ano/smoothing:
           (nmod, nmemb, sdate, nltime, nlat, nlon)
- then passed through spread(var, posdim = 2, narm = TRUE)
-                   & mean1dim(var, posdim = 3, narm = TRUE)
- or through trend(mean1dim(var, 2), posTR = 2):
+ then passed through spread(data, posdim = 2, narm = TRUE)
+                   & mean1dim(data, posdim = 3, narm = TRUE)
+ or through trend(mean1dim(data, 2), posTR = 2):
           (nmod, 3, nltime, nlat, nlon)
  animates average along start dates of IQR/MaxMin/SD/MAD across members 
  or trends of the ensemble-mean computed accross the start dates.
diff --git a/man/VizLayout.Rd b/man/VizLayout.Rd
index 0fd373c..dbed7de 100644
--- a/man/VizLayout.Rd
+++ b/man/VizLayout.Rd
@@ -7,7 +7,7 @@
 VizLayout(
   fun,
   plot_dims,
-  var,
+  data = NULL,
   ...,
   special_args = NULL,
   nrow = NULL,
@@ -50,25 +50,26 @@ VizLayout(
   height = NULL,
   size_units = "in",
   res = 100,
-  close_device = TRUE
+  close_device = TRUE,
+  var = NULL
 )
 }
 \arguments{
 \item{fun}{Plot function (or name of the function) to be called on the 
-arrays provided in 'var'. If multiple arrays are provided in 'var', a 
+arrays provided in 'data'. If multiple arrays are provided in 'data', a 
 vector of as many function names (character strings!) can be provided in 
-'fun', one for each array in 'var'.}
+'fun', one for each array in 'data'.}
 
 \item{plot_dims}{Numeric or character string vector with identifiers of the 
 input plot dimensions of the plot function specified in 'fun'. If 
-character labels are provided, names(dim(var)) or attr('dimensions', var) 
+character labels are provided, names(dim(data)) or attr('dimensions', data) 
 will be checked to locate the dimensions. As many plots as 
-prod(dim(var)[-plot_dims]) will be generated. If multiple arrays are 
-provided in 'var', 'plot_dims' can be sent a list with a vector of plot 
+prod(dim(data)[-plot_dims]) will be generated. If multiple arrays are 
+provided in 'data', 'plot_dims' can be sent a list with a vector of plot 
 dimensions for each. If a single vector is provided, it will be used for 
-all the arrays in 'var'.}
+all the arrays in 'data'.}
 
-\item{var}{Multi-dimensional array with at least the dimensions expected by 
+\item{data}{Multi-dimensional array with at least the dimensions expected by 
 the specified plot function in 'fun'. The dimensions reqired by the 
 function must be specified in 'plot_dims'. The dimensions can be 
 disordered and will be reordered automatically. Dimensions can optionally 
@@ -83,7 +84,7 @@ blank cell in the layout, which can be populated after
 (see .SwitchToFigure).}
 
 \item{\dots}{Parameters to be sent to the plotting function 'fun'. If 
-multiple arrays are provided in 'var' and multiple functions are provided 
+multiple arrays are provided in 'data' and multiple functions are provided 
 in 'fun', the parameters provided through \dots will be sent to all the 
 plot functions, as common parameters. To specify concrete arguments for 
 each of the plot functions see parameter 'special_args'.}
@@ -92,13 +93,13 @@ each of the plot functions see parameter 'special_args'.}
 arguments for each of the plot functions provided in 'fun'. If you want to 
 fix a different value for each plot in the layout you can do so by 
 a) splitting your array into a list of sub-arrays (each with the data for 
-one plot) and providing it as parameter 'var', 
+one plot) and providing it as parameter 'data', 
 b) providing a list of named sub-lists in 'special_args', where the names 
 of each sub-list match the names of the parameters to be adjusted, and 
 each value in a sub-list contains the value of the corresponding parameter.
 For example, if the plots are two maps with different arguments, the 
 structure would be like:\cr
-var:\cr
+data:\cr
  List of 2\cr
   $ : num [1:360, 1:181] 1 3.82 5.02 6.63 8.72 ...\cr
   $ : num [1:360, 1:181] 2.27 2.82 4.82 7.7 10.32 ...\cr
@@ -159,7 +160,7 @@ subtitles. Takes 1 by default.}
 \item{brks, cols, bar_limits, triangle_ends}{Usually only providing 'brks' is 
 enough to generate the desired colour bar. These parameters allow to 
 define n breaks that define n - 1 intervals to classify each of the values 
-in 'var'. The corresponding grid cell of a given value in 'var' will be 
+in 'data'. The corresponding grid cell of a given value in 'data' will be 
 coloured in function of the interval it belongs to. These parameters are 
 sent to \code{ColorBarContinuous()} to generate the breaks and colours. Additional 
 colours for values beyond the limits of the colour bar are also generated 
@@ -176,7 +177,7 @@ FALSE or:\cr
 \item{titles}{Character string vector with titles for each of the figures in 
 the multi-pannel, from top-left to bottom-right. Blank by default.}
 
-\item{col_inf, col_sup}{Colour identifiers to colour the values in 'var' that 
+\item{col_inf, col_sup}{Colour identifiers to colour the values in 'data' that 
 go beyond the extremes of the colour bar and to colour NA values, 
 respectively. 'colNA' takes 'white' by default. 'col_inf' and 'col_sup' 
 will take the value of 'colNA' if not specified. See ?ColorBarContinuous for a full 
@@ -185,7 +186,7 @@ explanation on 'col_inf' and 'col_sup'.}
 \item{color_fun, subsampleg, bar_extra_labels, draw_bar_ticks, draw_separators, triangle_ends_scale, bar_label_digits, bar_label_scale, units_scale, bar_tick_scale, bar_extra_margin}{Set of parameters to control the visual aspect of the drawn colour bar. See ?ColorBarContinuous for a full explanation.}
 
 \item{units}{Title at the top of the colour bar, most commonly the units of 
-the variable provided in parameter 'var'.}
+the variable provided in parameter 'data'.}
 
 \item{bar_left_shift_scale}{When plotting row titles, a shift is added to 
 the horizontal positioning of the colour bar in order to center it to the 
@@ -223,6 +224,8 @@ the layout and a 'fileout' has been specified. This is useful to avoid
 closing the device when saving the layout into a file and willing to add 
 extra elements or figures. Takes TRUE by default. Disregarded if no 
 'fileout' has been specified.}
+
+\item{var}{Deprecated. Use 'data' instead.}
 }
 \value{
 \item{brks}{
@@ -254,7 +257,7 @@ dimensions of each of the functions have to be specified, either with the
 names or the indices of the corresponding input dimensions. It is possible 
 to draw a common colour bar at any of the sides of the multi-pannel for all 
 the s2dv plots that use a colour bar. Common plotting arguments 
-for all the arrays in 'var' can be specified via the '...' parameter, and 
+for all the arrays in 'data' can be specified via the '...' parameter, and 
 specific plotting arguments for each array can be fully adjusted via 
 'special_args'. It is possible to draw titles for each of the figures, 
 layout rows, layout columns and for the whole figure. A number of parameters 
@@ -268,12 +271,12 @@ nested in complex layouts.
  \dontrun{
 ano <- s2dv::Ano_CrossValid(map_temp$exp, map_temp$obs, memb = FALSE,
                            dat_dim = c('dat', 'member'), memb_dim = 'member')
-var <- s2dv::MeanDims(ano$exp, "member")
-lats <- attr(map_temp$exp, "Variables")$common$lat
+data <- s2dv::MeanDims(ano$exp, "member")
+lats <- attr(map_temp$exp, "dataiables")$common$lat
 lons <- attr(map_temp$exp, "Variables")$common$lon
 
 VizLayout(fun = VizEquiMap, plot_dims = c('lat', 'lon'),
-         var = var[, 1, 1, 1, , ], lon = lons, lat = lats,
+         data = data[, 1, 1, 1, , ], lon = lons, lat = lats,
          filled.continents = FALSE, 
          toptitle = 'Near-surface temperature Nov.',
          titles = paste(2000:2005))
diff --git a/man/VizMatrix.Rd b/man/VizMatrix.Rd
index 016603c..6f080ab 100644
--- a/man/VizMatrix.Rd
+++ b/man/VizMatrix.Rd
@@ -5,7 +5,7 @@
 \title{Function to convert any numerical table to a grid of coloured squares.}
 \usage{
 VizMatrix(
-  var,
+  data = NULL,
   brks = NULL,
   cols = NULL,
   toptitle = NULL,
@@ -24,11 +24,12 @@ VizMatrix(
   fileout = NULL,
   size_units = "px",
   res = 100,
+  var = NULL,
   ...
 )
 }
 \arguments{
-\item{var}{A numerical matrix containing the values to be displayed in a 
+\item{data}{A numerical matrix containing the values to be displayed in a 
 colored image.}
 
 \item{brks}{A vector of the color bar intervals. The length must be one more 
@@ -49,15 +50,15 @@ color. Set "royalblue4" as default.}
 \item{ytitle}{A string of title of the y-axis. Set NULL as default.}
 
 \item{xlabels}{A vector of labels of the x-axis. The length must be 
-length of the column of parameter 'var'. Set the sequence from 1 to the 
-length of the column of parameter 'var' as default.}
+length of the column of parameter 'data'. Set the sequence from 1 to the 
+length of the column of parameter 'data' as default.}
 
 \item{xvert}{A logical value to decide whether to place x-axis labels 
 vertically. Set FALSE as default, which keeps the labels horizontally.}
 
 \item{ylabels}{A vector of labels of the y-axis The length must be 
-length of the row of parameter 'var'. Set the sequence from 1 to the 
-length of the row of parameter 'var' as default.}
+length of the row of parameter 'data'. Set the sequence from 1 to the 
+length of the row of parameter 'data' as default.}
 
 \item{line}{An integer specifying the distance between the title of the 
 x-axis and the x-axis. Set 3 as default. Adjust if the x-axis labels 
@@ -73,10 +74,10 @@ Set TRUE as default.}
 Set 0.15 as default.}
 
 \item{xlab_dist}{A number specifying the distance between the x labels and 
-the x axis. If not specified, it equals to -1 - (nrow(var) / 10 - 1).}
+the x axis. If not specified, it equals to -1 - (nrow(data) / 10 - 1).}
 
 \item{ylab_dist}{A number specifying the distance between the y labels and 
-the y axis. If not specified, it equals to 0.5 - ncol(var) / 10.}
+the y axis. If not specified, it equals to 0.5 - ncol(data) / 10.}
 
 \item{fileout}{A string of full directory path and file name indicating where 
 to save the plot. If not specified (default), a graphics device will pop up.}
@@ -88,6 +89,8 @@ creator function of the corresponding device.}
 \item{res}{A positive number indicating resolution of the device (file or window) 
 to plot in. See ?Devices and the creator function of the corresponding device.}
 
+\item{var}{Deprecated. Use 'data' instead.}
+
 \item{...}{The additional parameters to be passed to function 
 ColorBarContinuous() in s2dv for color legend creation.}
 }
@@ -102,7 +105,7 @@ colors instead of numbers.
 \examples{
 #Example with random data
  \dontrun{
-esviz:::VizMatrix(var = matrix(rnorm(n = 120, mean = 0.3), 10, 12),
+esviz:::VizMatrix(data = matrix(rnorm(n = 120, mean = 0.3), 10, 12),
            cols = c('white','#fef0d9','#fdd49e','#fdbb84','#fc8d59',
                      '#e34a33','#b30000', '#7f0000'),
            brks = c(-1, 0, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 1),
diff --git a/man/VizSection.Rd b/man/VizSection.Rd
index bc2947b..cb7fe69 100644
--- a/man/VizSection.Rd
+++ b/man/VizSection.Rd
@@ -5,7 +5,7 @@
 \title{Plots A Vertical Section}
 \usage{
 VizSection(
-  var,
+  data = NULL,
   horiz,
   depth,
   toptitle = "",
@@ -22,11 +22,12 @@ VizSection(
   height = 8,
   size_units = "in",
   res = 100,
+  var = NULL,
   ...
 )
 }
 \arguments{
-\item{var}{Matrix to plot with (longitude/latitude, depth) dimensions.}
+\item{data}{Matrix to plot with (longitude/latitude, depth) dimensions.}
 
 \item{horiz}{Array of longitudes or latitudes.}
 
@@ -68,6 +69,8 @@ corresponding device.}
 \item{res}{Resolution of the device (file or window) to plot in. See 
 ?Devices and the creator function of the corresponding device.}
 
+\item{var}{Deprecated. Use 'data' instead.}
+
 \item{...}{Arguments to be passed to the method. Only accepts the following
 graphical parameters:\cr
 adj ann ask bg bty cex.lab cex.sub cin col.axis col.lab col.main col.sub 
diff --git a/man/VizVsLTime.Rd b/man/VizVsLTime.Rd
index 7ff5ad4..0b4c8aa 100644
--- a/man/VizVsLTime.Rd
+++ b/man/VizVsLTime.Rd
@@ -5,7 +5,7 @@
 \title{Plot a score along the forecast time with its confidence interval}
 \usage{
 VizVsLTime(
-  var,
+  data = NULL,
   toptitle = "",
   ytitle = "",
   monini = 1,
@@ -25,11 +25,12 @@ VizVsLTime(
   height = 5,
   size_units = "in",
   res = 100,
+  var = NULL,
   ...
 )
 }
 \arguments{
-\item{var}{Matrix containing any Prediction Score with dimensions:\cr
+\item{data}{Matrix containing any Prediction Score with dimensions:\cr
 (nexp/nmod, 3/4 ,nltime)\cr
 or (nexp/nmod, nobs, 3/4 ,nltime).}
 
@@ -82,6 +83,8 @@ corresponding device.}
 \item{res}{Resolution of the device (file or window) to plot in. See 
 ?Devices and the creator function of the corresponding device.}
 
+\item{var}{Deprecated. Use 'data' instead.}
+
 \item{...}{Arguments to be passed to the method. Only accepts the following
 graphical parameters:\cr
 adj ann ask bg bty cex.sub cin col.axis col.lab col.main col.sub cra crt 
-- 
GitLab


From 5e89bececa43c6d06902169f778adc18123f4763 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Mon, 10 Mar 2025 10:32:50 +0100
Subject: [PATCH 20/72] Alternative to 'data = NULL'. VizEquiMap.R example

---
 R/VizEquiMap.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/VizEquiMap.R b/R/VizEquiMap.R
index bae6999..d905a35 100644
--- a/R/VizEquiMap.R
+++ b/R/VizEquiMap.R
@@ -261,7 +261,7 @@
 #'@importFrom stats cor
 #'@importFrom s2dv InsertDim
 #'@export
-VizEquiMap <- function(data = NULL, lon, lat, varu = NULL, varv = NULL,
+VizEquiMap <- function(data, lon, lat, varu = NULL, varv = NULL,
                        toptitle = NULL, sizetit = NULL, caption = NULL,
                        units = NULL, brks = NULL, cols = NULL, bar_limits = NULL, 
                        triangle_ends = NULL, col_inf = NULL, col_sup = NULL, 
@@ -314,7 +314,7 @@ VizEquiMap <- function(data = NULL, lon, lat, varu = NULL, varv = NULL,
   }
 
   # Check data
-  if (is.null(data)) {
+  if (missing(data)) {
     if (!is.null(var)) {
       data <- var
       warning("The parameter 'var' is deprecated. Use 'data' instead.")
-- 
GitLab


From 0f47145ccc45ecfe74ac8e975e249f65c4dadd49 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Mon, 10 Mar 2025 10:43:02 +0100
Subject: [PATCH 21/72] Fix on previous commit

---
 R/VizEquiMap.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/VizEquiMap.R b/R/VizEquiMap.R
index d905a35..0e1ce5b 100644
--- a/R/VizEquiMap.R
+++ b/R/VizEquiMap.R
@@ -314,7 +314,7 @@ VizEquiMap <- function(data, lon, lat, varu = NULL, varv = NULL,
   }
 
   # Check data
-  if (missing(data)) {
+  if (missing(data) || is.null(data)) {
     if (!is.null(var)) {
       data <- var
       warning("The parameter 'var' is deprecated. Use 'data' instead.")
-- 
GitLab


From ac506cdfdb0bf65a86170c4694c5232d15568a64 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Tue, 11 Mar 2025 16:55:00 +0100
Subject: [PATCH 22/72] Change 'coastlines_width' for 'coast_width' (not in UT)

---
 R/VizRobinson.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/VizRobinson.R b/R/VizRobinson.R
index f77db5f..74e088a 100644
--- a/R/VizRobinson.R
+++ b/R/VizRobinson.R
@@ -80,7 +80,7 @@
 #'@param dots_size A number of the size of the dots. The default is 0.5.
 #'@param dots_shape A number indicating the dot shape recognized by parameter 
 #'  'shape' in \code{geom_point()}.
-#'@param coastlines_width A number indicating the width of the coastlines.
+#'@param coast_width A number indicating the width of the coastlines.
 #'@param fileout A character string of the path to save the plot. If not 
 #'  specified (default), a graphic device will pop up. The extension should be  
 #'  accepted by \code{ggsave()}.
@@ -130,7 +130,7 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
                         toptitle = NULL, caption = NULL, units = NULL,
                         crop_coastlines = NULL, point_size = "auto",
                         title_scale = 16, title_size = NULL, dots_size = 0.5,
-                        dots_shape = 47, coastlines_width = 0.3, fileout = NULL,
+                        dots_shape = 47, coast_width = 0.3, fileout = NULL,
                         width = 8, height = 4, size_units = "in", res = 300) {
 
   # Sanity check
@@ -487,7 +487,7 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
     coord_sf_lim <- c(range(lonlat_df_ori$long), range(lonlat_df_ori$lat))
   }
   res_p <- res_p +
-           geom_sf(data = coastlines, colour ='black', size = coastlines_width) +
+           geom_sf(data = coastlines, colour ='black', size = coast_width) +
            # Remove background grid and lat/lon label; add white background
            theme_void() + theme(plot.background = element_rect(fill = 'white', colour = 'white')) +
            # crop the projection
-- 
GitLab


From eedbaf69393a1df94aff44cd488cc7bf02c61048 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Tue, 11 Mar 2025 17:01:36 +0100
Subject: [PATCH 23/72] Change 'dots_shape' for 'dot_symbol' in VizRobinson.R
 (not in UT)

---
 R/VizRobinson.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/VizRobinson.R b/R/VizRobinson.R
index 74e088a..a771d54 100644
--- a/R/VizRobinson.R
+++ b/R/VizRobinson.R
@@ -78,7 +78,7 @@
 #'@param title_scale A number of the size of the top title. The default is 16.
 #'@param title_size Deprecated. Use 'title_scale' instead.
 #'@param dots_size A number of the size of the dots. The default is 0.5.
-#'@param dots_shape A number indicating the dot shape recognized by parameter 
+#'@param dot_symbol A number indicating the dot shape recognized by parameter 
 #'  'shape' in \code{geom_point()}.
 #'@param coast_width A number indicating the width of the coastlines.
 #'@param fileout A character string of the path to save the plot. If not 
@@ -130,7 +130,7 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
                         toptitle = NULL, caption = NULL, units = NULL,
                         crop_coastlines = NULL, point_size = "auto",
                         title_scale = 16, title_size = NULL, dots_size = 0.5,
-                        dots_shape = 47, coast_width = 0.3, fileout = NULL,
+                        dot_symbol = 47, coast_width = 0.3, fileout = NULL,
                         width = 8, height = 4, size_units = "in", res = 300) {
 
   # Sanity check
@@ -496,7 +496,7 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
 
   if (!is.null(dots)) {
     res_p <- res_p + geom_point(data = dots_df, aes(x = .data$long, y = .data$lat),
-                                shape = dots_shape, size = dots_size)
+                                shape = dot_symbol, size = dots_size)
                                 #NOTE: This line makes point size vary with lat
                                 #size = dots_size / (dots_df$lat / min(dots_df$lat)))
   }
-- 
GitLab


From 702f739ac277a891a26ae8e363301fda0f500f7a Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Tue, 11 Mar 2025 17:27:49 +0100
Subject: [PATCH 24/72] Change 'dots_size' for 'dot_size' in VizRobinson.R (not
 in UT)

---
 R/VizRobinson.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/VizRobinson.R b/R/VizRobinson.R
index a771d54..e8f3aaa 100644
--- a/R/VizRobinson.R
+++ b/R/VizRobinson.R
@@ -77,7 +77,7 @@
 #'  The default is 'auto' and the function tries to find the appropriate size.
 #'@param title_scale A number of the size of the top title. The default is 16.
 #'@param title_size Deprecated. Use 'title_scale' instead.
-#'@param dots_size A number of the size of the dots. The default is 0.5.
+#'@param dot_size A number of the size of the dots. The default is 0.5.
 #'@param dot_symbol A number indicating the dot shape recognized by parameter 
 #'  'shape' in \code{geom_point()}.
 #'@param coast_width A number indicating the width of the coastlines.
@@ -129,7 +129,7 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
                         bar_extra_margin = rep(0, 4), vertical = TRUE,
                         toptitle = NULL, caption = NULL, units = NULL,
                         crop_coastlines = NULL, point_size = "auto",
-                        title_scale = 16, title_size = NULL, dots_size = 0.5,
+                        title_scale = 16, title_size = NULL, dot_size = 0.5,
                         dot_symbol = 47, coast_width = 0.3, fileout = NULL,
                         width = 8, height = 4, size_units = "in", res = 300) {
 
@@ -496,9 +496,9 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
 
   if (!is.null(dots)) {
     res_p <- res_p + geom_point(data = dots_df, aes(x = .data$long, y = .data$lat),
-                                shape = dot_symbol, size = dots_size)
+                                shape = dot_symbol, size = dot_size)
                                 #NOTE: This line makes point size vary with lat
-                                #size = dots_size / (dots_df$lat / min(dots_df$lat)))
+                                #size = dot_size / (dots_df$lat / min(dots_df$lat)))
   }
 
   if (identical(drawleg, 'ggplot2')) {
-- 
GitLab


From 85502fb59302b4936a23d65e0dd121da00b79ea1 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Tue, 11 Mar 2025 17:33:06 +0100
Subject: [PATCH 25/72] Change 'col_mask' for 'mask_color' in VizCombinedMap.R
 (not in UT)

---
 R/VizCombinedMap.R | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/R/VizCombinedMap.R b/R/VizCombinedMap.R
index 5119385..bb587d2 100644
--- a/R/VizCombinedMap.R
+++ b/R/VizCombinedMap.R
@@ -50,8 +50,8 @@
 #'@param mask Optional numeric array with dimensions (latitude, longitude), with 
 #'  values in the range [0, 1], indicating the opacity of the mask over each 
 #'  grid point. Cells with a 0 will result in no mask, whereas cells with a 1 
-#'  will result in a totally opaque superimposed pixel coloured in 'col_mask'.
-#'@param col_mask Colour to be used for the superimposed mask (if specified in 
+#'  will result in a totally opaque superimposed pixel coloured in 'mask_color'.
+#'@param mask_color Colour to be used for the superimposed mask (if specified in 
 #'  'mask'). Takes the value 'grey' by default.
 #'@param dots Array of same dimensions as 'var' or with dimensions 
 #'  c(n, dim(var)), where n is the number of dot/symbol layers to add to the 
@@ -142,7 +142,7 @@ VizCombinedMap <- function(maps, lon, lat,
                            bar_limits = NULL, triangle_ends = c(FALSE, FALSE), 
                            col_inf = NULL, col_sup = NULL,
                            col_unknown_map = 'white',
-                           mask = NULL, col_mask = 'grey',
+                           mask = NULL, mask_color = 'grey',
                            dots = NULL,
                            bar_titles = NULL, legend_scale = 1,
                            cex_bar_titles = 1.5,
@@ -295,9 +295,9 @@ VizCombinedMap <- function(maps, lon, lat,
     stop("Parameter 'col_unknown_map' must be a character string.")
   }
   
-  # Check col_mask
-  if (!is.character(col_mask)) {
-    stop("Parameter 'col_mask' must be a character string.")
+  # Check mask_color
+  if (!is.character(mask_color)) {
+    stop("Parameter 'mask_color' must be a character string.")
   }
   
   # Check mask
@@ -480,7 +480,7 @@ VizCombinedMap <- function(maps, lon, lat,
     lonb <- sort(lon, index.return = TRUE)
 
     cols_mask <- sapply(seq(from = 0, to = 1, length.out = 10), 
-                        function(x) adjustcolor(col_mask, alpha.f = x))
+                        function(x) adjustcolor(mask_color, alpha.f = x))
     image(lonb$x, latb$x, t(mask)[lonb$ix, latb$ix], 
           axes = FALSE, col = cols_mask, 
           breaks = seq(from = 0, to = 1, by = 0.1), 
-- 
GitLab


From e5f3f5eab1c7fd8b1cd226672055b312549a703e Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 13 Mar 2025 10:15:09 +0100
Subject: [PATCH 26/72] Change 'extra_labels' for 'bar_extra_labels' in
 ColorBarContinous.R + functions that call it

---
 R/ColorBarContinuous.R | 34 +++++++++++++++++-----------------
 R/VizEquiMap.R         |  4 ++--
 R/VizLayout.R          |  2 +-
 R/VizRobinson.R        |  4 ++--
 R/VizStereoMap.R       |  4 ++--
 5 files changed, 24 insertions(+), 24 deletions(-)

diff --git a/R/ColorBarContinuous.R b/R/ColorBarContinuous.R
index b7727ba..fe801a8 100644
--- a/R/ColorBarContinuous.R
+++ b/R/ColorBarContinuous.R
@@ -45,7 +45,7 @@
 #'  colorbar. Takes by default an approximation of a value that yields a 
 #'  readable tick arrangement (extreme breaks always ticked). If set to 0 or 
 #'  lower, no labels are drawn. See the code of the function for details or 
-#'  use 'extra_labels' for customized tick arrangements.
+#'  use 'bar_extra_labels' for customized tick arrangements.
 #'@param bar_limits Vector of two numeric values with the extremes of the 
 #'  range of values represented in the colour bar. If 'var_limits' go beyond 
 #'  this interval, the drawing of triangle extremes is triggered at the 
@@ -91,7 +91,7 @@
 #'  colour bar, if drawn at all. Takes 1 by default (rectangle triangle 
 #'  proportional to the thickness of the colour bar). Disregarded if 
 #'  'plot = FALSE'.
-#'@param extra_labels Numeric vector of extra labels to draw along axis of 
+#'@param bar_extra_labels Numeric vector of extra labels to draw along axis of 
 #'  the colour bar. The number of provided decimals will be conserved. 
 #'  Disregarded if 'plot = FALSE'.
 #'@param title Title to draw on top of the colour bar, most commonly with the 
@@ -108,7 +108,7 @@
 #'@param label_digits Number of significant digits to be displayed in the 
 #'  labels of the colour bar, usually to avoid too many decimal digits 
 #'  overflowing the figure region. This does not have effect over the labels 
-#'  provided in 'extra_labels'. Takes 4 by default.
+#'  provided in 'bar_extra_labels'. Takes 4 by default.
 #'@param ... Arguments to be passed to the method. Only accepts the following 
 #'  graphical parameters:\cr adj ann ask bg bty cex.lab cex.main cex.sub cin 
 #'  col.axis col.lab col.main col.sub cra crt csi cxy err family fg fig fin 
@@ -148,7 +148,7 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
                      triangle_ends = NULL, col_inf = NULL, col_sup = NULL, 
                      color_fun = ClimPalette(), plot = TRUE, 
                      draw_ticks = TRUE, draw_separators = FALSE, 
-                     triangle_ends_scale = 1, extra_labels = NULL, 
+                     triangle_ends_scale = 1, bar_extra_labels = NULL, 
                      title = NULL, title_scale = 1, 
                      label_scale = 1, tick_scale = 1, 
                      extra_margin = rep(0, 4), label_digits = 4, ...) {
@@ -325,18 +325,18 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
     stop("Parameter 'vertical' must be TRUE or FALSE.")
   }
 
-  # Check extra_labels
-  if (is.null(extra_labels)) {
-    extra_labels <- numeric(0)
+  # Check bar_extra_labels
+  if (is.null(bar_extra_labels)) {
+    bar_extra_labels <- numeric(0)
   }
-  if (!is.numeric(extra_labels)) {
-    stop("Parameter 'extra_labels' must be numeric.")
+  if (!is.numeric(bar_extra_labels)) {
+    stop("Parameter 'bar_extra_labels' must be numeric.")
   } else {
-    if (any(extra_labels > bar_limits[2]) || any(extra_labels < bar_limits[1])) {
-      stop("Parameter 'extra_labels' must not contain ticks beyond the color bar limits.")
+    if (any(bar_extra_labels > bar_limits[2]) || any(bar_extra_labels < bar_limits[1])) {
+      stop("Parameter 'bar_extra_labels' must not contain ticks beyond the color bar limits.")
     }
   }
-  extra_labels <- sort(extra_labels)
+  bar_extra_labels <- sort(bar_extra_labels)
 
   # Check subsampleg
   primes <- function(x) {
@@ -358,7 +358,7 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
     }
     if (subsampleg > (length(brks) - 1) / 4) {
       subsampleg <- max(1, round(length(brks) / 4))
-      extra_labels <- c(extra_labels, bar_limits[2])
+      bar_extra_labels <- c(bar_extra_labels, bar_limits[2])
       added_final_tick <- TRUE
       if ((length(brks) - 1) %% subsampleg < (length(brks) - 1) / 4 / 2) {
         remove_final_tick <- TRUE
@@ -565,7 +565,7 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
     # Put the ticks
     plot_range <- length(brks) - 1
     var_range <- tail(brks, 1) - head(brks, 1)
-    extra_labels_at <- ((extra_labels - head(brks, 1)) / var_range) * plot_range + 0.5
+    bar_extra_labels_at <- ((bar_extra_labels - head(brks, 1)) / var_range) * plot_range + 0.5
     at <- seq(1, length(brks), subsampleg)
     labels <- brks[at]
     # Getting rid of next-to-last tick if too close to last one
@@ -575,11 +575,11 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
     }
     labels <- signif(labels, label_digits)
     if (added_final_tick) {
-      extra_labels[length(extra_labels)] <- signif(tail(extra_labels, 1), label_digits)
+      bar_extra_labels[length(bar_extra_labels)] <- signif(tail(bar_extra_labels, 1), label_digits)
     }
     at <- at - 0.5
-    at <- c(at, extra_labels_at)
-    labels <- c(labels, extra_labels)
+    at <- c(at, bar_extra_labels_at)
+    labels <- c(labels, bar_extra_labels)
     tick_reorder <- sort(at, index.return = TRUE)
     at <- tick_reorder$x
     if (draw_labels) {
diff --git a/R/VizEquiMap.R b/R/VizEquiMap.R
index 0e1ce5b..0abbdb4 100644
--- a/R/VizEquiMap.R
+++ b/R/VizEquiMap.R
@@ -575,7 +575,7 @@ VizEquiMap <- function(data, lon, lat, varu = NULL, varv = NULL,
   # Build: brks, cols, bar_limits, col_inf, col_sup
   colorbar <- ColorBarContinuous(brks, cols, vertical = vertical, subsampleg, bar_limits, 
                        var_limits, triangle_ends, col_inf, col_sup, color_fun, FALSE, 
-                       extra_labels = bar_extra_labels, draw_ticks = draw_bar_ticks,
+                       bar_extra_labels = bar_extra_labels, draw_ticks = draw_bar_ticks,
                        draw_separators = draw_separators, 
                        triangle_ends_scale = triangle_ends_scale,
                        label_scale = bar_label_scale, title = units, 
@@ -1448,7 +1448,7 @@ VizEquiMap <- function(data, lon, lat, varu = NULL, varv = NULL,
     }
     ColorBarContinuous(brks, cols, vertical = vertical, subsampleg, bar_limits,
              var_limits, triangle_ends, col_inf = col_inf, col_sup = col_sup, 
-             extra_labels = bar_extra_labels, draw_ticks = draw_bar_ticks,
+             bar_extra_labels = bar_extra_labels, draw_ticks = draw_bar_ticks,
              draw_separators = draw_separators, title = units, 
              title_scale = units_scale, triangle_ends_scale = triangle_ends_scale, 
              label_scale = bar_label_scale, tick_scale = bar_tick_scale,
diff --git a/R/VizLayout.R b/R/VizLayout.R
index 11f094e..f356508 100644
--- a/R/VizLayout.R
+++ b/R/VizLayout.R
@@ -637,7 +637,7 @@ VizLayout <- function(fun, plot_dims, data = NULL, ..., special_args = NULL,
                triangle_ends = triangle_ends, col_inf = colorbar$col_inf,
                col_sup = colorbar$col_sup, color_fun = color_fun, plot = TRUE, draw_ticks = draw_bar_ticks,
                draw_separators = draw_separators, triangle_ends_scale = triangle_ends_scale,
-               extra_labels = bar_extra_labels,
+               bar_extra_labels = bar_extra_labels,
                title = units, title_scale = units_scale, label_scale = bar_label_scale, tick_scale = bar_tick_scale,
                extra_margin = bar_extra_margin, label_digits = bar_label_digits)
 
diff --git a/R/VizRobinson.R b/R/VizRobinson.R
index e8f3aaa..419de89 100644
--- a/R/VizRobinson.R
+++ b/R/VizRobinson.R
@@ -281,7 +281,7 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
                        bar_limits = bar_limits, var_limits = var_limits, triangle_ends = triangle_ends, 
                        col_inf = col_inf, col_sup = col_sup, color_fun = color_fun, 
                        plot = FALSE, draw_ticks = TRUE, draw_separators = FALSE,
-                       triangle_ends_scale = 1, extra_labels = NULL,
+                       triangle_ends_scale = 1, bar_extra_labels = NULL,
                        title = units, title_scale = 1, # units_scale
                        label_scale = 1, tick_scale = 1, # bar_tick_scale
                        extra_margin = bar_extra_margin, label_digits = 4)
@@ -548,7 +548,7 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
                bar_limits = bar_limits, var_limits = var_limits, triangle_ends = triangle_ends,
                col_inf = col_inf, col_sup = col_sup, color_fun = color_fun,
                plot = TRUE, draw_ticks = TRUE, draw_separators = FALSE,
-               triangle_ends_scale = 1, extra_labels = NULL,
+               triangle_ends_scale = 1, bar_extra_labels = NULL,
                title = units, title_scale = 1, # units_scale
                label_scale = 1, tick_scale = 1, #bar_tick_scale
                extra_margin = bar_extra_margin, label_digits = 4)
diff --git a/R/VizStereoMap.R b/R/VizStereoMap.R
index 49235ec..56f4db7 100644
--- a/R/VizStereoMap.R
+++ b/R/VizStereoMap.R
@@ -353,7 +353,7 @@ VizStereoMap <- function(data = NULL, lon, lat, varu = NULL, varv = NULL,
   # Build: brks, cols, bar_limits, col_inf, col_sup
   colorbar <- ColorBarContinuous(brks, cols, FALSE, subsampleg, bar_limits, var_limits,
                        triangle_ends, col_inf, col_sup, color_fun, FALSE,
-                       extra_labels = bar_extra_labels, draw_ticks = draw_bar_ticks,
+                       bar_extra_labels = bar_extra_labels, draw_ticks = draw_bar_ticks,
                        draw_separators = draw_separators, 
                        triangle_ends_scale = triangle_ends_scale,
                        label_scale = bar_label_scale, title = units, 
@@ -868,7 +868,7 @@ VizStereoMap <- function(data = NULL, lon, lat, varu = NULL, varv = NULL,
   if (drawleg) {
     ColorBarContinuous(brks, cols, TRUE, subsampleg, bar_limits, var_limits,
              triangle_ends, col_inf = col_inf, col_sup = col_sup, 
-             extra_labels = bar_extra_labels, draw_ticks = draw_bar_ticks,
+             bar_extra_labels = bar_extra_labels, draw_ticks = draw_bar_ticks,
              draw_separators = draw_separators, title = units,
              title_scale = units_scale, triangle_ends_scale = triangle_ends_scale, 
              label_scale = bar_label_scale, tick_scale = bar_tick_scale,
-- 
GitLab


From abd837566a8819e50ab96fcc9ab2438b14607687 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 13 Mar 2025 10:28:09 +0100
Subject: [PATCH 27/72] Change 'extra_labels' for 'bar_extra_labels' in
 ColorBarDiscrete.R

---
 R/ColorBarDiscrete.R | 34 +++++++++++++++++-----------------
 1 file changed, 17 insertions(+), 17 deletions(-)

diff --git a/R/ColorBarDiscrete.R b/R/ColorBarDiscrete.R
index 0f4d854..f7e1f73 100644
--- a/R/ColorBarDiscrete.R
+++ b/R/ColorBarDiscrete.R
@@ -42,7 +42,7 @@
 #'  colorbar. Takes by default an approximation of a value that yields a 
 #'  readable tick arrangement (extreme breaks always ticked). If set to 0 or 
 #'  lower, no labels are drawn. See the code of the function for details or 
-#'  use 'extra_labels' for customized tick arrangements.
+#'  use 'bar_extra_labels' for customized tick arrangements.
 #'@param bar_limits Vector of two numeric values with the extremes of the 
 #'  range of values represented in the colour bar. If 'var_limits' go beyond 
 #'  this interval, the drawing of triangle extremes is triggered at the 
@@ -70,7 +70,7 @@
 #'  default. Disregarded if 'plot = FALSE'.
 #'@param labels A charater string vector of the names of colors. Must be the
 #'  same length as 'cols'. 
-#'@param extra_labels Numeric vector of extra labels to draw along axis of 
+#'@param bar_extra_labels Numeric vector of extra labels to draw along axis of 
 #'  the colour bar. The number of provided decimals will be conserved. 
 #'  Disregarded if 'plot = FALSE'.
 #'@param title Title to draw on top of the colour bar, most commonly with the 
@@ -87,7 +87,7 @@
 #'@param label_digits Number of significant digits to be displayed in the 
 #'  labels of the colour bar, usually to avoid too many decimal digits 
 #'  overflowing the figure region. This does not have effect over the labels 
-#'  provided in 'extra_labels'. Takes 4 by default.
+#'  provided in 'bar_extra_labels'. Takes 4 by default.
 #'@param ... Arguments to be passed to the method. Only accepts the following 
 #'  graphical parameters:\cr adj ann ask bg bty cex.lab cex.main cex.sub cin 
 #'  col.axis col.lab col.main col.sub cra crt csi cxy err family fg fig fin 
@@ -118,7 +118,7 @@ ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE,
                      subsampleg = NULL, bar_limits = NULL, var_limits = NULL, 
                      color_fun = ClimPalette(), plot = TRUE, 
                      draw_ticks = FALSE, draw_separators = TRUE, labels = NULL, 
-                     extra_labels = NULL, 
+                     bar_extra_labels = NULL, 
                      title = NULL, title_scale = 1, 
                      label_scale = 1, tick_scale = 1, 
                      extra_margin = rep(0, 4), label_digits = 4, ...) {
@@ -234,18 +234,18 @@ ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE,
     stop("Parameter 'vertical' must be TRUE or FALSE.")
   }
 
-  ## extra_labels
-  if (is.null(extra_labels)) {
-    extra_labels <- numeric(0)
+  ## bar_extra_labels
+  if (is.null(bar_extra_labels)) {
+    bar_extra_labels <- numeric(0)
   }
-  if (!is.numeric(extra_labels)) {
-    stop("Parameter 'extra_labels' must be numeric.")
+  if (!is.numeric(bar_extra_labels)) {
+    stop("Parameter 'bar_extra_labels' must be numeric.")
   } else {
-    if (any(extra_labels > bar_limits[2]) || any(extra_labels < bar_limits[1])) {
-      stop("Parameter 'extra_labels' must not contain ticks beyond the color bar limits.")
+    if (any(bar_extra_labels > bar_limits[2]) || any(bar_extra_labels < bar_limits[1])) {
+      stop("Parameter 'bar_extra_labels' must not contain ticks beyond the color bar limits.")
     }
   }
-  extra_labels <- sort(extra_labels)
+  bar_extra_labels <- sort(bar_extra_labels)
 
   ## labels
   if (is.null(labels)) {
@@ -278,7 +278,7 @@ ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE,
     }
     if (subsampleg > (length(brks) - 1) / 4) {
       subsampleg <- max(1, round(length(brks) / 4))
-      extra_labels <- c(extra_labels, bar_limits[2])
+      bar_extra_labels <- c(bar_extra_labels, bar_limits[2])
       added_final_tick <- TRUE
       if ((length(brks) - 1) %% subsampleg < (length(brks) - 1) / 4 / 2) {
         remove_final_tick <- TRUE
@@ -445,7 +445,7 @@ ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE,
     # Put the ticks
     plot_range <- length(brks) - 1
     var_range <- tail(brks, 1) - head(brks, 1)
-    extra_labels_at <- ((extra_labels - head(brks, 1)) / var_range) * plot_range + 0.5
+    bar_extra_labels_at <- ((bar_extra_labels - head(brks, 1)) / var_range) * plot_range + 0.5
     at <- seq(1, length(cols), subsampleg)
 #    at <- seq(1, length(brks), subsampleg)
 #    labels <- brks[at]
@@ -456,11 +456,11 @@ ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE,
 #    }
 #    labels <- signif(labels, label_digits)
     if (added_final_tick) {
-      extra_labels[length(extra_labels)] <- signif(tail(extra_labels, 1), label_digits)
+      bar_extra_labels[length(bar_extra_labels)] <- signif(tail(bar_extra_labels, 1), label_digits)
     }
 #    at <- at - 0.5
-    at <- c(at, extra_labels_at)
-    labels <- c(labels, extra_labels)
+    at <- c(at, bar_extra_labels_at)
+    labels <- c(labels, bar_extra_labels)
     tick_reorder <- sort(at, index.return = TRUE)
     at <- tick_reorder$x
     if (draw_labels) {
-- 
GitLab


From d8a358565abb7000ea6f17a7bb2f6df60ed9ee0f Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 13 Mar 2025 10:52:11 +0100
Subject: [PATCH 28/72] Change 'draw_ticks' for 'draw_bar_ticks' in
 olorBarDiscrete.R

---
 R/ColorBarDiscrete.R | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/R/ColorBarDiscrete.R b/R/ColorBarDiscrete.R
index f7e1f73..0bfb93e 100644
--- a/R/ColorBarDiscrete.R
+++ b/R/ColorBarDiscrete.R
@@ -63,7 +63,7 @@
 #'  parameter is set by default to ClimPalette().
 #'@param plot Logical value indicating whether to only compute its breaks and 
 #'  colours (FALSE) or to also draw it on the current device (TRUE).
-#'@param draw_ticks Whether to draw ticks for the labels along the colour bar 
+#'@param draw_bar_ticks Whether to draw ticks for the labels along the colour bar 
 #' (TRUE) or not (FALSE). TRUE by default. Disregarded if 'plot = FALSE'.
 #'@param draw_separators Whether to draw black lines in the borders of each of 
 #'  the colour rectancles of the colour bar (TRUE) or not (FALSE). FALSE by 
@@ -117,7 +117,7 @@
 ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE, 
                      subsampleg = NULL, bar_limits = NULL, var_limits = NULL, 
                      color_fun = ClimPalette(), plot = TRUE, 
-                     draw_ticks = FALSE, draw_separators = TRUE, labels = NULL, 
+                     draw_bar_ticks = FALSE, draw_separators = TRUE, labels = NULL, 
                      bar_extra_labels = NULL, 
                      title = NULL, title_scale = 1, 
                      label_scale = 1, tick_scale = 1, 
@@ -303,9 +303,9 @@ ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE,
     stop("Parameter 'draw_separators' must be logical.")
   }
 
-  ## draw_ticks
-  if (!is.logical(draw_ticks)) {
-    stop("Parameter 'draw_ticks' must be logical.")
+  ## draw_bar_ticks
+  if (!is.logical(draw_bar_ticks)) {
+    stop("Parameter 'draw_bar_ticks' must be logical.")
   }
 
   ## title
@@ -469,7 +469,7 @@ ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE,
       labels <- FALSE
     }
     # Put box labels
-    axis(d, at = at, tick = draw_ticks, labels = labels, cex.axis = cex_labels, tcl = cex_ticks)
+    axis(d, at = at, tick = draw_bar_ticks, labels = labels, cex.axis = cex_labels, tcl = cex_ticks)
     par(saved_pars)
   }
   invisible(list(brks = brks, cols = cols))
-- 
GitLab


From b9b9fc129cfab989ec9866128dcc87b3bc9df0b0 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 13 Mar 2025 10:56:59 +0100
Subject: [PATCH 29/72] Change 'draw_ticks' for 'draw_bar_ticks' in
 ColorBarContinuous.R + functions that call it

---
 R/ColorBarContinuous.R | 12 ++++++------
 R/VizEquiMap.R         |  4 ++--
 R/VizLayout.R          |  2 +-
 R/VizRobinson.R        |  4 ++--
 R/VizStereoMap.R       |  4 ++--
 5 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/R/ColorBarContinuous.R b/R/ColorBarContinuous.R
index fe801a8..7dd89f3 100644
--- a/R/ColorBarContinuous.R
+++ b/R/ColorBarContinuous.R
@@ -82,7 +82,7 @@
 #'  parameter is set by default to ClimPalette().
 #'@param plot Logical value indicating whether to only compute its breaks and 
 #'  colours (FALSE) or to also draw it on the current device (TRUE).
-#'@param draw_ticks Whether to draw ticks for the labels along the colour bar 
+#'@param draw_bar_ticks Whether to draw ticks for the labels along the colour bar 
 #' (TRUE) or not (FALSE). TRUE by default. Disregarded if 'plot = FALSE'.
 #'@param draw_separators Whether to draw black lines in the borders of each of 
 #'  the colour rectancles of the colour bar (TRUE) or not (FALSE). FALSE by 
@@ -147,7 +147,7 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
                      subsampleg = NULL, bar_limits = NULL, var_limits = NULL, 
                      triangle_ends = NULL, col_inf = NULL, col_sup = NULL, 
                      color_fun = ClimPalette(), plot = TRUE, 
-                     draw_ticks = TRUE, draw_separators = FALSE, 
+                     draw_bar_ticks = TRUE, draw_separators = FALSE, 
                      triangle_ends_scale = 1, bar_extra_labels = NULL, 
                      title = NULL, title_scale = 1, 
                      label_scale = 1, tick_scale = 1, 
@@ -388,9 +388,9 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
     stop("Parameter 'triangle_ends_scale' must be numeric.")
   }
 
-  # Check draw_ticks
-  if (!is.logical(draw_ticks)) {
-    stop("Parameter 'draw_ticks' must be logical.")
+  # Check draw_bar_ticks
+  if (!is.logical(draw_bar_ticks)) {
+    stop("Parameter 'draw_bar_ticks' must be logical.")
   }
 
   # Check title
@@ -587,7 +587,7 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
     } else {
       labels <- FALSE
     }
-    axis(d, at = at, tick = draw_ticks, labels = labels, cex.axis = cex_labels, tcl = cex_ticks)
+    axis(d, at = at, tick = draw_bar_ticks, labels = labels, cex.axis = cex_labels, tcl = cex_ticks)
     par(saved_pars)
   }
   invisible(list(brks = brks, cols = cols, col_inf = col_inf, col_sup = col_sup))
diff --git a/R/VizEquiMap.R b/R/VizEquiMap.R
index 0abbdb4..4253121 100644
--- a/R/VizEquiMap.R
+++ b/R/VizEquiMap.R
@@ -575,7 +575,7 @@ VizEquiMap <- function(data, lon, lat, varu = NULL, varv = NULL,
   # Build: brks, cols, bar_limits, col_inf, col_sup
   colorbar <- ColorBarContinuous(brks, cols, vertical = vertical, subsampleg, bar_limits, 
                        var_limits, triangle_ends, col_inf, col_sup, color_fun, FALSE, 
-                       bar_extra_labels = bar_extra_labels, draw_ticks = draw_bar_ticks,
+                       bar_extra_labels = bar_extra_labels, draw_bar_ticks = draw_bar_ticks,
                        draw_separators = draw_separators, 
                        triangle_ends_scale = triangle_ends_scale,
                        label_scale = bar_label_scale, title = units, 
@@ -1448,7 +1448,7 @@ VizEquiMap <- function(data, lon, lat, varu = NULL, varv = NULL,
     }
     ColorBarContinuous(brks, cols, vertical = vertical, subsampleg, bar_limits,
              var_limits, triangle_ends, col_inf = col_inf, col_sup = col_sup, 
-             bar_extra_labels = bar_extra_labels, draw_ticks = draw_bar_ticks,
+             bar_extra_labels = bar_extra_labels, draw_bar_ticks = draw_bar_ticks,
              draw_separators = draw_separators, title = units, 
              title_scale = units_scale, triangle_ends_scale = triangle_ends_scale, 
              label_scale = bar_label_scale, tick_scale = bar_tick_scale,
diff --git a/R/VizLayout.R b/R/VizLayout.R
index f356508..0dbbd4d 100644
--- a/R/VizLayout.R
+++ b/R/VizLayout.R
@@ -635,7 +635,7 @@ VizLayout <- function(fun, plot_dims, data = NULL, ..., special_args = NULL,
       ColorBarContinuous(brks = colorbar$brks, cols = colorbar$cols, vertical = vertical, subsampleg = subsampleg,
                bar_limits = bar_limits, var_limits = var_limits,
                triangle_ends = triangle_ends, col_inf = colorbar$col_inf,
-               col_sup = colorbar$col_sup, color_fun = color_fun, plot = TRUE, draw_ticks = draw_bar_ticks,
+               col_sup = colorbar$col_sup, color_fun = color_fun, plot = TRUE, draw_bar_ticks = draw_bar_ticks,
                draw_separators = draw_separators, triangle_ends_scale = triangle_ends_scale,
                bar_extra_labels = bar_extra_labels,
                title = units, title_scale = units_scale, label_scale = bar_label_scale, tick_scale = bar_tick_scale,
diff --git a/R/VizRobinson.R b/R/VizRobinson.R
index 419de89..ee0d18f 100644
--- a/R/VizRobinson.R
+++ b/R/VizRobinson.R
@@ -280,7 +280,7 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
   colorbar <- ColorBarContinuous(brks = brks, cols = cols, vertical = vertical, subsampleg = NULL,
                        bar_limits = bar_limits, var_limits = var_limits, triangle_ends = triangle_ends, 
                        col_inf = col_inf, col_sup = col_sup, color_fun = color_fun, 
-                       plot = FALSE, draw_ticks = TRUE, draw_separators = FALSE,
+                       plot = FALSE, draw_bar_ticks = TRUE, draw_separators = FALSE,
                        triangle_ends_scale = 1, bar_extra_labels = NULL,
                        title = units, title_scale = 1, # units_scale
                        label_scale = 1, tick_scale = 1, # bar_tick_scale
@@ -547,7 +547,7 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
       ColorBarContinuous(brks = brks, cols = cols, vertical = vertical, subsampleg = NULL,
                bar_limits = bar_limits, var_limits = var_limits, triangle_ends = triangle_ends,
                col_inf = col_inf, col_sup = col_sup, color_fun = color_fun,
-               plot = TRUE, draw_ticks = TRUE, draw_separators = FALSE,
+               plot = TRUE, draw_bar_ticks = TRUE, draw_separators = FALSE,
                triangle_ends_scale = 1, bar_extra_labels = NULL,
                title = units, title_scale = 1, # units_scale
                label_scale = 1, tick_scale = 1, #bar_tick_scale
diff --git a/R/VizStereoMap.R b/R/VizStereoMap.R
index 56f4db7..281e025 100644
--- a/R/VizStereoMap.R
+++ b/R/VizStereoMap.R
@@ -353,7 +353,7 @@ VizStereoMap <- function(data = NULL, lon, lat, varu = NULL, varv = NULL,
   # Build: brks, cols, bar_limits, col_inf, col_sup
   colorbar <- ColorBarContinuous(brks, cols, FALSE, subsampleg, bar_limits, var_limits,
                        triangle_ends, col_inf, col_sup, color_fun, FALSE,
-                       bar_extra_labels = bar_extra_labels, draw_ticks = draw_bar_ticks,
+                       bar_extra_labels = bar_extra_labels, draw_bar_ticks = draw_bar_ticks,
                        draw_separators = draw_separators, 
                        triangle_ends_scale = triangle_ends_scale,
                        label_scale = bar_label_scale, title = units, 
@@ -868,7 +868,7 @@ VizStereoMap <- function(data = NULL, lon, lat, varu = NULL, varv = NULL,
   if (drawleg) {
     ColorBarContinuous(brks, cols, TRUE, subsampleg, bar_limits, var_limits,
              triangle_ends, col_inf = col_inf, col_sup = col_sup, 
-             bar_extra_labels = bar_extra_labels, draw_ticks = draw_bar_ticks,
+             bar_extra_labels = bar_extra_labels, draw_bar_ticks = draw_bar_ticks,
              draw_separators = draw_separators, title = units,
              title_scale = units_scale, triangle_ends_scale = triangle_ends_scale, 
              label_scale = bar_label_scale, tick_scale = bar_tick_scale,
-- 
GitLab


From 80ea293c7aacb005e29a56dd627d8740cf63c141 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 13 Mar 2025 12:38:42 +0100
Subject: [PATCH 30/72] Change 'label_digits' for 'bar_label_digits' in
 ColorBarDiscrete.R

---
 R/ColorBarDiscrete.R | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/R/ColorBarDiscrete.R b/R/ColorBarDiscrete.R
index 0bfb93e..122e1da 100644
--- a/R/ColorBarDiscrete.R
+++ b/R/ColorBarDiscrete.R
@@ -84,7 +84,7 @@
 #'@param extra_margin Extra margins to be added around the colour bar, 
 #'  in the format c(y1, x1, y2, x2). The units are margin lines. Takes 
 #'  rep(0, 4) by default.
-#'@param label_digits Number of significant digits to be displayed in the 
+#'@param bar_label_digits Number of significant digits to be displayed in the 
 #'  labels of the colour bar, usually to avoid too many decimal digits 
 #'  overflowing the figure region. This does not have effect over the labels 
 #'  provided in 'bar_extra_labels'. Takes 4 by default.
@@ -121,7 +121,7 @@ ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE,
                      bar_extra_labels = NULL, 
                      title = NULL, title_scale = 1, 
                      label_scale = 1, tick_scale = 1, 
-                     extra_margin = rep(0, 4), label_digits = 4, ...) {
+                     extra_margin = rep(0, 4), bar_label_digits = 4, ...) {
   # Sanity checks
   if ((is.null(brks) || length(brks) < 2) && is.null(bar_limits) && is.null(var_limits)) {
     stop("At least one of 'brks' with the desired breaks, 'bar_limits' or ",
@@ -250,7 +250,7 @@ ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE,
   ## labels
   if (is.null(labels)) {
     labels <- rep(NA, length(cols))
-    tmp <- signif(brks, label_digits)
+    tmp <- signif(brks, bar_label_digits)
     for (i_brks in 1:length(cols)) {
       labels[i_brks] <- paste0("(", tmp[i_brks], ", ", tmp[i_brks + 1], "]")
     }
@@ -336,11 +336,11 @@ ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE,
     stop("Parameter 'extra_margin' must be a numeric vector of length 4.")
   }
 
-  ## label_digits
-  if (!is.numeric(label_digits)) {
-    stop("Parameter 'label_digits' must be numeric.")
+  ## bar_label_digits
+  if (!is.numeric(bar_label_digits)) {
+    stop("Parameter 'bar_label_digits' must be numeric.")
   }
-  label_digits <- round(label_digits)
+  bar_label_digits <- round(bar_label_digits)
 
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
@@ -454,9 +454,9 @@ ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE,
 #      at <- at[-length(at)]
 #      labels <- labels[-length(labels)]
 #    }
-#    labels <- signif(labels, label_digits)
+#    labels <- signif(labels, bar_label_digits)
     if (added_final_tick) {
-      bar_extra_labels[length(bar_extra_labels)] <- signif(tail(bar_extra_labels, 1), label_digits)
+      bar_extra_labels[length(bar_extra_labels)] <- signif(tail(bar_extra_labels, 1), bar_label_digits)
     }
 #    at <- at - 0.5
     at <- c(at, bar_extra_labels_at)
-- 
GitLab


From cc5da7037e10f186bccf60bcaf065548463ee671 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 13 Mar 2025 12:54:42 +0100
Subject: [PATCH 31/72] Change 'label_digits' for 'bar_label_digits' in
 ColorBarContinuous.R + functions that call it

---
 R/ColorBarContinuous.R | 16 ++++++++--------
 R/VizEquiMap.R         |  4 ++--
 R/VizLayout.R          |  2 +-
 R/VizRobinson.R        |  4 ++--
 R/VizStereoMap.R       |  4 ++--
 5 files changed, 15 insertions(+), 15 deletions(-)

diff --git a/R/ColorBarContinuous.R b/R/ColorBarContinuous.R
index 7dd89f3..b55b14b 100644
--- a/R/ColorBarContinuous.R
+++ b/R/ColorBarContinuous.R
@@ -105,7 +105,7 @@
 #'@param extra_margin Extra margins to be added around the colour bar, 
 #'  in the format c(y1, x1, y2, x2). The units are margin lines. Takes 
 #'  rep(0, 4) by default.
-#'@param label_digits Number of significant digits to be displayed in the 
+#'@param bar_label_digits Number of significant digits to be displayed in the 
 #'  labels of the colour bar, usually to avoid too many decimal digits 
 #'  overflowing the figure region. This does not have effect over the labels 
 #'  provided in 'bar_extra_labels'. Takes 4 by default.
@@ -151,7 +151,7 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
                      triangle_ends_scale = 1, bar_extra_labels = NULL, 
                      title = NULL, title_scale = 1, 
                      label_scale = 1, tick_scale = 1, 
-                     extra_margin = rep(0, 4), label_digits = 4, ...) {
+                     extra_margin = rep(0, 4), bar_label_digits = 4, ...) {
   # Required checks
   if ((is.null(brks) || length(brks) < 2) && is.null(bar_limits) && is.null(var_limits)) {
     stop("At least one of 'brks' with the desired breaks, 'bar_limits' or ",
@@ -421,11 +421,11 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
     stop("Parameter 'extra_margin' must be a numeric vector of length 4.")
   }
 
-  # Check label_digits
-  if (!is.numeric(label_digits)) {
-    stop("Parameter 'label_digits' must be numeric.")
+  # Check bar_label_digits
+  if (!is.numeric(bar_label_digits)) {
+    stop("Parameter 'bar_label_digits' must be numeric.")
   }
-  label_digits <- round(label_digits)
+  bar_label_digits <- round(bar_label_digits)
 
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
@@ -573,9 +573,9 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
       at <- at[-length(at)]
       labels <- labels[-length(labels)]
     }
-    labels <- signif(labels, label_digits)
+    labels <- signif(labels, bar_label_digits)
     if (added_final_tick) {
-      bar_extra_labels[length(bar_extra_labels)] <- signif(tail(bar_extra_labels, 1), label_digits)
+      bar_extra_labels[length(bar_extra_labels)] <- signif(tail(bar_extra_labels, 1), bar_label_digits)
     }
     at <- at - 0.5
     at <- c(at, bar_extra_labels_at)
diff --git a/R/VizEquiMap.R b/R/VizEquiMap.R
index 4253121..fa6dee4 100644
--- a/R/VizEquiMap.R
+++ b/R/VizEquiMap.R
@@ -580,7 +580,7 @@ VizEquiMap <- function(data, lon, lat, varu = NULL, varv = NULL,
                        triangle_ends_scale = triangle_ends_scale,
                        label_scale = bar_label_scale, title = units, 
                        title_scale = units_scale, tick_scale = bar_tick_scale,
-                       extra_margin = bar_extra_margin, label_digits = bar_label_digits)
+                       extra_margin = bar_extra_margin, bar_label_digits = bar_label_digits)
   brks <- colorbar$brks
   cols <- colorbar$cols
   col_inf <- colorbar$col_inf
@@ -1452,7 +1452,7 @@ VizEquiMap <- function(data, lon, lat, varu = NULL, varv = NULL,
              draw_separators = draw_separators, title = units, 
              title_scale = units_scale, triangle_ends_scale = triangle_ends_scale, 
              label_scale = bar_label_scale, tick_scale = bar_tick_scale,
-             extra_margin = bar_extra_margin, label_digits = bar_label_digits)
+             extra_margin = bar_extra_margin, bar_label_digits = bar_label_digits)
   }
 
   # If the graphic was saved to file, close the connection with the device
diff --git a/R/VizLayout.R b/R/VizLayout.R
index 0dbbd4d..cecbc60 100644
--- a/R/VizLayout.R
+++ b/R/VizLayout.R
@@ -639,7 +639,7 @@ VizLayout <- function(fun, plot_dims, data = NULL, ..., special_args = NULL,
                draw_separators = draw_separators, triangle_ends_scale = triangle_ends_scale,
                bar_extra_labels = bar_extra_labels,
                title = units, title_scale = units_scale, label_scale = bar_label_scale, tick_scale = bar_tick_scale,
-               extra_margin = bar_extra_margin, label_digits = bar_label_digits)
+               extra_margin = bar_extra_margin, bar_label_digits = bar_label_digits)
 
     }
   }
diff --git a/R/VizRobinson.R b/R/VizRobinson.R
index ee0d18f..366fd6d 100644
--- a/R/VizRobinson.R
+++ b/R/VizRobinson.R
@@ -284,7 +284,7 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
                        triangle_ends_scale = 1, bar_extra_labels = NULL,
                        title = units, title_scale = 1, # units_scale
                        label_scale = 1, tick_scale = 1, # bar_tick_scale
-                       extra_margin = bar_extra_margin, label_digits = 4)
+                       extra_margin = bar_extra_margin, bar_label_digits = 4)
   brks <- colorbar$brks
   cols <- colorbar$cols
   col_inf <- colorbar$col_inf
@@ -551,7 +551,7 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
                triangle_ends_scale = 1, bar_extra_labels = NULL,
                title = units, title_scale = 1, # units_scale
                label_scale = 1, tick_scale = 1, #bar_tick_scale
-               extra_margin = bar_extra_margin, label_digits = 4)
+               extra_margin = bar_extra_margin, bar_label_digits = 4)
     }
     if (vertical) {
       res_p <- cowplot::plot_grid(res_p, fun_legend, rel_widths = c(6, 1))
diff --git a/R/VizStereoMap.R b/R/VizStereoMap.R
index 281e025..85030b5 100644
--- a/R/VizStereoMap.R
+++ b/R/VizStereoMap.R
@@ -358,7 +358,7 @@ VizStereoMap <- function(data = NULL, lon, lat, varu = NULL, varv = NULL,
                        triangle_ends_scale = triangle_ends_scale,
                        label_scale = bar_label_scale, title = units, 
                        title_scale = units_scale, tick_scale = bar_tick_scale,
-                       extra_margin = bar_extra_margin, label_digits = bar_label_digits)
+                       extra_margin = bar_extra_margin, bar_label_digits = bar_label_digits)
   brks <- colorbar$brks
   cols <- colorbar$cols
   col_inf <- colorbar$col_inf
@@ -872,7 +872,7 @@ VizStereoMap <- function(data = NULL, lon, lat, varu = NULL, varv = NULL,
              draw_separators = draw_separators, title = units,
              title_scale = units_scale, triangle_ends_scale = triangle_ends_scale, 
              label_scale = bar_label_scale, tick_scale = bar_tick_scale,
-             extra_margin = bar_extra_margin, label_digits = bar_label_digits)
+             extra_margin = bar_extra_margin, bar_label_digits = bar_label_digits)
   }
 
   # If the graphic was saved to file, close the connection with the device
-- 
GitLab


From f7eae5d1f21228b48a3c6b5e0eebd0a02e23c071 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Thu, 13 Mar 2025 15:40:25 +0100
Subject: [PATCH 32/72] 'label_scale' -> 'bar_label_scale', 'tick_scale' ->
 'bar_tick_scale', 'extra_margin' -> 'bar_extra_margin' in ColorBarContinuous
 and its calls in VizEquiMap, VizLayout, VizRobinson and VizStereoMap

---
 R/ColorBarContinuous.R | 36 +++++++++++++++++-----------------
 R/VizEquiMap.R         | 12 ++++++------
 R/VizLayout.R          | 44 ++++++++++++++++++++++++++++--------------
 R/VizRobinson.R        |  8 ++++----
 R/VizStereoMap.R       | 12 ++++++------
 5 files changed, 63 insertions(+), 49 deletions(-)

diff --git a/R/ColorBarContinuous.R b/R/ColorBarContinuous.R
index b55b14b..5974992 100644
--- a/R/ColorBarContinuous.R
+++ b/R/ColorBarContinuous.R
@@ -98,11 +98,11 @@
 #'  units of the represented field in the neighbour figures. Empty by default.
 #'@param title_scale Scale factor for the 'title' of the colour bar. 
 #'  Takes 1 by default.
-#'@param label_scale Scale factor for the labels of the colour bar. 
+#'@param bar_label_scale Scale factor for the labels of the colour bar. 
 #'  Takes 1 by default.
-#'@param tick_scale Scale factor for the length of the ticks of the labels 
+#'@param bar_tick_scale Scale factor for the length of the ticks of the labels 
 #'  along the colour bar. Takes 1 by default.
-#'@param extra_margin Extra margins to be added around the colour bar, 
+#'@param bar_extra_margin Extra margins to be added around the colour bar, 
 #'  in the format c(y1, x1, y2, x2). The units are margin lines. Takes 
 #'  rep(0, 4) by default.
 #'@param bar_label_digits Number of significant digits to be displayed in the 
@@ -150,8 +150,8 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
                      draw_bar_ticks = TRUE, draw_separators = FALSE, 
                      triangle_ends_scale = 1, bar_extra_labels = NULL, 
                      title = NULL, title_scale = 1, 
-                     label_scale = 1, tick_scale = 1, 
-                     extra_margin = rep(0, 4), bar_label_digits = 4, ...) {
+                     bar_label_scale = 1, bar_tick_scale = 1, 
+                     bar_extra_margin = rep(0, 4), bar_label_digits = 4, ...) {
   # Required checks
   if ((is.null(brks) || length(brks) < 2) && is.null(bar_limits) && is.null(var_limits)) {
     stop("At least one of 'brks' with the desired breaks, 'bar_limits' or ",
@@ -406,19 +406,19 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
     stop("Parameter 'title_scale' must be numeric.")
   }
 
-  # Check label_scale
-  if (!is.numeric(label_scale)) {
-    stop("Parameter 'label_scale' must be numeric.")
+  # Check bar_label_scale
+  if (!is.numeric(bar_label_scale)) {
+    stop("Parameter 'bar_label_scale' must be numeric.")
   }
 
-  # Check tick_scale
-  if (!is.numeric(tick_scale)) {
-    stop("Parameter 'tick_scale' must be numeric.")
+  # Check bar_tick_scale
+  if (!is.numeric(bar_tick_scale)) {
+    stop("Parameter 'bar_tick_scale' must be numeric.")
   }
 
-  # Check extra_margin
-  if (!is.numeric(extra_margin) || length(extra_margin) != 4) {
-    stop("Parameter 'extra_margin' must be a numeric vector of length 4.")
+  # Check bar_extra_margin
+  if (!is.numeric(bar_extra_margin) || length(bar_extra_margin) != 4) {
+    stop("Parameter 'bar_extra_margin' must be a numeric vector of length 4.")
   }
 
   # Check bar_label_digits
@@ -456,15 +456,15 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
     # Set up color bar plot region
     margins <- c(0.0, 0, 0.0, 0)
     cex_title <- 1 * title_scale
-    cex_labels <- 0.9 * label_scale
-    cex_ticks <- -0.3 * tick_scale
+    cex_labels <- 0.9 * bar_label_scale
+    cex_ticks <- -0.3 * bar_tick_scale
     spaceticklab <- max(-cex_ticks, 0)
     if (vertical) {
       margins[1] <- margins[1] + (1.2 * cex_labels * 3 + spaceticklab) * cs
-      margins <- margins + extra_margin[c(4, 1:3)] * cs
+      margins <- margins + bar_extra_margin[c(4, 1:3)] * cs
     } else {
       margins[1] <- margins[1] + (1.2 * cex_labels * 1 + spaceticklab) * cs
-      margins <- margins + extra_margin * cs
+      margins <- margins + bar_extra_margin * cs
     }
     if (title != '') {
       margins[3] <- margins[3] + (1.0 * cex_title) * cs
diff --git a/R/VizEquiMap.R b/R/VizEquiMap.R
index fa6dee4..940b750 100644
--- a/R/VizEquiMap.R
+++ b/R/VizEquiMap.R
@@ -570,7 +570,7 @@ VizEquiMap <- function(data, lon, lat, varu = NULL, varv = NULL,
   drawleg <- tmp$drawleg
 
   # Check: brks, cols, subsampleg, bar_limits, color_fun, bar_extra_labels, draw_bar_ticks
-  #        draw_separators, triangle_ends_scale, label_scale, units, units_scale, 
+  #        draw_separators, triangle_ends_scale, bar_label_scale, units, units_scale, 
   #        bar_label_digits
   # Build: brks, cols, bar_limits, col_inf, col_sup
   colorbar <- ColorBarContinuous(brks, cols, vertical = vertical, subsampleg, bar_limits, 
@@ -578,9 +578,9 @@ VizEquiMap <- function(data, lon, lat, varu = NULL, varv = NULL,
                        bar_extra_labels = bar_extra_labels, draw_bar_ticks = draw_bar_ticks,
                        draw_separators = draw_separators, 
                        triangle_ends_scale = triangle_ends_scale,
-                       label_scale = bar_label_scale, title = units, 
-                       title_scale = units_scale, tick_scale = bar_tick_scale,
-                       extra_margin = bar_extra_margin, bar_label_digits = bar_label_digits)
+                       bar_label_scale = bar_label_scale, title = units, 
+                       title_scale = units_scale, bar_tick_scale = bar_tick_scale,
+                       bar_extra_margin = bar_extra_margin, bar_label_digits = bar_label_digits)
   brks <- colorbar$brks
   cols <- colorbar$cols
   col_inf <- colorbar$col_inf
@@ -1451,8 +1451,8 @@ VizEquiMap <- function(data, lon, lat, varu = NULL, varv = NULL,
              bar_extra_labels = bar_extra_labels, draw_bar_ticks = draw_bar_ticks,
              draw_separators = draw_separators, title = units, 
              title_scale = units_scale, triangle_ends_scale = triangle_ends_scale, 
-             label_scale = bar_label_scale, tick_scale = bar_tick_scale,
-             extra_margin = bar_extra_margin, bar_label_digits = bar_label_digits)
+             bar_label_scale = bar_label_scale, bar_tick_scale = bar_tick_scale,
+             bar_extra_margin = bar_extra_margin, bar_label_digits = bar_label_digits)
   }
 
   # If the graphic was saved to file, close the connection with the device
diff --git a/R/VizLayout.R b/R/VizLayout.R
index cecbc60..c870f69 100644
--- a/R/VizLayout.R
+++ b/R/VizLayout.R
@@ -120,7 +120,9 @@
 #'  respectively. 'colNA' takes 'white' by default. 'col_inf' and 'col_sup' 
 #'  will take the value of 'colNA' if not specified. See ?ColorBarContinuous for a full 
 #'  explanation on 'col_inf' and 'col_sup'.
-#'@param color_fun,subsampleg,bar_extra_labels,draw_bar_ticks,draw_separators,triangle_ends_scale,bar_label_digits,bar_label_scale,units_scale,bar_tick_scale,bar_extra_margin Set of parameters to control the visual aspect of the drawn colour bar. See ?ColorBarContinuous for a full explanation.
+#'@param color_fun,subsampleg,bar_extra_labels,draw_bar_ticks,draw_separators,triangle_ends_scale,bar_label_digits,bar_label_scale,units_scale,bar_tick_scale,bar_extra_margin
+#'  Set of parameters to control the visual aspect of the drawn colour bar. See
+#'  ?ColorBarContinuous for a full explanation.
 #'@param drawleg Where to draw the common colour bar. Can take values TRUE, 
 #'  FALSE or:\cr
 #'  'up', 'u', 'U', 'top', 't', 'T', 'north', 'n', 'N'\cr
@@ -348,12 +350,20 @@ VizLayout <- function(fun, plot_dims, data = NULL, ..., special_args = NULL,
     drawleg <- tmp$drawleg
   }
 
-  colorbar <- ColorBarContinuous(brks, cols, FALSE, subsampleg, bar_limits,
-                       var_limits, triangle_ends, col_inf, col_sup, color_fun, 
-                       plot = FALSE, draw_bar_ticks, 
-                       draw_separators, triangle_ends_scale, bar_extra_labels,
-                       units, units_scale, bar_label_scale, bar_tick_scale,
-                       bar_extra_margin, bar_label_digits)
+  colorbar <- ColorBarContinuous(brks = brks, cols = cols, vertical = FALSE, 
+                                 subsampleg = subsampleg, bar_limits = bar_limits,
+                                 var_limits = var_limits, triangle_ends = triangle_ends,
+                                 col_inf = col_inf, col_sup = col_sup,
+                                 color_fun = color_fun, plot = FALSE,
+                                 draw_bar_ticks = draw_bar_ticks,
+                                 draw_separators = draw_separators,
+                                 triangle_ends_scale = triangle_ends_scale,
+                                 bar_extra_labels = bar_extra_labels,
+                                 title = units, title_scale = units_scale,
+                                 bar_label_scale = bar_label_scale,
+                                 bar_tick_scale = bar_tick_scale,
+                                 bar_extra_margin = bar_extra_margin,
+                                 bar_label_digits = bar_label_digits)
  
   # Check bar_scale
   if (!is.numeric(bar_scale)) {
@@ -632,14 +642,18 @@ VizLayout <- function(fun, plot_dims, data = NULL, ..., special_args = NULL,
                            label_scale = bar_label_scale, extra_margin = bar_extra_margin)
 
     } else {  # one colorbar
-      ColorBarContinuous(brks = colorbar$brks, cols = colorbar$cols, vertical = vertical, subsampleg = subsampleg,
-               bar_limits = bar_limits, var_limits = var_limits,
-               triangle_ends = triangle_ends, col_inf = colorbar$col_inf,
-               col_sup = colorbar$col_sup, color_fun = color_fun, plot = TRUE, draw_bar_ticks = draw_bar_ticks,
-               draw_separators = draw_separators, triangle_ends_scale = triangle_ends_scale,
-               bar_extra_labels = bar_extra_labels,
-               title = units, title_scale = units_scale, label_scale = bar_label_scale, tick_scale = bar_tick_scale,
-               extra_margin = bar_extra_margin, bar_label_digits = bar_label_digits)
+      ColorBarContinuous(brks = colorbar$brks, cols = colorbar$cols,
+                         vertical = vertical, subsampleg = subsampleg,
+                         bar_limits = bar_limits, var_limits = var_limits,
+                         triangle_ends = triangle_ends, col_inf = colorbar$col_inf,
+                         col_sup = colorbar$col_sup, color_fun = color_fun,
+                         plot = TRUE, draw_bar_ticks = draw_bar_ticks,
+                         draw_separators = draw_separators,
+                         triangle_ends_scale = triangle_ends_scale,
+                         bar_extra_labels = bar_extra_labels, title = units,
+                         title_scale = units_scale, bar_label_scale = bar_label_scale,
+                         bar_tick_scale = bar_tick_scale, bar_extra_margin = bar_extra_margin,
+                         bar_label_digits = bar_label_digits)
 
     }
   }
diff --git a/R/VizRobinson.R b/R/VizRobinson.R
index 366fd6d..0a9d8eb 100644
--- a/R/VizRobinson.R
+++ b/R/VizRobinson.R
@@ -283,8 +283,8 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
                        plot = FALSE, draw_bar_ticks = TRUE, draw_separators = FALSE,
                        triangle_ends_scale = 1, bar_extra_labels = NULL,
                        title = units, title_scale = 1, # units_scale
-                       label_scale = 1, tick_scale = 1, # bar_tick_scale
-                       extra_margin = bar_extra_margin, bar_label_digits = 4)
+                       bar_label_scale = 1, bar_tick_scale = 1,
+                       bar_extra_margin = bar_extra_margin, bar_label_digits = 4)
   brks <- colorbar$brks
   cols <- colorbar$cols
   col_inf <- colorbar$col_inf
@@ -550,8 +550,8 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
                plot = TRUE, draw_bar_ticks = TRUE, draw_separators = FALSE,
                triangle_ends_scale = 1, bar_extra_labels = NULL,
                title = units, title_scale = 1, # units_scale
-               label_scale = 1, tick_scale = 1, #bar_tick_scale
-               extra_margin = bar_extra_margin, bar_label_digits = 4)
+               bar_label_scale = 1, bar_tick_scale = 1,
+               bar_extra_margin = bar_extra_margin, bar_label_digits = 4)
     }
     if (vertical) {
       res_p <- cowplot::plot_grid(res_p, fun_legend, rel_widths = c(6, 1))
diff --git a/R/VizStereoMap.R b/R/VizStereoMap.R
index 85030b5..6e98c5b 100644
--- a/R/VizStereoMap.R
+++ b/R/VizStereoMap.R
@@ -348,7 +348,7 @@ VizStereoMap <- function(data = NULL, lon, lat, varu = NULL, varv = NULL,
   drawleg <- tmp$drawleg
 
   # Check: brks, cols, subsampleg, bar_limits, color_fun, bar_extra_labels, draw_bar_ticks
-  #        draw_separators, triangle_ends_scale, label_scale, units, units_scale, 
+  #        draw_separators, triangle_ends_scale, bar_label_scale, units, units_scale, 
   #        bar_label_digits
   # Build: brks, cols, bar_limits, col_inf, col_sup
   colorbar <- ColorBarContinuous(brks, cols, FALSE, subsampleg, bar_limits, var_limits,
@@ -356,9 +356,9 @@ VizStereoMap <- function(data = NULL, lon, lat, varu = NULL, varv = NULL,
                        bar_extra_labels = bar_extra_labels, draw_bar_ticks = draw_bar_ticks,
                        draw_separators = draw_separators, 
                        triangle_ends_scale = triangle_ends_scale,
-                       label_scale = bar_label_scale, title = units, 
-                       title_scale = units_scale, tick_scale = bar_tick_scale,
-                       extra_margin = bar_extra_margin, bar_label_digits = bar_label_digits)
+                       bar_label_scale = bar_label_scale, title = units, 
+                       title_scale = units_scale, bar_tick_scale = bar_tick_scale,
+                       bar_extra_margin = bar_extra_margin, bar_label_digits = bar_label_digits)
   brks <- colorbar$brks
   cols <- colorbar$cols
   col_inf <- colorbar$col_inf
@@ -871,8 +871,8 @@ VizStereoMap <- function(data = NULL, lon, lat, varu = NULL, varv = NULL,
              bar_extra_labels = bar_extra_labels, draw_bar_ticks = draw_bar_ticks,
              draw_separators = draw_separators, title = units,
              title_scale = units_scale, triangle_ends_scale = triangle_ends_scale, 
-             label_scale = bar_label_scale, tick_scale = bar_tick_scale,
-             extra_margin = bar_extra_margin, bar_label_digits = bar_label_digits)
+             bar_label_scale = bar_label_scale, bar_tick_scale = bar_tick_scale,
+             bar_extra_margin = bar_extra_margin, bar_label_digits = bar_label_digits)
   }
 
   # If the graphic was saved to file, close the connection with the device
-- 
GitLab


From 593e47fb2064aca31de9f0809e515d948be0e49a Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 14 Mar 2025 12:31:03 +0100
Subject: [PATCH 33/72] Change 'legend_scale' for 'bar_label_scale' in
 VizCombinedMap.R

---
 R/VizCombinedMap.R | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/R/VizCombinedMap.R b/R/VizCombinedMap.R
index bb587d2..3f0afaf 100644
--- a/R/VizCombinedMap.R
+++ b/R/VizCombinedMap.R
@@ -61,7 +61,7 @@
 #'  layers via the parameter 'dot_symbol'.
 #'@param bar_titles Optional vector of character strings providing the titles to 
 #'  be shown on top of each of the colour bars.
-#'@param legend_scale Scale factor for the size of the colour bar labels. Takes 
+#'@param bar_label_scale Scale factor for the size of the colour bar labels. Takes 
 #'  1 by default.
 #'@param cex_bar_titles Scale factor for the sizes of the bar titles. Takes 1.5 
 #'  by default.
@@ -144,7 +144,7 @@ VizCombinedMap <- function(maps, lon, lat,
                            col_unknown_map = 'white',
                            mask = NULL, mask_color = 'grey',
                            dots = NULL,
-                           bar_titles = NULL, legend_scale = 1,
+                           bar_titles = NULL, bar_label_scale = 1,
                            cex_bar_titles = 1.5,
                            plot_margin = NULL, bar_extra_margin = c(2, 0, 2, 0),
                            fileout = NULL, width = 8, height = 5, 
@@ -282,12 +282,12 @@ VizCombinedMap <- function(maps, lon, lat,
                                    subsampleg = NULL, bar_limits = bar_limits,
                                    var_limits = var_limits_maps,
                                    triangle_ends = triangle_ends, col_inf = col_inf, col_sup = col_sup, plot = FALSE, draw_separators = TRUE,
-                                   bar_titles = bar_titles, title_scale = cex_bar_titles, label_scale = legend_scale * 1.5,
+                                   bar_titles = bar_titles, title_scale = cex_bar_titles, label_scale = bar_label_scale * 1.5,
                                    extra_margin = bar_extra_margin)
   
-  # Check legend_scale
-  if (!is.numeric(legend_scale)) {
-    stop("Parameter 'legend_scale' must be numeric.")
+  # Check bar_label_scale
+  if (!is.numeric(bar_label_scale)) {
+    stop("Parameter 'bar_label_scale' must be numeric.")
   }
   
   # Check col_unknown_map
@@ -516,7 +516,7 @@ VizCombinedMap <- function(maps, lon, lat,
                          var_limits = var_limits_maps,
                          triangle_ends = triangle_ends, col_inf = colorbar$col_inf, col_sup = colorbar$col_sup,
                          plot = TRUE, draw_separators = TRUE,
-                         bar_titles = bar_titles, title_scale = cex_bar_titles, label_scale = legend_scale * 1.5,
+                         bar_titles = bar_titles, title_scale = cex_bar_titles, label_scale = bar_label_scale * 1.5,
                          extra_margin = bar_extra_margin)
   }
 
@@ -532,7 +532,7 @@ VizCombinedMap <- function(maps, lon, lat,
                 var_limits = var_limits_maps,
                 triangle_ends = triangle_ends, col_inf = colorbar$col_inf, col_sup = colorbar$col_sup,
                 plot = TRUE, draw_separators = TRUE,
-                bar_titles = bar_titles, title_scale = cex_bar_titles, label_scale = legend_scale * 1.5,
+                bar_titles = bar_titles, title_scale = cex_bar_titles, label_scale = bar_label_scale * 1.5,
                 extra_margin = bar_extra_margin)
     warning("The device is not off yet. Use dev.off() after plotting the color bars.")
     return(tmp)
-- 
GitLab


From 9c89c9b0788dc8cb5b844cc2c1d2994edd71563a Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Mon, 17 Mar 2025 09:59:51 +0100
Subject: [PATCH 34/72] Remove default NULL value for data in VizLayout

---
 R/VizLayout.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/VizLayout.R b/R/VizLayout.R
index c870f69..1efe302 100644
--- a/R/VizLayout.R
+++ b/R/VizLayout.R
@@ -141,7 +141,7 @@
 #'  format c(y1, x1, y2, x2). The units are margin lines. Takes rep(0, 4) 
 #'  by default.
 #'@param layout_by_rows Logical indicating wether the panels should be filled 
-#'  by columns (FALSE) or by raws (TRUE, default).
+#'  by columns (FALSE) or by rows (TRUE, default).
 #'@param fileout File where to save the plot. If not specified (default) a 
 #'  graphics device will pop up. Extensions allowed: eps/ps, jpeg, png, pdf, 
 #'  bmp and tiff.
@@ -199,7 +199,7 @@
 #'@importFrom grDevices dev.cur dev.new dev.off
 #'@importFrom s2dv Reorder
 #'@export
-VizLayout <- function(fun, plot_dims, data = NULL, ..., special_args = NULL,
+VizLayout <- function(fun, plot_dims, data, ..., special_args = NULL,
                       nrow = NULL, ncol = NULL, toptitle = NULL,
                       row_titles = NULL, col_titles = NULL, bar_scale = 1, 
                       title_scale = 1, title_margin_scale = 1,
@@ -228,7 +228,7 @@ VizLayout <- function(fun, plot_dims, data = NULL, ..., special_args = NULL,
   is_single_na <- function(x) ifelse(length(x) > 1, FALSE, is.na(x))
   
   # Check data
-  if (is.null(data)) {
+  if (missing(data) || is.null(data)) {
     if (!is.null(var)) {
       data <- var
       warning("The parameter 'var' is deprecated. Use 'data' instead.")
-- 
GitLab


From 2aac581ee076d0a161bb1beedcee24153f3e9f1f Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Mon, 17 Mar 2025 10:13:05 +0100
Subject: [PATCH 35/72] Remove default NULL value for 'data' in VizAnimateMap,
 VizMatrix, VizSection and VizVsLTime

---
 R/VizAnimateMap.R | 14 +++++++-------
 R/VizMatrix.R     |  4 ++--
 R/VizSection.R    |  4 ++--
 R/VizVsLTime.R    |  4 ++--
 4 files changed, 13 insertions(+), 13 deletions(-)

diff --git a/R/VizAnimateMap.R b/R/VizAnimateMap.R
index 30cf632..222928a 100644
--- a/R/VizAnimateMap.R
+++ b/R/VizAnimateMap.R
@@ -103,12 +103,12 @@
 #'  }
 #'@importFrom grDevices postscript dev.off
 #'@importFrom s2dv InsertDim
-VizAnimateMap <- function(data = NULL, lon, lat, toptitle = rep("", 11),
-                          sizetit = 1, units = "", monini = 1, freq = 12,
-                          msk95lev = FALSE, brks = NULL, cols = NULL,
-                          filled.continents = FALSE, lonmin = 0, lonmax = 360,
-                          latmin = -90, latmax = 90, intlon = 20, intlat = 30,
-                          drawleg = TRUE, subsampleg = 1, colNA = "white",
+VizAnimateMap <- function(data, lon, lat, toptitle = rep("", 11), sizetit = 1,
+                          units = "", monini = 1, freq = 12, msk95lev = FALSE,
+                          brks = NULL, cols = NULL, filled.continents = FALSE,
+                          lonmin = 0, lonmax = 360, latmin = -90, latmax = 90,
+                          intlon = 20, intlat = 30, drawleg = TRUE,
+                          subsampleg = 1, colNA = "white",
                           equi = TRUE, fileout = c("output1_animvsltime.gif",
                                                    "output2_animvsltime.gif",
                                                    "output3_animvsltime.gif"),
@@ -127,7 +127,7 @@ VizAnimateMap <- function(data = NULL, lon, lat, toptitle = rep("", 11),
   fileout <- sub("\\.[a-zA-Z0-9]*$", "", fileout)
 
   # Check data
-  if (is.null(data)) {
+  if (missing(data) || is.null(data)) {
     if (!is.null(var)) {
       data <- var
       warning("The parameter 'var' is deprecated. Use 'data' instead.")
diff --git a/R/VizMatrix.R b/R/VizMatrix.R
index 9043a6b..6560381 100644
--- a/R/VizMatrix.R
+++ b/R/VizMatrix.R
@@ -64,7 +64,7 @@
 #'  }
 #'
 #'@importFrom grDevices dev.new dev.off dev.cur 
-VizMatrix <- function(data = NULL, brks = NULL, cols = NULL, toptitle = NULL,
+VizMatrix <- function(data, brks = NULL, cols = NULL, toptitle = NULL,
                       title.color = "royalblue4", xtitle = NULL, ytitle = NULL,
                       xlabels = NULL, xvert = FALSE, ylabels = NULL, line = 3,
                       figure.width = 1, legend = TRUE, legend.width = 0.15,
@@ -72,7 +72,7 @@ VizMatrix <- function(data = NULL, brks = NULL, cols = NULL, toptitle = NULL,
                       size_units = 'px', res = 100, var = NULL, ...) {
 
   # Check data:
-  if (is.null(data)) {
+  if (missing(data) || is.null(data)) {
     if (!is.null(var)) {
       data <- var
       warning("The parameter 'var' is deprecated. Use 'data' instead.")
diff --git a/R/VizSection.R b/R/VizSection.R
index 14ed580..3235e38 100644
--- a/R/VizSection.R
+++ b/R/VizSection.R
@@ -44,7 +44,7 @@
 #'esviz:::VizSection(data, horiz = 0:20, depth = seq(0, 300, length.out = 7),
 #'           toptitle = 'Temperature cross-section', units = "degC")
 #'@importFrom grDevices dev.cur dev.new dev.off rainbow
-VizSection <- function(data = NULL, horiz, depth, toptitle = '', sizetit = 1,
+VizSection <- function(data, horiz, depth, toptitle = '', sizetit = 1,
                        units = '', brks = NULL, cols = NULL, axelab = TRUE,
                        intydep = 200, intxhoriz = 20, drawleg = TRUE,
                        fileout = NULL, width = 10, height = 8,
@@ -66,7 +66,7 @@ VizSection <- function(data = NULL, horiz, depth, toptitle = '', sizetit = 1,
   #  Input arguments 
   # ~~~~~~~~~~~~~~~~~
   #
-  if (is.null(data)) {
+  if (missing(data) || is.null(data)) {
     if (!is.null(var)) {
       data <- var
       warning("The parameter 'var' is deprecated. Use 'data' instead.")
diff --git a/R/VizVsLTime.R b/R/VizVsLTime.R
index 941bc3d..2b3bf73 100644
--- a/R/VizVsLTime.R
+++ b/R/VizVsLTime.R
@@ -85,7 +85,7 @@
 #'@importFrom grDevices dev.cur dev.new dev.off
 #'@importFrom stats ts
 #'@importFrom s2dv InsertDim
-VizVsLTime <- function(data = NULL, toptitle = '', ytitle = '', monini = 1,
+VizVsLTime <- function(data, toptitle = '', ytitle = '', monini = 1,
                        freq = 12, nticks = NULL, limits = NULL,
                        listexp = c('exp1', 'exp2', 'exp3'),
                        listobs = c('obs1', 'obs2', 'obs3'),
@@ -110,7 +110,7 @@ VizVsLTime <- function(data = NULL, toptitle = '', ytitle = '', monini = 1,
   #  Get some arguments
   # ~~~~~~~~~~~~~~~~~~~~
   #
-  if (is.null(data)) {
+  if (missing(data) || is.null(data)) {
     if (!is.null(var)) {
       data <- var
       warning("The parameter 'var' is deprecated. Use 'data' instead.")
-- 
GitLab


From 2d12dc176a3996965e9c9d6aa42ec2c3f6b9308b Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 28 Mar 2025 17:07:44 +0100
Subject: [PATCH 36/72] Change 'sizetit' for 'title_scale' in VizAnimateMap.R

---
 R/VizAnimateMap.R | 36 ++++++++++++++++++++++++++----------
 1 file changed, 26 insertions(+), 10 deletions(-)

diff --git a/R/VizAnimateMap.R b/R/VizAnimateMap.R
index 222928a..71fdea1 100644
--- a/R/VizAnimateMap.R
+++ b/R/VizAnimateMap.R
@@ -16,7 +16,9 @@
 #'@param toptitle c('','', \dots) array of main title for each animation, 
 #'  optional. If RMS, RMSSS, correlations: first exp with successive obs, then 
 #'  second exp with successive obs, etc ...
-#'@param sizetit Multiplicative factor to increase title size, optional.
+#'@param title_scale Scale factor for the figure top title. Defaults to 1.
+#'@param sizetit Scale factor for the figure top title provided in parameter 
+#'  'toptitle'. Deprecated. Use 'title_scale' instead.
 #'@param units Units, optional.
 #'@param monini Starting month between 1 and 12. Default = 1.
 #'@param freq 1 = yearly, 12 = monthly, 4 = seasonal ...
@@ -97,18 +99,18 @@
 #'lons <- attr(map_temp$exp, "Variables")$common$lon
 #'  \dontrun{
 #'esviz:::VizAnimateMap(clim$clim_exp[1, 1, , , ], lon = lons, lat = lats,
-#'  toptitle = "climatology of decadal prediction", sizetit = 1, 
+#'  toptitle = "climatology of decadal prediction", title_scale = 1, 
 #'  units = "K", brks = seq(270, 300, 3), monini = 11, freq = 12, 
 #'  msk95lev = FALSE, filled.continents = FALSE, intlon = 10, intlat = 10)
 #'  }
 #'@importFrom grDevices postscript dev.off
 #'@importFrom s2dv InsertDim
-VizAnimateMap <- function(data, lon, lat, toptitle = rep("", 11), sizetit = 1,
-                          units = "", monini = 1, freq = 12, msk95lev = FALSE,
-                          brks = NULL, cols = NULL, filled.continents = FALSE,
-                          lonmin = 0, lonmax = 360, latmin = -90, latmax = 90,
-                          intlon = 20, intlat = 30, drawleg = TRUE,
-                          subsampleg = 1, colNA = "white",
+VizAnimateMap <- function(data, lon, lat, toptitle = rep("", 11), title_scale = 1,
+                          sizetit = NULL, units = "", monini = 1, freq = 12,
+                          msk95lev = FALSE, brks = NULL, cols = NULL,
+                          filled.continents = FALSE, lonmin = 0, lonmax = 360,
+                          latmin = -90, latmax = 90, intlon = 20, intlat = 30,
+                          drawleg = TRUE, subsampleg = 1, colNA = "white",
                           equi = TRUE, fileout = c("output1_animvsltime.gif",
                                                    "output2_animvsltime.gif",
                                                    "output3_animvsltime.gif"),
@@ -152,6 +154,20 @@ VizAnimateMap <- function(data, lon, lat, toptitle = rep("", 11), sizetit = 1,
   if (length(dim(data)) == 5) {
     data <- InsertDim(data, posdim = 2, lendim = 1, name = 'new')
   }
+  
+  # Check title_scale
+  if (!is.numeric(title_scale)) {
+    stop("Parameter 'title_scale' must be numeric.")
+  }
+  
+  # Check sizetit
+  if (!is.null(sizetit)) {
+    warning("Parameter 'sizetit' is obsolete. Use 'title_scale' instead.")
+    if (!is.numeric(sizetit) || length(sizetit) != 1) {
+      stop("Parameter 'sizetit' must numeric.")
+    }
+    title_scale <- sizetit
+  }
 
   nleadtime <- dim(data)[4]
   nexp <- dim(data)[1]
@@ -227,13 +243,13 @@ VizAnimateMap <- function(data, lon, lat, toptitle = rep("", 11), sizetit = 1,
           (max(brks) - min(brks))/1000
         if (equi) {
           VizEquiMap(t(varbis), lonb$x, latb$x, toptitle = title, 
-          title_scale = sizetit, units = units, filled.continents = filled.continents, 
+          title_scale = title_scale, units = units, filled.continents = filled.continents, 
           dots = t(flag), brks = brks, cols = cols, 
           intxlon = intlon, intylat = intlat, drawleg = drawleg, 
           subsampleg = subsampleg, colNA = colNA, ...)
         } else {
           VizStereoMap(t(varbis), lonb$x, latb$x, latlims = c(latmin, 
-          latmax), toptitle = title, title_scale = sizetit, 
+          latmax), toptitle = title, title_scale = title_scale, 
           units = units, filled.continents = filled.continents, 
           dots = t(flag), brks = brks, cols = cols, 
           intlat = intlat, drawleg = drawleg, subsampleg = subsampleg, 
-- 
GitLab


From ed55ab7bcdad6d7340f0c882ce9cd25879ed2eed Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Mon, 31 Mar 2025 11:15:42 +0200
Subject: [PATCH 37/72] Change 'sizetit' for 'title_scale' in VizSection.R

---
 R/VizAnimateMap.R | 4 ++--
 R/VizSection.R    | 8 +++++---
 2 files changed, 7 insertions(+), 5 deletions(-)

diff --git a/R/VizAnimateMap.R b/R/VizAnimateMap.R
index 71fdea1..cf33697 100644
--- a/R/VizAnimateMap.R
+++ b/R/VizAnimateMap.R
@@ -17,8 +17,8 @@
 #'  optional. If RMS, RMSSS, correlations: first exp with successive obs, then 
 #'  second exp with successive obs, etc ...
 #'@param title_scale Scale factor for the figure top title. Defaults to 1.
-#'@param sizetit Scale factor for the figure top title provided in parameter 
-#'  'toptitle'. Deprecated. Use 'title_scale' instead.
+#'@param sizetit Scale factor for the figure top title. Deprecated. Use
+#'  'title_scale' instead.
 #'@param units Units, optional.
 #'@param monini Starting month between 1 and 12. Default = 1.
 #'@param freq 1 = yearly, 12 = monthly, 4 = seasonal ...
diff --git a/R/VizSection.R b/R/VizSection.R
index 3235e38..f60557a 100644
--- a/R/VizSection.R
+++ b/R/VizSection.R
@@ -7,7 +7,9 @@
 #'@param horiz Array of longitudes or latitudes.
 #'@param depth Array of depths.
 #'@param toptitle Title, optional.
-#'@param sizetit Multiplicative factor to increase title size, optional.
+#'@param title_scale Scale factor for the figure top title. Defaults to 1.
+#'@param sizetit Scale factor for the figure top title. Deprecated. Use
+#' 'title_scale' instead.
 #'@param units Units, optional.
 #'@param brks Colour levels, optional.
 #'@param cols List of colours, optional.
@@ -44,7 +46,7 @@
 #'esviz:::VizSection(data, horiz = 0:20, depth = seq(0, 300, length.out = 7),
 #'           toptitle = 'Temperature cross-section', units = "degC")
 #'@importFrom grDevices dev.cur dev.new dev.off rainbow
-VizSection <- function(data, horiz, depth, toptitle = '', sizetit = 1,
+VizSection <- function(data, horiz, depth, toptitle = '', title_scale = 1,
                        units = '', brks = NULL, cols = NULL, axelab = TRUE,
                        intydep = 200, intxhoriz = 20, drawleg = TRUE,
                        fileout = NULL, width = 10, height = 8,
@@ -151,7 +153,7 @@ VizSection <- function(data, horiz, depth, toptitle = '', sizetit = 1,
       mgp = c(2.5, 0.5, 0), las = 1)
   image(horizb$x, depthb$x, array(0, dims), col = 'grey', breaks = c(-1, 1),
         axes = FALSE, xlab = "", ylab = "", main = toptitle, 
-        cex.main = 1.5 * sizetit)
+        cex.main = 1.5 * title_scale)
   image(horizb$x, depthb$x, data[horizb$ix, depthb$ix], col = cols, 
         breaks = brks, axes = FALSE, xlab = "", ylab = "", add = TRUE)
   if (axelab) {
-- 
GitLab


From 67e701694c6f09ec5915a4376919ebe47849a603 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Mon, 31 Mar 2025 11:16:25 +0200
Subject: [PATCH 38/72] Change 'sizetit' for 'title_scale' in VizVsLTime.R

---
 R/VizVsLTime.R | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/R/VizVsLTime.R b/R/VizVsLTime.R
index 2b3bf73..414f22f 100644
--- a/R/VizVsLTime.R
+++ b/R/VizVsLTime.R
@@ -29,7 +29,9 @@
 #'@param siglev TRUE/FALSE if significance level should replace confidence 
 #'  interval.\cr
 #'  Default = FALSE.
-#'@param sizetit Multiplicative factor to change title size, optional.
+#'@param title_scale Scale factor for the figure top title. Defaults to 1.
+#'@param sizetit Scale factor for the figure top title. Deprecated. Use
+#' 'title_scale' instead.
 #'@param show_conf TRUE/FALSE to show/not confidence intervals for input 
 #'  variables.
 #'@param fileout Name of output file. Extensions allowed: eps/ps, jpeg, png, 
@@ -90,7 +92,7 @@ VizVsLTime <- function(data, toptitle = '', ytitle = '', monini = 1,
                        listexp = c('exp1', 'exp2', 'exp3'),
                        listobs = c('obs1', 'obs2', 'obs3'),
                        biglab = FALSE, hlines = NULL, leg = TRUE,
-                       siglev = FALSE, sizetit = 1, show_conf = TRUE,
+                       siglev = FALSE, title_scale = 1, show_conf = TRUE,
                        fileout = NULL, width = 8, height = 5, size_units = 'in',
                        res = 100, var = NULL, ...) {
   # Process the user graphical parameters that may be passed in the call
@@ -212,7 +214,7 @@ VizVsLTime <- function(data, toptitle = '', ytitle = '', monini = 1,
     legsize <- 1
   }
   plot(empty, ylim = c(ll, ul), xlab = "Time (months)", ylab = ytitle, 
-       main = toptitle, cex.main = cexmain*sizetit, axes = FALSE)
+       main = toptitle, cex.main = cexmain*title_scale, axes = FALSE)
   axis(1, at = labind, labels = labmonth)
   axis(2)
   box()
-- 
GitLab


From b89dbb3c6131e1b72a2d5d52bac3f55b8cea9a9c Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Mon, 31 Mar 2025 17:17:14 +0200
Subject: [PATCH 39/72] Change 'legend' for 'drawleg' in VizMatrix.R

---
 R/VizMatrix.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/R/VizMatrix.R b/R/VizMatrix.R
index 6560381..61ce4bf 100644
--- a/R/VizMatrix.R
+++ b/R/VizMatrix.R
@@ -31,7 +31,7 @@
 #'  are long.
 #'@param figure.width A positive number as a ratio adjusting the width of the 
 #'  grids. Set 1 as default.
-#'@param legend A logical value to decide to draw the grid color legend or not. 
+#'@param drawleg A logical value to decide to draw the grid color legend or not. 
 #'  Set TRUE as default.
 #'@param legend.width A number between 0 and 0.5 to adjust the legend width.
 #'  Set 0.15 as default.
@@ -67,7 +67,7 @@
 VizMatrix <- function(data, brks = NULL, cols = NULL, toptitle = NULL,
                       title.color = "royalblue4", xtitle = NULL, ytitle = NULL,
                       xlabels = NULL, xvert = FALSE, ylabels = NULL, line = 3,
-                      figure.width = 1, legend = TRUE, legend.width = 0.15,
+                      figure.width = 1, drawleg = TRUE, legend.width = 0.15,
                       xlab_dist = NULL, ylab_dist = NULL, fileout = NULL,
                       size_units = 'px', res = 100, var = NULL, ...) {
 
@@ -117,7 +117,7 @@ VizMatrix <- function(data, brks = NULL, cols = NULL, toptitle = NULL,
   if (!is.numeric(legend.width) || legend.width < 0 || legend.width > 0.5)
       stop("legend.width must be a number from 0 to 0.5")
 
-    
+
   # If there is any filenames to store the graphics, process them
   # to select the right device 
   if (!is.null(fileout)) {
@@ -228,7 +228,7 @@ VizMatrix <- function(data, brks = NULL, cols = NULL, toptitle = NULL,
   }
 
   # Draw color legend:
-  if (legend) {
+  if (drawleg) {
     par(fig = c(1 - legend.width - 0.01, 
                 1 - legend.width + legend.width * min(1, 10 / ncols), 
                 0.3, 0.8), new = TRUE)
-- 
GitLab


From 93f519bfeb76625b14ebbb3caf40162d400c5d61 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Mon, 31 Mar 2025 17:17:37 +0200
Subject: [PATCH 40/72] Change 'leg' for'drawleg' in R/VizVsLTime.R

---
 R/VizVsLTime.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/VizVsLTime.R b/R/VizVsLTime.R
index 414f22f..1775542 100644
--- a/R/VizVsLTime.R
+++ b/R/VizVsLTime.R
@@ -24,7 +24,7 @@
 #'@param biglab TRUE/FALSE for presentation/paper plot. Default = FALSE.
 #'@param hlines c(a,b, ..) Add horizontal black lines at Y-positions a,b, ...\cr
 #'  Default = NULL.
-#'@param leg TRUE/FALSE if legend should be added or not to the plot. 
+#'@param drawleg TRUE/FALSE if legend should be added or not to the plot. 
 #'  Default = TRUE.
 #'@param siglev TRUE/FALSE if significance level should replace confidence 
 #'  interval.\cr
@@ -91,7 +91,7 @@ VizVsLTime <- function(data, toptitle = '', ytitle = '', monini = 1,
                        freq = 12, nticks = NULL, limits = NULL,
                        listexp = c('exp1', 'exp2', 'exp3'),
                        listobs = c('obs1', 'obs2', 'obs3'),
-                       biglab = FALSE, hlines = NULL, leg = TRUE,
+                       biglab = FALSE, hlines = NULL, drawleg = TRUE,
                        siglev = FALSE, title_scale = 1, show_conf = TRUE,
                        fileout = NULL, width = 8, height = 5, size_units = 'in',
                        res = 100, var = NULL, ...) {
@@ -256,7 +256,7 @@ VizVsLTime <- function(data, toptitle = '', ytitle = '', monini = 1,
       }
     }
   }
-  if (leg) {
+  if (drawleg) {
     if (nobs == 1) {
       legendnames <- listexp[1:nexp]
     }  
-- 
GitLab


From 523694fd09d8ec29ee8fb2b80feb47d846e6f18f Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 11 Apr 2025 18:28:02 +0200
Subject: [PATCH 41/72] Ensure deprecated parameters maintain compatibility

---
 R/ColorBarContinuous.R | 35 +++++++++++++++++++++++++----
 R/ColorBarDiscrete.R   | 16 +++++++++++++
 R/VizAnimateMap.R      | 18 +++++----------
 R/VizCombinedMap.R     |  7 +++++-
 R/VizMatrix.R          | 17 +++++++++++---
 R/VizRobinson.R        | 51 +++++++++++++++++++++++++++++++++++-------
 R/VizSection.R         | 20 ++++++++++++-----
 R/VizStereoMap.R       |  2 +-
 R/VizVsLTime.R         | 28 ++++++++++++++++++-----
 9 files changed, 154 insertions(+), 40 deletions(-)

diff --git a/R/ColorBarContinuous.R b/R/ColorBarContinuous.R
index 5974992..f7e02ad 100644
--- a/R/ColorBarContinuous.R
+++ b/R/ColorBarContinuous.R
@@ -94,21 +94,26 @@
 #'@param bar_extra_labels Numeric vector of extra labels to draw along axis of 
 #'  the colour bar. The number of provided decimals will be conserved. 
 #'  Disregarded if 'plot = FALSE'.
+#'@param extra_labels Deprecated. Use 'bar_extra_labels' instead.
 #'@param title Title to draw on top of the colour bar, most commonly with the 
 #'  units of the represented field in the neighbour figures. Empty by default.
 #'@param title_scale Scale factor for the 'title' of the colour bar. 
 #'  Takes 1 by default.
 #'@param bar_label_scale Scale factor for the labels of the colour bar. 
 #'  Takes 1 by default.
+#'@param label_scale Deprecated. Use 'bar_label_scale' instead.
 #'@param bar_tick_scale Scale factor for the length of the ticks of the labels 
 #'  along the colour bar. Takes 1 by default.
+#'@param tick_scale Deprecated. Use 'bar_tick_scale' instead.
 #'@param bar_extra_margin Extra margins to be added around the colour bar, 
 #'  in the format c(y1, x1, y2, x2). The units are margin lines. Takes 
 #'  rep(0, 4) by default.
+#'@param extra_margin Deprecated. Use 'bar_extra_margin' instead.
 #'@param bar_label_digits Number of significant digits to be displayed in the 
 #'  labels of the colour bar, usually to avoid too many decimal digits 
 #'  overflowing the figure region. This does not have effect over the labels 
 #'  provided in 'bar_extra_labels'. Takes 4 by default.
+#'@param label_digits Deprecated. Use 'bar_label_digits' instead.
 #'@param ... Arguments to be passed to the method. Only accepts the following 
 #'  graphical parameters:\cr adj ann ask bg bty cex.lab cex.main cex.sub cin 
 #'  col.axis col.lab col.main col.sub cra crt csi cxy err family fg fig fin 
@@ -148,10 +153,12 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
                      triangle_ends = NULL, col_inf = NULL, col_sup = NULL, 
                      color_fun = ClimPalette(), plot = TRUE, 
                      draw_bar_ticks = TRUE, draw_separators = FALSE, 
-                     triangle_ends_scale = 1, bar_extra_labels = NULL, 
-                     title = NULL, title_scale = 1, 
-                     bar_label_scale = 1, bar_tick_scale = 1, 
-                     bar_extra_margin = rep(0, 4), bar_label_digits = 4, ...) {
+                     triangle_ends_scale = 1, bar_extra_labels = NULL,
+                     extra_labels = NULL, title = NULL, title_scale = 1, 
+                     bar_label_scale = 1, label_scale = NULL,
+                     bar_tick_scale = 1, tick_scale = NULL,
+                     bar_extra_margin = rep(0, 4), extra_margin = NULL,
+                     bar_label_digits = 4, label_digits = NULL, ...) {
   # Required checks
   if ((is.null(brks) || length(brks) < 2) && is.null(bar_limits) && is.null(var_limits)) {
     stop("At least one of 'brks' with the desired breaks, 'bar_limits' or ",
@@ -326,6 +333,10 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
   }
 
   # Check bar_extra_labels
+  if (missing(bar_extra_labels) && !missing(extra_labels)) {
+    warning("The parameter 'extra_labels' is deprecated. Use 'bar_extra_labels' instead.")
+    bar_extra_labels <- extra_labels
+  }
   if (is.null(bar_extra_labels)) {
     bar_extra_labels <- numeric(0)
   }
@@ -407,21 +418,37 @@ ColorBarContinuous <- function(brks = NULL, cols = NULL, vertical = TRUE,
   }
 
   # Check bar_label_scale
+  if (missing(bar_label_scale) && !missing(label_scale)) {
+    warning("The parameter 'label_scale' is deprecated. Use 'bar_label_scale' instead.")
+    bar_label_scale <- label_scale
+  }
   if (!is.numeric(bar_label_scale)) {
     stop("Parameter 'bar_label_scale' must be numeric.")
   }
 
   # Check bar_tick_scale
+  if (missing(bar_tick_scale) && !missing(tick_scale)) {
+    warning("The parameter 'tick_scale' is deprecated. Use 'bar_tick_scale' instead.")
+    bar_tick_scale <- tick_scale
+  }
   if (!is.numeric(bar_tick_scale)) {
     stop("Parameter 'bar_tick_scale' must be numeric.")
   }
 
   # Check bar_extra_margin
+  if (missing(bar_extra_margin) && !missing(extra_margin)) {
+    warning("The parameter 'extra_margin' is deprecated. Use 'bar_extra_margin' instead.")
+    bar_extra_margin <- extra_margin
+  }
   if (!is.numeric(bar_extra_margin) || length(bar_extra_margin) != 4) {
     stop("Parameter 'bar_extra_margin' must be a numeric vector of length 4.")
   }
 
   # Check bar_label_digits
+  if (missing(bar_label_digits) && !missing(label_digits)) {
+    warning("The parameter 'label_digits' is deprecated. Use 'bar_label_digits' instead.")
+    bar_label_digits <- label_digits
+  }
   if (!is.numeric(bar_label_digits)) {
     stop("Parameter 'bar_label_digits' must be numeric.")
   }
diff --git a/R/ColorBarDiscrete.R b/R/ColorBarDiscrete.R
index 122e1da..5e0f619 100644
--- a/R/ColorBarDiscrete.R
+++ b/R/ColorBarDiscrete.R
@@ -322,21 +322,37 @@ ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE,
   }
 
   ## label_scale
+  if (missing(bar_label_scale) && !missing(label_scale)) {
+    warning("The parameter 'label_scale' is deprecated. Use 'bar_label_scale' instead.")
+    bar_label_scale <- label_scale
+  }
   if (!is.numeric(label_scale)) {
     stop("Parameter 'label_scale' must be numeric.")
   }
 
   ## tick_scale
+  if (missing(bar_tick_scale) && !missing(tick_scale)) {
+    warning("The parameter 'tick_scale' is deprecated. Use 'bar_tick_scale' instead.")
+    bar_tick_scale <- tick_scale
+  }
   if (!is.numeric(tick_scale)) {
     stop("Parameter 'tick_scale' must be numeric.")
   }
 
   ## extra_margin
+  if (missing(bar_extra_margin) && !missing(extra_margin)) {
+    warning("The parameter 'extra_margin' is deprecated. Use 'bar_extra_margin' instead.")
+    bar_extra_margin <- extra_margin
+  }
   if (!is.numeric(extra_margin) || length(extra_margin) != 4) {
     stop("Parameter 'extra_margin' must be a numeric vector of length 4.")
   }
 
   ## bar_label_digits
+  if (missing(bar_label_digits) && !missing(label_digits)) {
+    warning("The parameter 'label_digits' is deprecated. Use 'bar_label_digits' instead.")
+    bar_label_digits <- label_digits
+  }
   if (!is.numeric(bar_label_digits)) {
     stop("Parameter 'bar_label_digits' must be numeric.")
   }
diff --git a/R/VizAnimateMap.R b/R/VizAnimateMap.R
index cf33697..f90a355 100644
--- a/R/VizAnimateMap.R
+++ b/R/VizAnimateMap.R
@@ -17,8 +17,7 @@
 #'  optional. If RMS, RMSSS, correlations: first exp with successive obs, then 
 #'  second exp with successive obs, etc ...
 #'@param title_scale Scale factor for the figure top title. Defaults to 1.
-#'@param sizetit Scale factor for the figure top title. Deprecated. Use
-#'  'title_scale' instead.
+#'@param sizetit Deprecated. Use 'title_scale' instead.
 #'@param units Units, optional.
 #'@param monini Starting month between 1 and 12. Default = 1.
 #'@param freq 1 = yearly, 12 = monthly, 4 = seasonal ...
@@ -156,18 +155,13 @@ VizAnimateMap <- function(data, lon, lat, toptitle = rep("", 11), title_scale =
   }
   
   # Check title_scale
-  if (!is.numeric(title_scale)) {
-    stop("Parameter 'title_scale' must be numeric.")
-  }
-  
-  # Check sizetit
-  if (!is.null(sizetit)) {
-    warning("Parameter 'sizetit' is obsolete. Use 'title_scale' instead.")
-    if (!is.numeric(sizetit) || length(sizetit) != 1) {
-      stop("Parameter 'sizetit' must numeric.")
-    }
+  if (missing(title_scale) && !missing(sizetit)) {
+    warning("The parameter 'sizetit' is deprecated. Use 'title_scale' instead.")
     title_scale <- sizetit
   }
+  if (!is.numeric(title_scale) || length(title_scale) != 1) {
+    stop("Parameter 'title_scale' must be a single numerical value.")
+  }
 
   nleadtime <- dim(data)[4]
   nexp <- dim(data)[1]
diff --git a/R/VizCombinedMap.R b/R/VizCombinedMap.R
index 3f0afaf..aa3b50c 100644
--- a/R/VizCombinedMap.R
+++ b/R/VizCombinedMap.R
@@ -53,6 +53,7 @@
 #'  will result in a totally opaque superimposed pixel coloured in 'mask_color'.
 #'@param mask_color Colour to be used for the superimposed mask (if specified in 
 #'  'mask'). Takes the value 'grey' by default.
+#'@param col_mask Deprecated. Use 'mask_color' instead.
 #'@param dots Array of same dimensions as 'var' or with dimensions 
 #'  c(n, dim(var)), where n is the number of dot/symbol layers to add to the 
 #'  plot. A value of TRUE at a grid cell will draw a dot/symbol on the 
@@ -142,7 +143,7 @@ VizCombinedMap <- function(maps, lon, lat,
                            bar_limits = NULL, triangle_ends = c(FALSE, FALSE), 
                            col_inf = NULL, col_sup = NULL,
                            col_unknown_map = 'white',
-                           mask = NULL, mask_color = 'grey',
+                           mask = NULL, mask_color = 'grey', col_mask = NULL,
                            dots = NULL,
                            bar_titles = NULL, bar_label_scale = 1,
                            cex_bar_titles = 1.5,
@@ -296,6 +297,10 @@ VizCombinedMap <- function(maps, lon, lat,
   }
   
   # Check mask_color
+  if (missing(mask_color) && !missing(col_mask)) {
+    warning("The parameter 'col_mask' is deprecated. Use 'mask_color' instead.")
+    mask_color <- col_mask
+  }
   if (!is.character(mask_color)) {
     stop("Parameter 'mask_color' must be a character string.")
   }
diff --git a/R/VizMatrix.R b/R/VizMatrix.R
index 61ce4bf..fdee366 100644
--- a/R/VizMatrix.R
+++ b/R/VizMatrix.R
@@ -33,6 +33,7 @@
 #'  grids. Set 1 as default.
 #'@param drawleg A logical value to decide to draw the grid color legend or not. 
 #'  Set TRUE as default.
+#'@param legend Deprecated. Use 'drawleg' instead.
 #'@param legend.width A number between 0 and 0.5 to adjust the legend width.
 #'  Set 0.15 as default.
 #'@param xlab_dist A number specifying the distance between the x labels and 
@@ -67,9 +68,10 @@
 VizMatrix <- function(data, brks = NULL, cols = NULL, toptitle = NULL,
                       title.color = "royalblue4", xtitle = NULL, ytitle = NULL,
                       xlabels = NULL, xvert = FALSE, ylabels = NULL, line = 3,
-                      figure.width = 1, drawleg = TRUE, legend.width = 0.15,
-                      xlab_dist = NULL, ylab_dist = NULL, fileout = NULL,
-                      size_units = 'px', res = 100, var = NULL, ...) {
+                      figure.width = 1, drawleg = TRUE, legend = NULL,
+                      legend.width = 0.15, xlab_dist = NULL, ylab_dist = NULL,
+                      fileout = NULL, size_units = 'px', res = 100, var = NULL,
+                      ...) {
 
   # Check data:
   if (missing(data) || is.null(data)) {
@@ -88,6 +90,15 @@ VizMatrix <- function(data, brks = NULL, cols = NULL, toptitle = NULL,
   if (!is.numeric(data)){
     stop("Input values are not always numbers")
   }
+  
+  # Check drawleg
+  if (missing(drawleg) && !missing(legend)) {
+    warning("The parameter 'legend' is deprecated. Use 'drawleg' instead.")
+    drawleg <- legend
+  }
+  if (!is.logical(drawleg) || length(drawleg) != 1) {
+    stop("Parameter 'drawleg' must be a single logical value")
+  }
 
   # Build: brks, cols 
   colorbar <- ColorBarContinuous(brks = brks, cols = cols, vertical = FALSE, 
diff --git a/R/VizRobinson.R b/R/VizRobinson.R
index 0a9d8eb..46ac73a 100644
--- a/R/VizRobinson.R
+++ b/R/VizRobinson.R
@@ -78,9 +78,13 @@
 #'@param title_scale A number of the size of the top title. The default is 16.
 #'@param title_size Deprecated. Use 'title_scale' instead.
 #'@param dot_size A number of the size of the dots. The default is 0.5.
+#'@param dots_size Deprecated. Use 'dot_size' instead.
 #'@param dot_symbol A number indicating the dot shape recognized by parameter 
 #'  'shape' in \code{geom_point()}.
-#'@param coast_width A number indicating the width of the coastlines.
+#'@param dots_shape Deprecated. Use 'dot_symbol' instead.
+#'@param coast_width A number indicating the width of the coastlines. Default is
+#'  0.3.
+#'@param coastlines_width Deprecated. Use 'coast_width' instead.
 #'@param fileout A character string of the path to save the plot. If not 
 #'  specified (default), a graphic device will pop up. The extension should be  
 #'  accepted by \code{ggsave()}.
@@ -130,8 +134,10 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
                         toptitle = NULL, caption = NULL, units = NULL,
                         crop_coastlines = NULL, point_size = "auto",
                         title_scale = 16, title_size = NULL, dot_size = 0.5,
-                        dot_symbol = 47, coast_width = 0.3, fileout = NULL,
-                        width = 8, height = 4, size_units = "in", res = 300) {
+                        dots_size = NULL, dot_symbol = 47, dots_shape = NULL,
+                        coast_width = 0.3, coastlines_width = NULL,
+                        fileout = NULL, width = 8, height = 4,
+                        size_units = "in", res = 300) {
 
   # Sanity check
   # data
@@ -263,10 +269,13 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
       stop("Parameter 'mask' must be a logical or numerical array.")
     }
   }
-  # title_scale
-  if (missing(title_scale) && !is.null(title_size)) {
-    title_scale <- title_size
+  # Check title_scale
+  if (missing(title_scale) && !missing(title_size)) {
     warning("The parameter 'title_size' is deprecated. Use 'title_scale' instead.")
+    title_scale <- title_size
+  }
+  if (!is.numeric(title_scale) || length(title_scale) != 1) {
+    stop("Parameter 'title_scale' must be a single numerical value.")
   }
 
   tmp <- .create_var_limits(data = data, brks = brks, 
@@ -326,9 +335,35 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
     # 360x181 with default setting, 0.05
     point_size <- round(0.05 * (360 * 181) / (length(lon) * length(lat)), 2)
   } else if (!is.numeric(point_size)) {
-    stop("Parameter 'point_size' must be a number.")
+    stop("Parameter 'point_size' must be a numerical value")
+  }
+  
+  # dot_symbol
+  if (missing(dot_symbol) && !missing(dots_shape)) {
+    warning("The parameter 'dots_shape' is deprecated. Use 'dot_symbol' instead.")
+    dot_symbol <- dots_shape
+  }
+  if (!is.numeric(dot_symbol)) {
+    stop("Parameter 'dot_symbol' must be a numerical value.")
+  }
+  
+  # dot_size
+  if (missing(dot_size) && !missing(dots_size)) {
+    warning("The parameter 'dots_size' is deprecated. Use 'dot_size' instead.")
+    dot_size <- dots_size
+  }
+  if (!is.numeric(dot_size)) {
+    stop("Parameter 'dot_size' must be a numerical value.")
+  }
+  
+  # coast_width
+  if (missing(coast_width) && !missing(coastlines_width)) {
+    warning("The parameter 'coastlines_width' is deprecated. Use 'coast_width' instead.")
+    coast_width <- coastlines_width
+  }
+  if (!is.numeric(coast_width)) {
+    stop("Parameter 'coast_width' must be a numerical value.")
   }
-  #
 
 #=================================================================
 
diff --git a/R/VizSection.R b/R/VizSection.R
index f60557a..8742ef6 100644
--- a/R/VizSection.R
+++ b/R/VizSection.R
@@ -8,8 +8,7 @@
 #'@param depth Array of depths.
 #'@param toptitle Title, optional.
 #'@param title_scale Scale factor for the figure top title. Defaults to 1.
-#'@param sizetit Scale factor for the figure top title. Deprecated. Use
-#' 'title_scale' instead.
+#'@param sizetit Deprecated. Use 'title_scale' instead.
 #'@param units Units, optional.
 #'@param brks Colour levels, optional.
 #'@param cols List of colours, optional.
@@ -47,9 +46,9 @@
 #'           toptitle = 'Temperature cross-section', units = "degC")
 #'@importFrom grDevices dev.cur dev.new dev.off rainbow
 VizSection <- function(data, horiz, depth, toptitle = '', title_scale = 1,
-                       units = '', brks = NULL, cols = NULL, axelab = TRUE,
-                       intydep = 200, intxhoriz = 20, drawleg = TRUE,
-                       fileout = NULL, width = 10, height = 8,
+                       sizetit = NULL, units = '', brks = NULL, cols = NULL,
+                       axelab = TRUE, intydep = 200, intxhoriz = 20,
+                       drawleg = TRUE, fileout = NULL, width = 10, height = 8,
                        size_units = 'in', res = 100, var = NULL, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
@@ -90,6 +89,15 @@ VizSection <- function(data, horiz, depth, toptitle = '', title_scale = 1,
       stop("Inconsistent data dimensions and longitudes/latitudes + depth")
     }
   }
+  # Check title_scale
+  if (missing(title_scale) && !missing(sizetit)) {
+    warning("The parameter 'sizetit' is deprecated. Use 'title_scale' instead.")
+    title_scale <- sizetit
+  }
+  if (!is.numeric(title_scale) || length(title_scale) != 1) {
+    stop("Parameter 'title_scale' must be a single numerical value.")
+  }
+  
   dhoriz <- horiz[2:dims[1]] - horiz[1:(dims[1] - 1)]
   wher <- which(dhoriz > (mean(dhoriz) + 5))
   if (length(wher) > 0) {
@@ -120,11 +128,11 @@ VizSection <- function(data, horiz, depth, toptitle = '', title_scale = 1,
       }
     }
   }
+  
   #
   #  Plotting the section
   # ~~~~~~~~~~~~~~~~~~
   #
-
   # Open connection to graphical device
   if (!is.null(fileout)) {
     saveToFile(fileout)
diff --git a/R/VizStereoMap.R b/R/VizStereoMap.R
index 6e98c5b..5c73210 100644
--- a/R/VizStereoMap.R
+++ b/R/VizStereoMap.R
@@ -460,7 +460,7 @@ VizStereoMap <- function(data = NULL, lon, lat, varu = NULL, varv = NULL,
   }
 
   # Check contour_draw_label
-  if (missing(contour_draw_label) && !is.null(contour_label_draw)) {
+  if (missing(contour_draw_label) && !missing(contour_label_draw)) {
     contour_draw_label <- contour_label_draw
     warning("The parameter 'contour_label_draw' is deprecated. Use 'contour_draw_label' instead.")
   }
diff --git a/R/VizVsLTime.R b/R/VizVsLTime.R
index 1775542..9fac301 100644
--- a/R/VizVsLTime.R
+++ b/R/VizVsLTime.R
@@ -26,12 +26,12 @@
 #'  Default = NULL.
 #'@param drawleg TRUE/FALSE if legend should be added or not to the plot. 
 #'  Default = TRUE.
+#'@param leg Deprecated. Use 'drawleg' instead.
 #'@param siglev TRUE/FALSE if significance level should replace confidence 
 #'  interval.\cr
 #'  Default = FALSE.
 #'@param title_scale Scale factor for the figure top title. Defaults to 1.
-#'@param sizetit Scale factor for the figure top title. Deprecated. Use
-#' 'title_scale' instead.
+#'@param sizetit Deprecated. Use 'title_scale' instead.
 #'@param show_conf TRUE/FALSE to show/not confidence intervals for input 
 #'  variables.
 #'@param fileout Name of output file. Extensions allowed: eps/ps, jpeg, png, 
@@ -92,9 +92,10 @@ VizVsLTime <- function(data, toptitle = '', ytitle = '', monini = 1,
                        listexp = c('exp1', 'exp2', 'exp3'),
                        listobs = c('obs1', 'obs2', 'obs3'),
                        biglab = FALSE, hlines = NULL, drawleg = TRUE,
-                       siglev = FALSE, title_scale = 1, show_conf = TRUE,
-                       fileout = NULL, width = 8, height = 5, size_units = 'in',
-                       res = 100, var = NULL, ...) {
+                       leg = NULL, siglev = FALSE, title_scale = 1,
+                       sizetit = NULL, show_conf = TRUE, fileout = NULL,
+                       width = 8, height = 5, size_units = 'in', res = 100,
+                       var = NULL, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("cex", "cex.axis", "cex.lab", "cex.main", "col", "fin", "lab", "las", "lend", "lty", "lwd", "mai", "mgp", "new", "pin", "ps", "pty")
@@ -127,6 +128,23 @@ VizVsLTime <- function(data, toptitle = '', ytitle = '', monini = 1,
   } else if (length(dim(data)) != 4) {
     stop("Parameter 'data' should have 3 or 4 dimensions: c(n. exp[, n. obs], 3/4, n. lead-times)")
   }
+  # Check title_scale
+  if (missing(title_scale) && !missing(sizetit)) {
+    warning("The parameter 'sizetit' is deprecated. Use 'title_scale' instead.")
+    title_scale <- sizetit
+  }
+  if (!is.numeric(title_scale) || length(title_scale) != 1) {
+    stop("Parameter 'title_scale' must be a single numerical value.")
+  }
+  # Check drawleg
+  if (missing(drawleg) && !missing(leg)) {
+    warning("The parameter 'leg' is deprecated. Use 'drawleg' instead.")
+    drawleg <- leg
+  }
+  if (!is.logical(drawleg) || length(drawleg) != 1) {
+    stop("Parameter 'drawleg' must be a single logical value")
+  }
+  
   nleadtime <- dim(data)[4]
   nexp <- dim(data)[1]
   nobs <- dim(data)[2]
-- 
GitLab


From f33c3ca227c41991b514b73278645cd84fd84595 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Mon, 14 Apr 2025 10:04:42 +0200
Subject: [PATCH 42/72] Update test-VizRobinson.R 'point_size' check

---
 R/VizRobinson.R                   | 2 +-
 tests/testthat/test-VizRobinson.R | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/VizRobinson.R b/R/VizRobinson.R
index 46ac73a..9134151 100644
--- a/R/VizRobinson.R
+++ b/R/VizRobinson.R
@@ -335,7 +335,7 @@ VizRobinson <- function(data, lon, lat, lon_dim = NULL, lat_dim = NULL,
     # 360x181 with default setting, 0.05
     point_size <- round(0.05 * (360 * 181) / (length(lon) * length(lat)), 2)
   } else if (!is.numeric(point_size)) {
-    stop("Parameter 'point_size' must be a numerical value")
+    stop("Parameter 'point_size' must be a numerical value.")
   }
   
   # dot_symbol
diff --git a/tests/testthat/test-VizRobinson.R b/tests/testthat/test-VizRobinson.R
index d460aa2..6e8aeda 100644
--- a/tests/testthat/test-VizRobinson.R
+++ b/tests/testthat/test-VizRobinson.R
@@ -89,7 +89,7 @@ test_that("1. Input checks", {
   # point_size
   expect_error(
     VizRobinson(data1, lon = lon1_1, lat = lat1, point_size = 'small'),
-    "Parameter 'point_size' must be a number."
+    "Parameter 'point_size' must be a numerical value."
   )
 
 })
-- 
GitLab


From c8f93050db45bc7b49cc038c8b4d9c7dbf29cae2 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Mon, 14 Apr 2025 11:22:06 +0200
Subject: [PATCH 43/72] Update 'bar_' parameters in R/ColorBarDiscrete.R

---
 R/ColorBarDiscrete.R | 69 +++++++++++++++++++++++++-------------------
 1 file changed, 40 insertions(+), 29 deletions(-)

diff --git a/R/ColorBarDiscrete.R b/R/ColorBarDiscrete.R
index 5e0f619..f44c0e0 100644
--- a/R/ColorBarDiscrete.R
+++ b/R/ColorBarDiscrete.R
@@ -73,21 +73,26 @@
 #'@param bar_extra_labels Numeric vector of extra labels to draw along axis of 
 #'  the colour bar. The number of provided decimals will be conserved. 
 #'  Disregarded if 'plot = FALSE'.
+#'@param extra_labels Deprecated. Use 'bar_extra_labels' instead.
 #'@param title Title to draw on top of the colour bar, most commonly with the 
 #'  units of the represented field in the neighbour figures. Empty by default.
 #'@param title_scale Scale factor for the 'title' of the colour bar. 
 #'  Takes 1 by default.
-#'@param label_scale Scale factor for the labels of the colour bar. 
+#'@param bar_label_scale Scale factor for the labels of the colour bar. 
 #'  Takes 1 by default.
-#'@param tick_scale Scale factor for the length of the ticks of the labels 
+#'@param label_scale Deprecated. Use 'bar_label_scale' instead.
+#'@param bar_tick_scale Scale factor for the length of the ticks of the labels 
 #'  along the colour bar. Takes 1 by default.
-#'@param extra_margin Extra margins to be added around the colour bar, 
+#'@param tick_scale Deprecated. Use 'bar_tick_scale' instead.
+#'@param bar_extra_margin Extra margins to be added around the colour bar, 
 #'  in the format c(y1, x1, y2, x2). The units are margin lines. Takes 
 #'  rep(0, 4) by default.
+#'@param extra_margin Deprecated. Use 'bar_extra_margin' instead.
 #'@param bar_label_digits Number of significant digits to be displayed in the 
 #'  labels of the colour bar, usually to avoid too many decimal digits 
 #'  overflowing the figure region. This does not have effect over the labels 
 #'  provided in 'bar_extra_labels'. Takes 4 by default.
+#'@param label_digits. Deprecated. Use 'bar_label_digits' instead.
 #'@param ... Arguments to be passed to the method. Only accepts the following 
 #'  graphical parameters:\cr adj ann ask bg bty cex.lab cex.main cex.sub cin 
 #'  col.axis col.lab col.main col.sub cra crt csi cxy err family fg fig fin 
@@ -108,8 +113,8 @@
 #'@examples
 #'cb <- ColorBarDiscrete(
 #'  brks = 0:4, cols = c("green1", "green2", "green3", "green4"),
-#'  vertical = FALSE, labels = paste0('lev ', 1:4), label_scale = 1.5, 
-#'  extra_margin = c(0.5, 2, 0.5, 2), plot = FALSE)
+#'  vertical = FALSE, labels = paste0('lev ', 1:4), bar_label_scale = 1.5, 
+#'  bar_extra_margin = c(0.5, 2, 0.5, 2), plot = FALSE)
 #'
 #'@import utils
 #'@importFrom grDevices col2rgb rgb
@@ -117,11 +122,13 @@
 ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE, 
                      subsampleg = NULL, bar_limits = NULL, var_limits = NULL, 
                      color_fun = ClimPalette(), plot = TRUE, 
-                     draw_bar_ticks = FALSE, draw_separators = TRUE, labels = NULL, 
-                     bar_extra_labels = NULL, 
-                     title = NULL, title_scale = 1, 
-                     label_scale = 1, tick_scale = 1, 
-                     extra_margin = rep(0, 4), bar_label_digits = 4, ...) {
+                     draw_bar_ticks = FALSE, draw_separators = TRUE,
+                     labels = NULL, bar_extra_labels = NULL,
+                     extra_labels = NULL, title = NULL, title_scale = 1, 
+                     bar_label_scale = 1, label_scale = NULL,
+                     bar_tick_scale = 1, tick_scale = NULL,
+                     bar_extra_margin = rep(0, 4), extra_margin = NULL,
+                     bar_label_digits = 4, label_digits = NULL, ...) {
   # Sanity checks
   if ((is.null(brks) || length(brks) < 2) && is.null(bar_limits) && is.null(var_limits)) {
     stop("At least one of 'brks' with the desired breaks, 'bar_limits' or ",
@@ -235,6 +242,10 @@ ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE,
   }
 
   ## bar_extra_labels
+  if (missing(bar_extra_labels) && !missing(extra_labels)) {
+    warning("The parameter 'extra_labels' is deprecated. Use 'bar_extra_labels' instead.")
+    bar_extra_labels <- extra_labels
+  }
   if (is.null(bar_extra_labels)) {
     bar_extra_labels <- numeric(0)
   }
@@ -246,6 +257,16 @@ ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE,
     }
   }
   bar_extra_labels <- sort(bar_extra_labels)
+  
+  ## bar_label_digits
+  if (missing(bar_label_digits) && !missing(label_digits)) {
+    warning("The parameter 'label_digits' is deprecated. Use 'bar_label_digits' instead.")
+    bar_label_digits <- label_digits
+  }
+  if (!is.numeric(bar_label_digits)) {
+    stop("Parameter 'bar_label_digits' must be numeric.")
+  }
+  bar_label_digits <- round(bar_label_digits)
 
   ## labels
   if (is.null(labels)) {
@@ -321,43 +342,33 @@ ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE,
     stop("Parameter 'title_scale' must be numeric.")
   }
 
-  ## label_scale
+  ## bar_label_scale
   if (missing(bar_label_scale) && !missing(label_scale)) {
     warning("The parameter 'label_scale' is deprecated. Use 'bar_label_scale' instead.")
     bar_label_scale <- label_scale
   }
-  if (!is.numeric(label_scale)) {
-    stop("Parameter 'label_scale' must be numeric.")
+  if (!is.numeric(bar_label_scale)) {
+    stop("Parameter 'bar_label_scale' must be numeric.")
   }
 
-  ## tick_scale
+  ## bar_tick_scale
   if (missing(bar_tick_scale) && !missing(tick_scale)) {
     warning("The parameter 'tick_scale' is deprecated. Use 'bar_tick_scale' instead.")
     bar_tick_scale <- tick_scale
   }
-  if (!is.numeric(tick_scale)) {
-    stop("Parameter 'tick_scale' must be numeric.")
+  if (!is.numeric(bar_tick_scale)) {
+    stop("Parameter 'bar_tick_scale' must be numeric.")
   }
 
-  ## extra_margin
+  ## bar_extra_margin
   if (missing(bar_extra_margin) && !missing(extra_margin)) {
     warning("The parameter 'extra_margin' is deprecated. Use 'bar_extra_margin' instead.")
     bar_extra_margin <- extra_margin
   }
-  if (!is.numeric(extra_margin) || length(extra_margin) != 4) {
-    stop("Parameter 'extra_margin' must be a numeric vector of length 4.")
+  if (!is.numeric(bar_extra_margin) || length(extra_margin) != 4) {
+    stop("Parameter 'bar_extra_margin' must be a numeric vector of length 4.")
   }
 
-  ## bar_label_digits
-  if (missing(bar_label_digits) && !missing(label_digits)) {
-    warning("The parameter 'label_digits' is deprecated. Use 'bar_label_digits' instead.")
-    bar_label_digits <- label_digits
-  }
-  if (!is.numeric(bar_label_digits)) {
-    stop("Parameter 'bar_label_digits' must be numeric.")
-  }
-  bar_label_digits <- round(bar_label_digits)
-
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("cex", "cex.axis", "col", "lab", "las", "mar", "mgp", "new", "ps")
-- 
GitLab


From 4816a079db701e7a623c08b99d4264604e7feb7d Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Mon, 14 Apr 2025 11:23:25 +0200
Subject: [PATCH 44/72] Update man documentation 'devtools::document()'

---
 man/ColorBarContinuous.Rd | 41 ++++++++++++++++++++++++++-------------
 man/ColorBarDiscrete.Rd   | 16 +++++++--------
 man/VizAnimateMap.Rd      | 11 +++++++----
 man/VizCombinedMap.Rd     | 13 ++++++++-----
 man/VizEquiMap.Rd         |  2 +-
 man/VizLayout.Rd          |  7 ++++---
 man/VizMatrix.Rd          |  9 ++++++---
 man/VizRobinson.Rd        | 22 +++++++++++++++------
 man/VizSection.Rd         |  9 ++++++---
 man/VizVsLTime.Rd         | 16 ++++++++++-----
 10 files changed, 95 insertions(+), 51 deletions(-)

diff --git a/man/ColorBarContinuous.Rd b/man/ColorBarContinuous.Rd
index f4dee97..df6e0a2 100644
--- a/man/ColorBarContinuous.Rd
+++ b/man/ColorBarContinuous.Rd
@@ -16,16 +16,21 @@ ColorBarContinuous(
   col_sup = NULL,
   color_fun = ClimPalette(),
   plot = TRUE,
-  draw_ticks = TRUE,
+  draw_bar_ticks = TRUE,
   draw_separators = FALSE,
   triangle_ends_scale = 1,
+  bar_extra_labels = NULL,
   extra_labels = NULL,
   title = NULL,
   title_scale = 1,
-  label_scale = 1,
-  tick_scale = 1,
-  extra_margin = rep(0, 4),
-  label_digits = 4,
+  bar_label_scale = 1,
+  label_scale = NULL,
+  bar_tick_scale = 1,
+  tick_scale = NULL,
+  bar_extra_margin = rep(0, 4),
+  extra_margin = NULL,
+  bar_label_digits = 4,
+  label_digits = NULL,
   ...
 )
 }
@@ -63,7 +68,7 @@ ends the colours have been provided for.}
 colorbar. Takes by default an approximation of a value that yields a 
 readable tick arrangement (extreme breaks always ticked). If set to 0 or 
 lower, no labels are drawn. See the code of the function for details or 
-use 'extra_labels' for customized tick arrangements.}
+use 'bar_extra_labels' for customized tick arrangements.}
 
 \item{bar_limits}{Vector of two numeric values with the extremes of the 
 range of values represented in the colour bar. If 'var_limits' go beyond 
@@ -108,7 +113,7 @@ parameter is set by default to ClimPalette().}
 \item{plot}{Logical value indicating whether to only compute its breaks and 
 colours (FALSE) or to also draw it on the current device (TRUE).}
 
-\item{draw_ticks}{Whether to draw ticks for the labels along the colour bar 
+\item{draw_bar_ticks}{Whether to draw ticks for the labels along the colour bar 
 (TRUE) or not (FALSE). TRUE by default. Disregarded if 'plot = FALSE'.}
 
 \item{draw_separators}{Whether to draw black lines in the borders of each of 
@@ -120,30 +125,40 @@ colour bar, if drawn at all. Takes 1 by default (rectangle triangle
 proportional to the thickness of the colour bar). Disregarded if 
 'plot = FALSE'.}
 
-\item{extra_labels}{Numeric vector of extra labels to draw along axis of 
+\item{bar_extra_labels}{Numeric vector of extra labels to draw along axis of 
 the colour bar. The number of provided decimals will be conserved. 
 Disregarded if 'plot = FALSE'.}
 
+\item{extra_labels}{Deprecated. Use 'bar_extra_labels' instead.}
+
 \item{title}{Title to draw on top of the colour bar, most commonly with the 
 units of the represented field in the neighbour figures. Empty by default.}
 
 \item{title_scale}{Scale factor for the 'title' of the colour bar. 
 Takes 1 by default.}
 
-\item{label_scale}{Scale factor for the labels of the colour bar. 
+\item{bar_label_scale}{Scale factor for the labels of the colour bar. 
 Takes 1 by default.}
 
-\item{tick_scale}{Scale factor for the length of the ticks of the labels 
+\item{label_scale}{Deprecated. Use 'bar_label_scale' instead.}
+
+\item{bar_tick_scale}{Scale factor for the length of the ticks of the labels 
 along the colour bar. Takes 1 by default.}
 
-\item{extra_margin}{Extra margins to be added around the colour bar, 
+\item{tick_scale}{Deprecated. Use 'bar_tick_scale' instead.}
+
+\item{bar_extra_margin}{Extra margins to be added around the colour bar, 
 in the format c(y1, x1, y2, x2). The units are margin lines. Takes 
 rep(0, 4) by default.}
 
-\item{label_digits}{Number of significant digits to be displayed in the 
+\item{extra_margin}{Deprecated. Use 'bar_extra_margin' instead.}
+
+\item{bar_label_digits}{Number of significant digits to be displayed in the 
 labels of the colour bar, usually to avoid too many decimal digits 
 overflowing the figure region. This does not have effect over the labels 
-provided in 'extra_labels'. Takes 4 by default.}
+provided in 'bar_extra_labels'. Takes 4 by default.}
+
+\item{label_digits}{Deprecated. Use 'bar_label_digits' instead.}
 
 \item{...}{Arguments to be passed to the method. Only accepts the following 
  graphical parameters:\cr adj ann ask bg bty cex.lab cex.main cex.sub cin 
diff --git a/man/ColorBarDiscrete.Rd b/man/ColorBarDiscrete.Rd
index 14c5ab6..fccc06d 100644
--- a/man/ColorBarDiscrete.Rd
+++ b/man/ColorBarDiscrete.Rd
@@ -13,16 +13,16 @@ ColorBarDiscrete(
   var_limits = NULL,
   color_fun = ClimPalette(),
   plot = TRUE,
-  draw_ticks = FALSE,
+  draw_bar_ticks = FALSE,
   draw_separators = TRUE,
   labels = NULL,
-  extra_labels = NULL,
+  bar_extra_labels = NULL,
   title = NULL,
   title_scale = 1,
   label_scale = 1,
   tick_scale = 1,
   extra_margin = rep(0, 4),
-  label_digits = 4,
+  bar_label_digits = 4,
   ...
 )
 }
@@ -60,7 +60,7 @@ ends the colours have been provided for.}
 colorbar. Takes by default an approximation of a value that yields a 
 readable tick arrangement (extreme breaks always ticked). If set to 0 or 
 lower, no labels are drawn. See the code of the function for details or 
-use 'extra_labels' for customized tick arrangements.}
+use 'bar_extra_labels' for customized tick arrangements.}
 
 \item{bar_limits}{Vector of two numeric values with the extremes of the 
 range of values represented in the colour bar. If 'var_limits' go beyond 
@@ -86,7 +86,7 @@ parameter is set by default to ClimPalette().}
 \item{plot}{Logical value indicating whether to only compute its breaks and 
 colours (FALSE) or to also draw it on the current device (TRUE).}
 
-\item{draw_ticks}{Whether to draw ticks for the labels along the colour bar 
+\item{draw_bar_ticks}{Whether to draw ticks for the labels along the colour bar 
 (TRUE) or not (FALSE). TRUE by default. Disregarded if 'plot = FALSE'.}
 
 \item{draw_separators}{Whether to draw black lines in the borders of each of 
@@ -96,7 +96,7 @@ default. Disregarded if 'plot = FALSE'.}
 \item{labels}{A charater string vector of the names of colors. Must be the
 same length as 'cols'.}
 
-\item{extra_labels}{Numeric vector of extra labels to draw along axis of 
+\item{bar_extra_labels}{Numeric vector of extra labels to draw along axis of 
 the colour bar. The number of provided decimals will be conserved. 
 Disregarded if 'plot = FALSE'.}
 
@@ -116,10 +116,10 @@ along the colour bar. Takes 1 by default.}
 in the format c(y1, x1, y2, x2). The units are margin lines. Takes 
 rep(0, 4) by default.}
 
-\item{label_digits}{Number of significant digits to be displayed in the 
+\item{bar_label_digits}{Number of significant digits to be displayed in the 
 labels of the colour bar, usually to avoid too many decimal digits 
 overflowing the figure region. This does not have effect over the labels 
-provided in 'extra_labels'. Takes 4 by default.}
+provided in 'bar_extra_labels'. Takes 4 by default.}
 
 \item{...}{Arguments to be passed to the method. Only accepts the following 
  graphical parameters:\cr adj ann ask bg bty cex.lab cex.main cex.sub cin 
diff --git a/man/VizAnimateMap.Rd b/man/VizAnimateMap.Rd
index 236a327..fa28cd7 100644
--- a/man/VizAnimateMap.Rd
+++ b/man/VizAnimateMap.Rd
@@ -5,11 +5,12 @@
 \title{Animate Maps of Forecast/Observed Values or Scores Over Forecast Time}
 \usage{
 VizAnimateMap(
-  data = NULL,
+  data,
   lon,
   lat,
   toptitle = rep("", 11),
-  sizetit = 1,
+  title_scale = 1,
+  sizetit = NULL,
   units = "",
   monini = 1,
   freq = 12,
@@ -46,7 +47,9 @@ VizAnimateMap(
 optional. If RMS, RMSSS, correlations: first exp with successive obs, then 
 second exp with successive obs, etc ...}
 
-\item{sizetit}{Multiplicative factor to increase title size, optional.}
+\item{title_scale}{Scale factor for the figure top title. Defaults to 1.}
+
+\item{sizetit}{Deprecated. Use 'title_scale' instead.}
 
 \item{units}{Units, optional.}
 
@@ -156,7 +159,7 @@ lats <- attr(map_temp$exp, "Variables")$common$lat
 lons <- attr(map_temp$exp, "Variables")$common$lon
  \dontrun{
 esviz:::VizAnimateMap(clim$clim_exp[1, 1, , , ], lon = lons, lat = lats,
- toptitle = "climatology of decadal prediction", sizetit = 1, 
+ toptitle = "climatology of decadal prediction", title_scale = 1, 
  units = "K", brks = seq(270, 300, 3), monini = 11, freq = 12, 
  msk95lev = FALSE, filled.continents = FALSE, intlon = 10, intlat = 10)
  }
diff --git a/man/VizCombinedMap.Rd b/man/VizCombinedMap.Rd
index fc59267..a9e9654 100644
--- a/man/VizCombinedMap.Rd
+++ b/man/VizCombinedMap.Rd
@@ -19,10 +19,11 @@ VizCombinedMap(
   col_sup = NULL,
   col_unknown_map = "white",
   mask = NULL,
-  col_mask = "grey",
+  mask_color = "grey",
+  col_mask = NULL,
   dots = NULL,
   bar_titles = NULL,
-  legend_scale = 1,
+  bar_label_scale = 1,
   cex_bar_titles = 1.5,
   plot_margin = NULL,
   bar_extra_margin = c(2, 0, 2, 0),
@@ -93,11 +94,13 @@ values that go beyond 'display_range'. Takes the value 'white' by default.}
 \item{mask}{Optional numeric array with dimensions (latitude, longitude), with 
 values in the range [0, 1], indicating the opacity of the mask over each 
 grid point. Cells with a 0 will result in no mask, whereas cells with a 1 
-will result in a totally opaque superimposed pixel coloured in 'col_mask'.}
+will result in a totally opaque superimposed pixel coloured in 'mask_color'.}
 
-\item{col_mask}{Colour to be used for the superimposed mask (if specified in 
+\item{mask_color}{Colour to be used for the superimposed mask (if specified in 
 'mask'). Takes the value 'grey' by default.}
 
+\item{col_mask}{Deprecated. Use 'mask_color' instead.}
+
 \item{dots}{Array of same dimensions as 'var' or with dimensions 
 c(n, dim(var)), where n is the number of dot/symbol layers to add to the 
 plot. A value of TRUE at a grid cell will draw a dot/symbol on the 
@@ -108,7 +111,7 @@ layers via the parameter 'dot_symbol'.}
 \item{bar_titles}{Optional vector of character strings providing the titles to 
 be shown on top of each of the colour bars.}
 
-\item{legend_scale}{Scale factor for the size of the colour bar labels. Takes 
+\item{bar_label_scale}{Scale factor for the size of the colour bar labels. Takes 
 1 by default.}
 
 \item{cex_bar_titles}{Scale factor for the sizes of the bar titles. Takes 1.5 
diff --git a/man/VizEquiMap.Rd b/man/VizEquiMap.Rd
index dc24552..5f6b37b 100644
--- a/man/VizEquiMap.Rd
+++ b/man/VizEquiMap.Rd
@@ -5,7 +5,7 @@
 \title{Maps A Two-Dimensional Variable On A Cylindrical Equidistant Projection}
 \usage{
 VizEquiMap(
-  data = NULL,
+  data,
   lon,
   lat,
   varu = NULL,
diff --git a/man/VizLayout.Rd b/man/VizLayout.Rd
index dbed7de..75335fe 100644
--- a/man/VizLayout.Rd
+++ b/man/VizLayout.Rd
@@ -7,7 +7,7 @@
 VizLayout(
   fun,
   plot_dims,
-  data = NULL,
+  data,
   ...,
   special_args = NULL,
   nrow = NULL,
@@ -183,7 +183,8 @@ respectively. 'colNA' takes 'white' by default. 'col_inf' and 'col_sup'
 will take the value of 'colNA' if not specified. See ?ColorBarContinuous for a full 
 explanation on 'col_inf' and 'col_sup'.}
 
-\item{color_fun, subsampleg, bar_extra_labels, draw_bar_ticks, draw_separators, triangle_ends_scale, bar_label_digits, bar_label_scale, units_scale, bar_tick_scale, bar_extra_margin}{Set of parameters to control the visual aspect of the drawn colour bar. See ?ColorBarContinuous for a full explanation.}
+\item{color_fun, subsampleg, bar_extra_labels, draw_bar_ticks, draw_separators, triangle_ends_scale, bar_label_digits, bar_label_scale, units_scale, bar_tick_scale, bar_extra_margin}{Set of parameters to control the visual aspect of the drawn colour bar. See
+?ColorBarContinuous for a full explanation.}
 
 \item{units}{Title at the top of the colour bar, most commonly the units of 
 the variable provided in parameter 'data'.}
@@ -200,7 +201,7 @@ format c(y1, x1, y2, x2). The units are margin lines. Takes rep(0, 4)
 by default.}
 
 \item{layout_by_rows}{Logical indicating wether the panels should be filled 
-by columns (FALSE) or by raws (TRUE, default).}
+by columns (FALSE) or by rows (TRUE, default).}
 
 \item{fileout}{File where to save the plot. If not specified (default) a 
 graphics device will pop up. Extensions allowed: eps/ps, jpeg, png, pdf, 
diff --git a/man/VizMatrix.Rd b/man/VizMatrix.Rd
index 6f080ab..49a5f0e 100644
--- a/man/VizMatrix.Rd
+++ b/man/VizMatrix.Rd
@@ -5,7 +5,7 @@
 \title{Function to convert any numerical table to a grid of coloured squares.}
 \usage{
 VizMatrix(
-  data = NULL,
+  data,
   brks = NULL,
   cols = NULL,
   toptitle = NULL,
@@ -17,7 +17,8 @@ VizMatrix(
   ylabels = NULL,
   line = 3,
   figure.width = 1,
-  legend = TRUE,
+  drawleg = TRUE,
+  legend = NULL,
   legend.width = 0.15,
   xlab_dist = NULL,
   ylab_dist = NULL,
@@ -67,9 +68,11 @@ are long.}
 \item{figure.width}{A positive number as a ratio adjusting the width of the 
 grids. Set 1 as default.}
 
-\item{legend}{A logical value to decide to draw the grid color legend or not. 
+\item{drawleg}{A logical value to decide to draw the grid color legend or not. 
 Set TRUE as default.}
 
+\item{legend}{Deprecated. Use 'drawleg' instead.}
+
 \item{legend.width}{A number between 0 and 0.5 to adjust the legend width.
 Set 0.15 as default.}
 
diff --git a/man/VizRobinson.Rd b/man/VizRobinson.Rd
index 3c7fd57..60c9f43 100644
--- a/man/VizRobinson.Rd
+++ b/man/VizRobinson.Rd
@@ -32,9 +32,12 @@ VizRobinson(
   point_size = "auto",
   title_scale = 16,
   title_size = NULL,
-  dots_size = 0.5,
-  dots_shape = 47,
-  coastlines_width = 0.3,
+  dot_size = 0.5,
+  dots_size = NULL,
+  dot_symbol = 47,
+  dots_shape = NULL,
+  coast_width = 0.3,
+  coastlines_width = NULL,
   fileout = NULL,
   width = 8,
   height = 4,
@@ -130,12 +133,19 @@ The default is 'auto' and the function tries to find the appropriate size.}
 
 \item{title_size}{Deprecated. Use 'title_scale' instead.}
 
-\item{dots_size}{A number of the size of the dots. The default is 0.5.}
+\item{dot_size}{A number of the size of the dots. The default is 0.5.}
 
-\item{dots_shape}{A number indicating the dot shape recognized by parameter 
+\item{dots_size}{Deprecated. Use 'dot_size' instead.}
+
+\item{dot_symbol}{A number indicating the dot shape recognized by parameter 
 'shape' in \code{geom_point()}.}
 
-\item{coastlines_width}{A number indicating the width of the coastlines.}
+\item{dots_shape}{Deprecated. Use 'dot_symbol' instead.}
+
+\item{coast_width}{A number indicating the width of the coastlines. Default is
+0.3.}
+
+\item{coastlines_width}{Deprecated. Use 'coast_width' instead.}
 
 \item{fileout}{A character string of the path to save the plot. If not 
 specified (default), a graphic device will pop up. The extension should be  
diff --git a/man/VizSection.Rd b/man/VizSection.Rd
index cb7fe69..fac59ff 100644
--- a/man/VizSection.Rd
+++ b/man/VizSection.Rd
@@ -5,11 +5,12 @@
 \title{Plots A Vertical Section}
 \usage{
 VizSection(
-  data = NULL,
+  data,
   horiz,
   depth,
   toptitle = "",
-  sizetit = 1,
+  title_scale = 1,
+  sizetit = NULL,
   units = "",
   brks = NULL,
   cols = NULL,
@@ -35,7 +36,9 @@ VizSection(
 
 \item{toptitle}{Title, optional.}
 
-\item{sizetit}{Multiplicative factor to increase title size, optional.}
+\item{title_scale}{Scale factor for the figure top title. Defaults to 1.}
+
+\item{sizetit}{Deprecated. Use 'title_scale' instead.}
 
 \item{units}{Units, optional.}
 
diff --git a/man/VizVsLTime.Rd b/man/VizVsLTime.Rd
index 0b4c8aa..5b69ad2 100644
--- a/man/VizVsLTime.Rd
+++ b/man/VizVsLTime.Rd
@@ -5,7 +5,7 @@
 \title{Plot a score along the forecast time with its confidence interval}
 \usage{
 VizVsLTime(
-  data = NULL,
+  data,
   toptitle = "",
   ytitle = "",
   monini = 1,
@@ -16,9 +16,11 @@ VizVsLTime(
   listobs = c("obs1", "obs2", "obs3"),
   biglab = FALSE,
   hlines = NULL,
-  leg = TRUE,
+  drawleg = TRUE,
+  leg = NULL,
   siglev = FALSE,
-  sizetit = 1,
+  title_scale = 1,
+  sizetit = NULL,
   show_conf = TRUE,
   fileout = NULL,
   width = 8,
@@ -55,14 +57,18 @@ or (nexp/nmod, nobs, 3/4 ,nltime).}
 \item{hlines}{c(a,b, ..) Add horizontal black lines at Y-positions a,b, ...\cr
 Default = NULL.}
 
-\item{leg}{TRUE/FALSE if legend should be added or not to the plot. 
+\item{drawleg}{TRUE/FALSE if legend should be added or not to the plot. 
 Default = TRUE.}
 
+\item{leg}{Deprecated. Use 'drawleg' instead.}
+
 \item{siglev}{TRUE/FALSE if significance level should replace confidence 
 interval.\cr
 Default = FALSE.}
 
-\item{sizetit}{Multiplicative factor to change title size, optional.}
+\item{title_scale}{Scale factor for the figure top title. Defaults to 1.}
+
+\item{sizetit}{Deprecated. Use 'title_scale' instead.}
 
 \item{show_conf}{TRUE/FALSE to show/not confidence intervals for input 
 variables.}
-- 
GitLab


From a66df49bead2cbd0f6c210d1cd2d0c8098fe2da3 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 16 Apr 2025 13:57:07 +0200
Subject: [PATCH 45/72] Change 'plot_margin' for 'margin_scale' in
 VizCombinedMap.R

---
 R/VizCombinedMap.R | 32 ++++++++++++++++++++++----------
 1 file changed, 22 insertions(+), 10 deletions(-)

diff --git a/R/VizCombinedMap.R b/R/VizCombinedMap.R
index aa3b50c..4f176a4 100644
--- a/R/VizCombinedMap.R
+++ b/R/VizCombinedMap.R
@@ -66,10 +66,10 @@
 #'  1 by default.
 #'@param cex_bar_titles Scale factor for the sizes of the bar titles. Takes 1.5 
 #'  by default.
-#'@param plot_margin Numeric vector of length 4 for the margin sizes in the 
-#'  following order: bottom, left, top, and right. If not specified, use the 
-#'  default of par("mar"), c(5.1, 4.1, 4.1, 2.1). Used as 'margin_scale' in 
-#'  VizEquiMap.
+#'@param margin_scale Numeric vector of length 4 for the margin sizes in the 
+#'  following order: bottom, left, top, and right. If not specified (NULL), the 
+#'  default of par("mar"), c(5.1, 4.1, 4.1, 2.1), is used. Default is NULL.
+#'@param plot_margin Deprecated. Use 'margin_scale' instead.
 #'@param bar_extra_margin A numeric vector of 4 indicating the extra margins to
 #'  be added around the color bar, in the format c(y1, x1, y2, x2). The units 
 #'  are margin lines. The default values are c(2, 0, 2, 0).
@@ -146,11 +146,11 @@ VizCombinedMap <- function(maps, lon, lat,
                            mask = NULL, mask_color = 'grey', col_mask = NULL,
                            dots = NULL,
                            bar_titles = NULL, bar_label_scale = 1,
-                           cex_bar_titles = 1.5,
+                           cex_bar_titles = 1.5, margin_scale = NULL,
                            plot_margin = NULL, bar_extra_margin = c(2, 0, 2, 0),
                            fileout = NULL, width = 8, height = 5, 
-                           size_units = 'in', res = 100, drawleg = T, return_leg = FALSE,
-                            ...) {
+                           size_units = 'in', res = 100, drawleg = T,
+                           return_leg = FALSE, ...) {
   args <- list(...)
 
   # If there is any filenames to store the graphics, process them
@@ -318,6 +318,7 @@ VizCombinedMap <- function(maps, lon, lat,
       stop("Parameter 'mask' must have dimensions c(lat, lon).")
     }
   }
+  
   # Check dots
   if (!is.null(dots)) {
     if (length(dim(dots)) != 2) {
@@ -328,6 +329,17 @@ VizCombinedMap <- function(maps, lon, lat,
       stop("Parameter 'mask' must have dimensions c(lat, lon).")
     }
   }
+  
+  # Check margin_scale
+  if (missing(margin_scale) && !missing(plot_margin)) {
+    warning("The parameter 'plot_margin' is deprecated. Use 'margin_scale' instead.")
+    margin_scale <- plot_margin
+  }
+  if (!is.null(margin_scale)) {
+    if (!is.numeric(margin_scale) || length(margin_scale) != 4) {
+      stop("Parameter 'margin_scale' must be a numeric vector of length 4: c(bottom, left, top, right).")
+    }
+  }
  
   #----------------------
   # Identify the most likely map
@@ -463,13 +475,13 @@ VizCombinedMap <- function(maps, lon, lat,
     }
   }
 
-  if (is.null(plot_margin)) {
-    plot_margin <- c(5, 4, 4, 2) + 0.1  # default of par()$mar
+  if (is.null(margin_scale)) {
+    margin_scale <- c(5, 4, 4, 2) + 0.1  # default of par()$mar
   }
 
   VizEquiMap(var = ml_map, lon = lon, lat = lat, 
              brks = tbrks, cols = tcols, drawleg = FALSE, 
-             filled.continents = FALSE, dots = dots, margin_scale = plot_margin, ...)
+             filled.continents = FALSE, dots = dots, margin_scale = margin_scale, ...)
   
   #----------------------
   # Add overplot on top
-- 
GitLab


From cf6cab2767759dc68d6a6d2bc1826e2f6497019d Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 23 Apr 2025 16:05:31 +0200
Subject: [PATCH 46/72] Change 'title' for 'toptitle' in VizForecastPDF.R

---
 R/VizForecastPDF.R | 22 +++++++++++++++++-----
 1 file changed, 17 insertions(+), 5 deletions(-)

diff --git a/R/VizForecastPDF.R b/R/VizForecastPDF.R
index c477bd6..644e37a 100644
--- a/R/VizForecastPDF.R
+++ b/R/VizForecastPDF.R
@@ -30,7 +30,8 @@
 #'  (Default: observation is not shown).
 #'@param plotfile (optional) A filename (pdf, png...) where the plot will be 
 #'  saved. (Default: the plot is not saved).
-#'@param title A string with the plot title.
+#'@param toptitle A string with the plot title.
+#'@param title Deprecated. Use 'data' instead.
 #'@param var.name A string with the variable name and units.
 #'@param fcst.names (optional) An array of strings with the titles of each 
 #'  individual forecast.
@@ -53,9 +54,12 @@
 #'@importFrom plyr . dlply
 #'@importFrom s2dv InsertDim
 #'@export
-VizForecastPDF <- function(fcst, tercile.limits, extreme.limits = NULL, obs = NULL, 
-                           plotfile = NULL, title = "Set a title", var.name = "Varname (units)", 
-                           fcst.names = NULL, add.ensmemb = c("above", "below", "no"), 
+VizForecastPDF <- function(fcst, tercile.limits, extreme.limits = NULL,
+                           obs = NULL, plotfile = NULL,
+                           toptitle = "Set a title", title = NULL,
+                           var.name = "Varname (units)", 
+                           fcst.names = NULL,
+                           add.ensmemb = c("above", "below", "no"), 
                            color.set = c("ggplot", "s2s4e", "hydro", "vitigeoss"), 
                            memb_dim = 'member') {
     value <- init <- extremes <- x <- ymin <- ymax <- tercile <- NULL
@@ -99,6 +103,14 @@ VizForecastPDF <- function(fcst, tercile.limits, extreme.limits = NULL, obs = NU
     # Check input arguments
     #------------------------
     add.ensmemb <- match.arg(add.ensmemb)
+    # Check toptitle
+    if (missing(toptitle) && !missing(title)) {
+      warning("The parameter 'title' is deprecated. Use 'toptitle' instead.")
+      toptitle <- title
+    }
+    if (!is.character(toptitle)) {
+      stop("Parameter 'toptitle' must be a character string.")
+    }
     #------------------------
     # Check fcst type and convert to data.frame if needed
     #------------------------
@@ -431,7 +443,7 @@ VizForecastPDF <- function(fcst, tercile.limits, extreme.limits = NULL, obs = NU
                             values = c(3)) + 
         labs(x = var.name, 
                 y = "Probability density\n(total area=1)",
-                title = title) +
+                title = toptitle) +
         theme(axis.text.x = element_blank(),
                 panel.grid.minor.x = element_blank(), 
                 legend.key.size = unit(0.3, "in"),
-- 
GitLab


From 2061f6f5ef3f2b48a70884ec6c5a2ed868f2e9ea Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 23 Apr 2025 16:12:00 +0200
Subject: [PATCH 47/72] Change 'plotfile' for 'fileout' in VizForecastPDF.R

---
 R/VizForecastPDF.R | 21 ++++++++++++++-------
 1 file changed, 14 insertions(+), 7 deletions(-)

diff --git a/R/VizForecastPDF.R b/R/VizForecastPDF.R
index 644e37a..902b2e2 100644
--- a/R/VizForecastPDF.R
+++ b/R/VizForecastPDF.R
@@ -28,10 +28,11 @@
 #'@param obs (optional) A vector providing the observed values for each forecast 
 #'  panel or a single value that will be reused for all forecast panels. 
 #'  (Default: observation is not shown).
-#'@param plotfile (optional) A filename (pdf, png...) where the plot will be 
+#'@param fileout (optional) A filename (pdf, png...) where the plot will be 
 #'  saved. (Default: the plot is not saved).
+#'@param plotfile Deprecated. Use 'fileout' instead.
 #'@param toptitle A string with the plot title.
-#'@param title Deprecated. Use 'data' instead.
+#'@param title Deprecated. Use 'toptitle' instead.
 #'@param var.name A string with the variable name and units.
 #'@param fcst.names (optional) An array of strings with the titles of each 
 #'  individual forecast.
@@ -55,12 +56,13 @@
 #'@importFrom s2dv InsertDim
 #'@export
 VizForecastPDF <- function(fcst, tercile.limits, extreme.limits = NULL,
-                           obs = NULL, plotfile = NULL,
+                           obs = NULL, fileout = NULL, plotfile = NULL,
                            toptitle = "Set a title", title = NULL,
                            var.name = "Varname (units)", 
                            fcst.names = NULL,
                            add.ensmemb = c("above", "below", "no"), 
-                           color.set = c("ggplot", "s2s4e", "hydro", "vitigeoss"), 
+                           color.set = c("ggplot", "s2s4e", "hydro",
+                                         "vitigeoss"), 
                            memb_dim = 'member') {
     value <- init <- extremes <- x <- ymin <- ymax <- tercile <- NULL
     y <- xend <- yend <- yjitter <- MLT <- lab.pos <- NULL
@@ -111,6 +113,11 @@ VizForecastPDF <- function(fcst, tercile.limits, extreme.limits = NULL,
     if (!is.character(toptitle)) {
       stop("Parameter 'toptitle' must be a character string.")
     }
+    # Check fileout
+    if (missing(fileout) && !missing(plotfile)) {
+      warning("The parameter 'plotfile' is deprecated. Use 'fileout' instead.")
+      fileout <- plotfile
+    }
     #------------------------
     # Check fcst type and convert to data.frame if needed
     #------------------------
@@ -458,10 +465,10 @@ VizForecastPDF <- function(fcst, tercile.limits, extreme.limits = NULL,
                 shape = guide_legend(order = 3, label = F),
                 size = guide_legend(order = 4, label = F))
     #------------------------
-    # Save to plotfile if needed, and return plot
+    # Save to fileout if needed, and return plot
     #------------------------
-    if (!is.null(plotfile)) {
-        ggsave(plotfile, plot)
+    if (!is.null(fileout)) {
+        ggsave(fileout, plot)
     }
     return(plot)
 }
-- 
GitLab


From 1caf30d183aebe82505c9c95ea576eee12b54247 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 23 Apr 2025 16:35:25 +0200
Subject: [PATCH 48/72] Change 'sizetit' for 'title_scale' in
 R/Viz2VarsVsLTime.R

---
 R/Viz2VarsVsLTime.R | 29 ++++++++++++++++++++---------
 1 file changed, 20 insertions(+), 9 deletions(-)

diff --git a/R/Viz2VarsVsLTime.R b/R/Viz2VarsVsLTime.R
index f4a6345..e041ac6 100644
--- a/R/Viz2VarsVsLTime.R
+++ b/R/Viz2VarsVsLTime.R
@@ -22,7 +22,8 @@
 #'@param siglev TRUE/FALSE if significance level should replace confidence 
 #'  interval.\cr 
 #'  Default = FALSE.
-#'@param sizetit Multiplicative factor to change title size, optional.
+#'@param title_scale Multiplicative factor to change title size, optional.
+#'@param sizetit Deprecated. Use 'title_scale' instead.
 #'@param show_conf TRUE/FALSE to show/not confidence intervals for input 
 #'  variables.
 #'@param fileout Name of output file. Extensions allowed: eps/ps, jpeg, png, 
@@ -65,7 +66,7 @@
 #'input_rms[, 3, ] <- rms_ano$conf.upper[, 1, 1, ]
 #'esviz:::Viz2VarsVsLTime(input_cor, input_rms,
 #'                toptitle = "Time correlation and RMSE with ERA5",
-#'                ytitle = "K", sizetit = 0.7,
+#'                ytitle = "K", title_scale = 0.7,
 #'                monini = 11, freq = 1, limits = c(-1, 5),
 #'                listexp = c('SEAS5'), listvars = c('Corr', 'RMSE'),
 #'                fileout = NULL)
@@ -73,12 +74,12 @@
 #'@importFrom grDevices png jpeg postscript pdf svg bmp tiff postscript dev.cur dev.new dev.off
 #'@importFrom stats ts 
 Viz2VarsVsLTime <- function(var1, var2, toptitle = '', ytitle = '', monini = 1,
-                             freq = 12, nticks = NULL, limits = NULL, listexp =
-                             c('exp1', 'exp2', 'exp3'), listvars = c('var1',
-                             'var2'), biglab = FALSE, hlines = NULL, leg = TRUE,
-                             siglev = FALSE, sizetit = 1, show_conf = TRUE,
-                             fileout = NULL, 
-                             width = 8, height = 5, size_units = 'in', res = 100, ...) {
+                            freq = 12, nticks = NULL, limits = NULL, listexp =
+                            c('exp1', 'exp2', 'exp3'), listvars = c('var1',
+                            'var2'), biglab = FALSE, hlines = NULL, leg = TRUE,
+                            siglev = FALSE, title_scale = 1, sizetit = NULL,
+                            show_conf = TRUE, fileout = NULL, width = 8,
+                            height = 5, size_units = 'in', res = 100, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("cex", "cex.axis", "cex.lab", "cex.main", "col", "fin", "lab", "las", "lty", "lwd", "mai", "mgp", "new", "pin", "ps", "pty")
@@ -130,6 +131,16 @@ Viz2VarsVsLTime <- function(var1, var2, toptitle = '', ytitle = '', monini = 1,
                  end = c(lastyear, (lastmonth - 1) %/% (12 / freq) + 1), 
                  frequency = freq)
   empty <- array(dim = length(empty_ts))
+  
+  # Check title_scale
+  if (missing(title_scale) && !missing(sizetit)) {
+    warning("The parameter 'sizetit' is deprecated. Use 'title_scale' instead.")
+    title_scale <- sizetit
+  }
+  if (!is.numeric(title_scale) || length(title_scale) != 1) {
+    stop("Parameter 'title_scale' must be a single numerical value.")
+  }
+  
   #
   #  Define some plot parameters
   # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -193,7 +204,7 @@ Viz2VarsVsLTime <- function(var1, var2, toptitle = '', ytitle = '', monini = 1,
     legsize <- 1
   }
   plot(empty, ylim = c(ll, ul), xlab = "Time (months)", ylab = ytitle, 
-       main = toptitle, cex.main = cexmain * sizetit, axes = FALSE)
+       main = toptitle, cex.main = cexmain * title_scale, axes = FALSE)
   axis(1, at = labind, labels = labmonth)
   axis(2)
   box()
-- 
GitLab


From d0cb7a8a8655cb8a200bf10cfb766834c48953f9 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 23 Apr 2025 16:36:04 +0200
Subject: [PATCH 49/72] Change 'sizetit' for 'title_scale' in R/VizACC.R

---
 R/VizACC.R | 28 ++++++++++++++++++----------
 1 file changed, 18 insertions(+), 10 deletions(-)

diff --git a/R/VizACC.R b/R/VizACC.R
index 2787383..b219707 100644
--- a/R/VizACC.R
+++ b/R/VizACC.R
@@ -15,7 +15,8 @@
 #'  interval and the 95\% significance level.
 #'@param sdates A character vector of startdates: c('YYYYMMDD','YYYYMMDD').
 #'@param toptitle A character string of the main title, optional.
-#'@param sizetit A multiplicative factor to scale title size, optional.
+#'@param title_scale A multiplicative factor to scale title size, optional.
+#'@param sizetit Deprecated. Use 'title_scale' instead.
 #'@param ytitle A character string of the title of Y-axis for each experiment:
 #'  c('', ''), optional.
 #'@param limits A numeric vector c(lower limit, upper limit): limits of the 
@@ -64,16 +65,16 @@
 #'sdates <- paste0(2000:2005, '1101')
 #'esviz:::VizACC(input_acc, sdates, 
 #'       toptitle = "Spatial anomaly corr. coeff. with ERA5",
-#'       ytitle = "K", sizetit = 0.7, freq = 12,
+#'       ytitle = "K", title_scale = 0.7, freq = 12,
 #'       legends = 'SEAS5', fileout = NULL)
 #'  }
 #'@importFrom grDevices dev.cur dev.new dev.off 
 #'@importFrom stats ts
-VizACC <- function(ACC, sdates, toptitle = "", sizetit = 1, ytitle = "", 
-                    limits = NULL, legends = NULL, freq = 12, biglab = FALSE, 
-                    fill = FALSE, linezero = FALSE, points = TRUE, vlines = NULL, 
-                    fileout = NULL, 
-                    width = 8, height = 5, size_units = 'in', res = 100, ...) {
+VizACC <- function(ACC, sdates, toptitle = "", title_scale = 1, sizetit = NULL,
+                   ytitle = "", limits = NULL, legends = NULL, freq = 12,
+                   biglab = FALSE, fill = FALSE, linezero = FALSE,
+                   points = TRUE, vlines = NULL, fileout = NULL, 
+                   width = 8, height = 5, size_units = 'in', res = 100, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("cex", "cex.axis", "cex.lab", "cex.main", "col", "lab", "las", "lty",
@@ -87,8 +88,15 @@ VizACC <- function(ACC, sdates, toptitle = "", sizetit = 1, ytitle = "",
     saveToFile <- deviceInfo$fun
     fileout <- deviceInfo$files
   }
-
-  #
+  # Check title_scale
+  if (missing(title_scale) && !missing(sizetit)) {
+    warning("The parameter 'sizetit' is deprecated. Use 'title_scale' instead.")
+    title_scale <- sizetit
+  }
+  if (!is.numeric(title_scale) || length(title_scale) != 1) {
+    stop("Parameter 'title_scale' must be a single numerical value.")
+  }
+  # Check dim
   if (length(dim(ACC)) != 5 | dim(ACC)[5] != 4) {
     stop("5 dim needed : c(nexp, nobs, nsdates, nltime, 4)")
   }
@@ -145,7 +153,7 @@ VizACC <- function(ACC, sdates, toptitle = "", sizetit = 1, ytitle = "",
     legsize <- 1
   }
   plot(empty_ts, ylim = c(ll, ul), xlab = "Time (years)", ylab = ytitle, 
-       main = toptitle, cex.main = cexmain * sizetit)
+       main = toptitle, cex.main = cexmain * title_scale)
   for (jexp in 1:nexp) {
     for (jobs in 1:nobs) {
       numcol <- jobs + (jexp - 1) * nobs
-- 
GitLab


From f0bec5d36f4683a1588d79bdbd5b77c4d023eec3 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 30 Apr 2025 11:59:52 +0200
Subject: [PATCH 50/72] Change 'sizetit' for 'title_scale' in R/VizAno.R

---
 R/VizAno.R | 15 ++++++++++++---
 1 file changed, 12 insertions(+), 3 deletions(-)

diff --git a/R/VizAno.R b/R/VizAno.R
index 7a03420..e4ab324 100644
--- a/R/VizAno.R
+++ b/R/VizAno.R
@@ -28,7 +28,8 @@
 #'@param points TRUE/FALSE if points instead of lines should be shown. 
 #'  Default = FALSE.
 #'@param vlines List of x location where to add vertical black lines, optional.
-#'@param sizetit Multiplicative factor to scale title size, optional.
+#'@param title_scale Multiplicative factor to scale title size, optional.
+#'@param sizetit Deprecated. Use 'title_scale' instead.
 #'@param fileout Name of the output file for each experiment: c('',''). 
 #'  Extensions allowed: eps/ps, jpeg, png, pdf, bmp and tiff. If filenames 
 #'  with different extensions are passed, it will be considered only the first 
@@ -65,7 +66,7 @@ VizAno <- function(exp_ano, obs_ano = NULL, sdates, toptitle = rep('', 15),
                    ytitle = rep('', 15), limits = NULL, legends = NULL, 
                    freq = 12, biglab = FALSE, fill = TRUE, memb = TRUE, 
                    ensmean = TRUE, linezero = FALSE, points = FALSE, 
-                   vlines = NULL, sizetit = 1, 
+                   vlines = NULL, title_scale = 1, sizetit = NULL, 
                    fileout = NULL, 
                    width = 8, height = 5, size_units = 'in', res = 100, ...) {
   # Process the user graphical parameters that may be passed in the call
@@ -107,6 +108,14 @@ VizAno <- function(exp_ano, obs_ano = NULL, sdates, toptitle = rep('', 15),
   if (!all(nchar(sdates) == 8)) {
     stop ("The parameter 'sdates' must be formatted as YYYYMMDD.")
   }
+  # title_scale check
+    if (missing(title_scale) && !missing(sizetit)) {
+    warning("The parameter 'sizetit' is deprecated. Use 'title_scale' instead.")
+    title_scale <- sizetit
+  }
+  if (!is.numeric(title_scale) || length(title_scale) != 1) {
+    stop("Parameter 'title_scale' must be a single numerical value.")
+  }
 
   if (is.null(limits) == TRUE) {
     if (memb) {
@@ -187,7 +196,7 @@ VizAno <- function(exp_ano, obs_ano = NULL, sdates, toptitle = rep('', 15),
       legsize <- 1
     }
     plot(empty_ts, ylim = c(ll, ul), xlab = "Time (years)", ylab = ytitle[jexp],
-          main = toptitle[jexp], cex.main = cexmain * sizetit)
+          main = toptitle[jexp], cex.main = cexmain * title_scale)
     # 
     #  Plot experimental data + all observational datasets sdate by sdate
     # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-- 
GitLab


From ea9ad01d2a1147cddf1eaea7c85ac44f7d85437c Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 30 Apr 2025 12:07:35 +0200
Subject: [PATCH 51/72] Change 'sizetit' for 'title_scale' in R/VizClim.R

---
 R/VizAno.R  | 12 ++++++------
 R/VizClim.R | 16 +++++++++++++---
 2 files changed, 19 insertions(+), 9 deletions(-)

diff --git a/R/VizAno.R b/R/VizAno.R
index e4ab324..6122c04 100644
--- a/R/VizAno.R
+++ b/R/VizAno.R
@@ -63,12 +63,12 @@
 #'@importFrom stats ts
 #'@importFrom s2dv MeanDims
 VizAno <- function(exp_ano, obs_ano = NULL, sdates, toptitle = rep('', 15),
-                   ytitle = rep('', 15), limits = NULL, legends = NULL, 
-                   freq = 12, biglab = FALSE, fill = TRUE, memb = TRUE, 
-                   ensmean = TRUE, linezero = FALSE, points = FALSE, 
-                   vlines = NULL, title_scale = 1, sizetit = NULL, 
-                   fileout = NULL, 
-                   width = 8, height = 5, size_units = 'in', res = 100, ...) {
+                   ytitle = rep('', 15), limits = NULL, legends = NULL,
+                   freq = 12, biglab = FALSE, fill = TRUE, memb = TRUE,
+                   ensmean = TRUE, linezero = FALSE, points = FALSE,
+                   vlines = NULL, title_scale = 1, sizetit = NULL,
+                   fileout = NULL, width = 8, height = 5, size_units = 'in',
+                   res = 100, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("cex", "cex.axis", "cex.lab", "cex.main", "col", "fin", "lab", "las", "lty", "lwd", "mai", "mgp", "new", "pch", "pin", "ps", "pty")
diff --git a/R/VizClim.R b/R/VizClim.R
index 84dcd46..fa2f9fa 100644
--- a/R/VizClim.R
+++ b/R/VizClim.R
@@ -20,7 +20,8 @@
 #'@param listobs List of observational dataset names, optional.
 #'@param biglab TRUE/FALSE for presentation/paper plot. Default = FALSE.
 #'@param leg TRUE/FALSE to plot the legend or not.
-#'@param sizetit Multiplicative factor to scale title size, optional.
+#'@param title_scale Multiplicative factor to scale title size, optional.
+#'@param sizetit Deprecated. Use 'title_scale' instead.
 #'@param width File width, in the units specified in the parameter size_units 
 #'  (inches by default). Takes 8 by default.
 #'@param height File height, in the units specified in the parameter 
@@ -57,7 +58,7 @@ VizClim <- function(exp_clim, obs_clim = NULL, toptitle = '', ytitle = '',
                     monini = 1, freq = 12, limits = NULL,
                     listexp = c('exp1', 'exp2', 'exp3'),
                     listobs = c('obs1', 'obs2', 'obs3'), biglab = FALSE,
-                    leg = TRUE, sizetit = 1, fileout = NULL,
+                    leg = TRUE, title_scale = 1, sizetit = NULL, fileout = NULL,
                     width = 8, height = 5, size_units = 'in', res = 100, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
@@ -112,6 +113,15 @@ VizClim <- function(exp_clim, obs_clim = NULL, toptitle = '', ytitle = '',
   }
   lastyear <- (monini + (nleadtime - 1) * 12 / freq - 1) %/% 12
   lastmonth <- (monini + (nleadtime - 1) * 12 / freq - 1) %% 12 + 1
+  # Check title_scale
+  if (missing(title_scale) && !missing(sizetit)) {
+    warning("The parameter 'sizetit' is deprecated. Use 'title_scale' instead.")
+    title_scale <- sizetit
+  }
+  if (!is.numeric(title_scale) || length(title_scale) != 1) {
+    stop("Parameter 'title_scale' must be a single numerical value.")
+  }
+  
   #
   #  Define some plot parameters
   # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -166,7 +176,7 @@ VizClim <- function(exp_clim, obs_clim = NULL, toptitle = '', ytitle = '',
     legsize <- 1
   }
   plot(empty, ylim = c(ll, ul), xlab = "Time (months)", ylab = ytitle,
-       main = toptitle, cex.main = cexmain * sizetit, axes = FALSE)
+       main = toptitle, cex.main = cexmain * title_scale, axes = FALSE)
   axis(1, at = labind, labels = labmonth)
   axis(2)
   box()
-- 
GitLab


From 44d51209dc8f5dfb5c67d65550fba0f72e28831b Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 30 Apr 2025 12:28:25 +0200
Subject: [PATCH 52/72] Change 'title' for 'toptitle' in R/VizWeeklyClim.R

---
 R/VizWeeklyClim.R | 31 +++++++++++++++++++++----------
 1 file changed, 21 insertions(+), 10 deletions(-)

diff --git a/R/VizWeeklyClim.R b/R/VizWeeklyClim.R
index 9615c3b..3805a96 100644
--- a/R/VizWeeklyClim.R
+++ b/R/VizWeeklyClim.R
@@ -36,7 +36,8 @@
 #'@param ylim A numeric vector of length two providing limits of the scale. 
 #'  Use NA to refer to the existing minimum or maximum. For more information, 
 #'  see 'ggplot2' documentation of 'scale_y_continuous' parameter.
-#'@param title The text for the top title of the plot. It is NULL by default.
+#'@param toptitle The text for the top title of the plot. It is NULL by default.
+#'@param title Deprecated. Use 'toptitle' instead.
 #'@param subtitle The text for the subtitle of the plot. It is NULL bu default.
 #'@param ytitle Character string to be drawn as y-axis title. It is NULL by 
 #'  default.
@@ -66,7 +67,7 @@
 #'VizWeeklyClim(data = data, first_date = '2002-08-09', 
 #'              last_date = '2002-09-15', ref_period = 2010:2019, 
 #'              data_years = 2000:2019, time_dim = 'time', sdate_dim = 'sdate',
-#'              title = "Observed weekly means and climatology", 
+#'              toptitle = "Observed weekly means and climatology", 
 #'              subtitle = "Target years: 2010 to 2019", 
 #'              ytitle = paste0('tas', " (", "deg.C", ")"))
 #' 
@@ -78,12 +79,12 @@
 #' @importFrom rlang .data
 #'@export
 VizWeeklyClim <- function(data, first_date, ref_period, last_date = NULL, 
-                          data_years = NULL, time_dim = 'time', 
-                          sdate_dim = 'sdate', ylim = NULL, 
-                          title = NULL, subtitle = NULL, 
-                          ytitle = NULL, legend = TRUE,
-                          palette = "Blues", fileout = NULL, device = NULL, 
-                          width = 8, height = 6, units = 'in', dpi = 300) {
+                          data_years = NULL, time_dim = 'time',
+                          sdate_dim = 'sdate', ylim = NULL, toptitle = NULL,
+                          title = NULL, subtitle = NULL, ytitle = NULL,
+                          legend = TRUE, palette = "Blues", fileout = NULL,
+                          device = NULL, width = 8, height = 6, units = 'in',
+                          dpi = 300) {
   ## Check input arguments
   # data
   if (is.array(data)) {
@@ -201,7 +202,17 @@ VizWeeklyClim <- function(data, first_date, ref_period, last_date = NULL,
       warning("Parameter 'ylim' can't be a character string, it will not be used.")
       ylim <- NULL
     }
-
+    # toptitle
+    if (missing(toptitle) && !missing(title)) {
+      warning("The parameter 'title' is deprecated. Use 'toptitle' instead.")
+      toptitle <- title
+    }
+    if (!is.null(toptitle)) {
+      if (!is.character(toptitle)) {
+        stop("Parameter 'toptitle' must be a character string.")
+      }
+    }
+    
     index_first_date <- which(dates == first_date)
     index_last_date <- length(dates) - (length(dates) %% 7)
     last_date <- dates[index_last_date]
@@ -296,7 +307,7 @@ VizWeeklyClim <- function(data, first_date, ref_period, last_date = NULL,
                           alpha = 1, linewidth = 0.7, show.legend = legend)
   } 
   p = p + theme_bw() + ylab(ytitle) + xlab(NULL) + 
-      ggtitle(title, subtitle = subtitle) +
+      ggtitle(toptitle, subtitle = subtitle) +
       scale_x_date(breaks = seq(min(all$day), max(all$day), by = "7 days"),
                    minor_breaks = NULL, expand = c(0.03, 0.03),
                    labels = scales::date_format("%d %b %Y")) +
-- 
GitLab


From a8560211b994552386d2afb4e3c2cf7e147b4cd5 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 30 Apr 2025 13:26:04 +0200
Subject: [PATCH 53/72] Change 'leg' for 'drawleg' in R/Viz2VarsVsLTime.R

---
 R/Viz2VarsVsLTime.R | 23 +++++++++++++++++------
 1 file changed, 17 insertions(+), 6 deletions(-)

diff --git a/R/Viz2VarsVsLTime.R b/R/Viz2VarsVsLTime.R
index e041ac6..211ae40 100644
--- a/R/Viz2VarsVsLTime.R
+++ b/R/Viz2VarsVsLTime.R
@@ -17,8 +17,9 @@
 #'@param biglab TRUE/FALSE for presentation/paper plot. Default = FALSE.
 #'@param hlines c(a, b, ...) Add horizontal black lines at Y-positions a, b, 
 #'  ... The default value is NULL.
-#'@param leg TRUE/FALSE if legend should be added or not to the plot. 
+#'@param drawleg TRUE/FALSE if legend should be added or not to the plot. 
 #'  Default = TRUE.
+#'@param leg Deprecated. Use 'drawleg' instead.
 #'@param siglev TRUE/FALSE if significance level should replace confidence 
 #'  interval.\cr 
 #'  Default = FALSE.
@@ -76,10 +77,11 @@
 Viz2VarsVsLTime <- function(var1, var2, toptitle = '', ytitle = '', monini = 1,
                             freq = 12, nticks = NULL, limits = NULL, listexp =
                             c('exp1', 'exp2', 'exp3'), listvars = c('var1',
-                            'var2'), biglab = FALSE, hlines = NULL, leg = TRUE,
-                            siglev = FALSE, title_scale = 1, sizetit = NULL,
-                            show_conf = TRUE, fileout = NULL, width = 8,
-                            height = 5, size_units = 'in', res = 100, ...) {
+                            'var2'), biglab = FALSE, hlines = NULL, 
+                            drawleg = TRUE, leg = NULL, siglev = FALSE,
+                            title_scale = 1, sizetit = NULL, show_conf = TRUE,
+                            fileout = NULL, width = 8, height = 5,
+                            size_units = 'in', res = 100, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("cex", "cex.axis", "cex.lab", "cex.main", "col", "fin", "lab", "las", "lty", "lwd", "mai", "mgp", "new", "pin", "ps", "pty")
@@ -132,6 +134,15 @@ Viz2VarsVsLTime <- function(var1, var2, toptitle = '', ytitle = '', monini = 1,
                  frequency = freq)
   empty <- array(dim = length(empty_ts))
   
+  # Check drawleg
+  if (missing(drawleg) && !missing(leg)) {
+    warning("The parameter 'leg' is deprecated. Use 'drawleg' instead.")
+    drawleg <- leg
+  }
+  if (!is.logical(title_scale) || length(title_scale) != 1) {
+    stop("Parameter 'drawleg' must be a single logical value.")
+  }
+  
   # Check title_scale
   if (missing(title_scale) && !missing(sizetit)) {
     warning("The parameter 'sizetit' is deprecated. Use 'title_scale' instead.")
@@ -245,7 +256,7 @@ Viz2VarsVsLTime <- function(var1, var2, toptitle = '', ytitle = '', monini = 1,
       }
     }
   }
-  if (leg) {
+  if (drawleg) {
     legend(1, ul, legendnames, lty = legendsty, lwd = legendthick,
            col = legendcol, cex = legsize)
   }
-- 
GitLab


From 1f5cf7130126ec01365ea2ac4216f66fbdee3e72 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 30 Apr 2025 14:02:26 +0200
Subject: [PATCH 54/72] Change 'leg' for 'drawleg' in R/VizClim.R

---
 R/VizClim.R | 22 +++++++++++++++++-----
 1 file changed, 17 insertions(+), 5 deletions(-)

diff --git a/R/VizClim.R b/R/VizClim.R
index fa2f9fa..86691ac 100644
--- a/R/VizClim.R
+++ b/R/VizClim.R
@@ -19,7 +19,8 @@
 #'@param listexp List of experiment names, optional.
 #'@param listobs List of observational dataset names, optional.
 #'@param biglab TRUE/FALSE for presentation/paper plot. Default = FALSE.
-#'@param leg TRUE/FALSE to plot the legend or not.
+#'@param drawleg TRUE/FALSE to plot the legend or not. Default = TRUE.
+#'@param leg Deprecated. Use 'drawleg' instead.
 #'@param title_scale Multiplicative factor to scale title size, optional.
 #'@param sizetit Deprecated. Use 'title_scale' instead.
 #'@param width File width, in the units specified in the parameter size_units 
@@ -58,8 +59,9 @@ VizClim <- function(exp_clim, obs_clim = NULL, toptitle = '', ytitle = '',
                     monini = 1, freq = 12, limits = NULL,
                     listexp = c('exp1', 'exp2', 'exp3'),
                     listobs = c('obs1', 'obs2', 'obs3'), biglab = FALSE,
-                    leg = TRUE, title_scale = 1, sizetit = NULL, fileout = NULL,
-                    width = 8, height = 5, size_units = 'in', res = 100, ...) {
+                    drawleg = TRUE, leg = NULL, title_scale = 1, sizetit = NULL,
+                    fileout = NULL, width = 8, height = 5, size_units = 'in',
+                    res = 100, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("cex", "cex.axis", "cex.lab", "cex.main", "col", "fin", "lab", "las", "lty", "lwd", "mai", "mgp", "new", "pin", "ps", "pty", "tcl")
@@ -113,6 +115,16 @@ VizClim <- function(exp_clim, obs_clim = NULL, toptitle = '', ytitle = '',
   }
   lastyear <- (monini + (nleadtime - 1) * 12 / freq - 1) %/% 12
   lastmonth <- (monini + (nleadtime - 1) * 12 / freq - 1) %% 12 + 1
+  
+  # Check drawleg
+  if (missing(drawleg) && !missing(leg)) {
+    warning("The parameter 'leg' is deprecated. Use 'drawleg' instead.")
+    drawleg <- leg
+  }
+  if (!is.logical(title_scale) || length(title_scale) != 1) {
+    stop("Parameter 'drawleg' must be a single logical value.")
+  }
+  
   # Check title_scale
   if (missing(title_scale) && !missing(sizetit)) {
     warning("The parameter 'sizetit' is deprecated. Use 'title_scale' instead.")
@@ -201,14 +213,14 @@ VizClim <- function(exp_clim, obs_clim = NULL, toptitle = '', ytitle = '',
              axes = FALSE)
       }
     }
-    if (leg) {
+    if (drawleg) {
       legend(1, ul, c(listexp[1:nexp], listobs[1:nobs]), 
              lty = c(array(1, dim = nexp), type[1:nobs]),
              lwd = c(array(2, dim = nexp), thickness[1:nobs]),
              col = c(color[1:nexp], array(1, dim = nobs)), cex = legsize)
     }
   } else {
-    if (leg) {
+    if (drawleg) {
       legend(1, ul, listexp[1:nexp], lty = 1, lwd = 2, col = color[1:nexp],
              cex = legsize)
     }
-- 
GitLab


From e04bcd2e390cd60e66b92e259b6c009e976a56b2 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 30 Apr 2025 15:57:46 +0200
Subject: [PATCH 55/72] Change 'legend' for 'drawleg' in
 R/VizTriangles4Categories.R (+ bugfix in R/Viz2VarsVsLTime.R)

---
 R/Viz2VarsVsLTime.R         |  2 +-
 R/VizTriangles4Categories.R | 29 ++++++++++++++++++++---------
 2 files changed, 21 insertions(+), 10 deletions(-)

diff --git a/R/Viz2VarsVsLTime.R b/R/Viz2VarsVsLTime.R
index 211ae40..d96394e 100644
--- a/R/Viz2VarsVsLTime.R
+++ b/R/Viz2VarsVsLTime.R
@@ -139,7 +139,7 @@ Viz2VarsVsLTime <- function(var1, var2, toptitle = '', ytitle = '', monini = 1,
     warning("The parameter 'leg' is deprecated. Use 'drawleg' instead.")
     drawleg <- leg
   }
-  if (!is.logical(title_scale) || length(title_scale) != 1) {
+  if (!is.logical(drawleg) || length(drawleg) != 1) {
     stop("Parameter 'drawleg' must be a single logical value.")
   }
   
diff --git a/R/VizTriangles4Categories.R b/R/VizTriangles4Categories.R
index 15a9dd7..ca48f5f 100644
--- a/R/VizTriangles4Categories.R
+++ b/R/VizTriangles4Categories.R
@@ -32,8 +32,9 @@
 #'  length of the row of parameter 'data'. Set the sequence from 1 to the 
 #'  length of the row of parameter 'data' as default. 
 #'@param ytitle A string of title of the y-axis. Set NULL as default.
-#'@param legend A logical value to decide to draw the color bar legend or not. 
+#'@param drawleg A logical value to decide to draw the color bar legend or not. 
 #'  Set TRUE as default.
+#'@param legend Deprecated. Use 'drawleg' instead.
 #'@param lab_legend A vector of labels indicating what is represented in each 
 #'category (i.e. triangle). Set the sequence from 1 to the length of 
 #' the categories (2 or 4).  
@@ -83,11 +84,12 @@ VizTriangles4Categories <- function(data, brks = NULL, cols = NULL,
                                     cex_sig = 1, xlab = TRUE, ylab = TRUE,
                                     xlabels = NULL, xtitle = NULL, 
                                     ylabels = NULL, ytitle = NULL,
-                                    legend = TRUE, lab_legend = NULL,
-                                    cex_leg = 1, col_leg = 'black',
-                                    cex_axis = 1.5, mar = c(5, 4, 0, 0),
-                                    fileout = NULL, size_units = 'px',
-                                    res = 100, figure.width = 1, ...) {
+                                    drawleg = TRUE, legend = NULL,
+                                    lab_legend = NULL, cex_leg = 1,
+                                    col_leg = 'black', cex_axis = 1.5,
+                                    mar = c(5, 4, 0, 0), fileout = NULL,
+                                    size_units = 'px', res = 100,
+                                    figure.width = 1, ...) {
   # Checking the dimensions
   if (length(dim(data)) != 3) {
     stop("Parameter 'data' must be an array with three dimensions.")
@@ -125,7 +127,16 @@ VizTriangles4Categories <- function(data, brks = NULL, cols = NULL,
     stop(
       "Parameter 'data' should contain a dimcat dimension with length equals
       to two or four as only two or four categories can be plotted.")
-  }      
+  }
+  
+  # Check drawleg
+  if (missing(drawleg) && !missing(legend)) {
+    warning("The parameter 'legend' is deprecated. Use 'drawleg' instead.")
+    drawleg <- legend
+  }
+  if (!is.logical(drawleg) || length(drawleg) != 1) {
+    stop("Parameter 'drawleg' must be a single logical value.")
+  }
   
   # Checking what is available and generating missing information 
   if (!is.null(lab_legend) &&
@@ -183,7 +194,7 @@ VizTriangles4Categories <- function(data, brks = NULL, cols = NULL,
     data_cat[data < brks[i + 1]] <- cols[i]
   }
   
-  if(legend){
+  if(drawleg){
     layout(matrix(c(1, 2, 1, 3), 2, 2, byrow = T),
            widths = c(10, 3.4), heights = c(10, 3.5))
     par(oma = c(1, 1, 1, 1), mar = mar)
@@ -255,7 +266,7 @@ VizTriangles4Categories <- function(data, brks = NULL, cols = NULL,
   
   # legend
   
-  if(legend){
+  if(drawleg){
     # Colorbar
     par(mar=c(0,0,0,0))
     ColorBarContinuous(brks = brks, cols = cols, vertical = T, draw_ticks = T, draw_separators = T,
-- 
GitLab


From 0d2ae5004e0eaf36f2c6deb7d69ba7cc16340730 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 30 Apr 2025 16:20:58 +0200
Subject: [PATCH 56/72] Change 'plot_legend' for 'drawleg' in R/VizScorecard.R

---
 R/VizClim.R      |  2 +-
 R/VizScorecard.R | 19 ++++++++++++-------
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/R/VizClim.R b/R/VizClim.R
index 86691ac..b4902b2 100644
--- a/R/VizClim.R
+++ b/R/VizClim.R
@@ -121,7 +121,7 @@ VizClim <- function(exp_clim, obs_clim = NULL, toptitle = '', ytitle = '',
     warning("The parameter 'leg' is deprecated. Use 'drawleg' instead.")
     drawleg <- leg
   }
-  if (!is.logical(title_scale) || length(title_scale) != 1) {
+  if (!is.logical(drawleg) || length(drawleg) != 1) {
     stop("Parameter 'drawleg' must be a single logical value.")
   }
   
diff --git a/R/VizScorecard.R b/R/VizScorecard.R
index ab2e415..a4a89fe 100644
--- a/R/VizScorecard.R
+++ b/R/VizScorecard.R
@@ -45,8 +45,9 @@
 #'  be given as input if the 'legend_dims' require different breaks. This  
 #'  parameter is required even if the legend is not plotted, to define the 
 #'  colors in the scorecard table. It is set as NULL by default.
-#'@param plot_legend A logical value to determine if the legend is plotted. It 
+#'@param drawleg A logical value to determine if the legend is plotted. It 
 #'  is set as TRUE by default.
+#'@param plot_legend Deprecated. Use 'drawleg' instead.
 #'@param label_scale A numeric value to define the size of the legend labels. 
 #'  It is set as 1.4 by default.
 #'@param legend_width A numeric value to define the width of the legend bars. By 
@@ -117,7 +118,7 @@ VizScorecard <- function(data, sign = NULL, row_dim = 'region',
                          row_title = NULL, subrow_title = NULL, 
                          col_title = NULL, table_title = NULL, 
                          table_subtitle = NULL, legend_breaks = NULL, 
-                         plot_legend = TRUE, label_scale = 1.4, 
+                         drawleg = TRUE, plot_legend = NULL, label_scale = 1.4, 
                          legend_width = NULL, legend_height = 50, 
                          palette = NULL, colorunder = NULL, colorsup = NULL,
                          round_decimal = 2, font_size = 1.1,
@@ -268,9 +269,13 @@ VizScorecard <- function(data, sign = NULL, row_dim = 'region',
   } else {
     stop("Parameter 'legend_breaks' must be a numeric vector, a list or NULL.")
   }
-  # Check plot_legend
-  if (!inherits(plot_legend, 'logical')) {
-    stop("Parameter 'plot_legend' must be a logical value.")
+  # Check drawleg
+  if (missing(drawleg) && !missing(plot_legend)) {
+    warning("The parameter 'plot_legend' is deprecated. Use 'drawleg' instead.")
+    drawleg <- plot_legend
+  }
+  if (!inherits(drawleg, 'logical')) {
+    stop("Parameter 'drawleg' must be a logical value.")
   }
   # Check label_scale
   if (any(!is.numeric(label_scale), length(label_scale) != 1)) {
@@ -508,7 +513,7 @@ VizScorecard <- function(data, sign = NULL, row_dim = 'region',
                 column_spec(n_columns, border_right = "2px solid black") %>%
                 row_spec(seq(from = 0, to = n_subrow_names * n_row_names, by = n_subrow_names), 
                          extra_css = "border-bottom: 2px solid black", hline_after = TRUE)
-  if (plot_legend == TRUE) {
+  if (drawleg == TRUE) {
     # Save the scorecard (without legend)
     save_kable(table_html, file = paste0(fileout, '_tmpScorecard.png'), vheight = 1)
     
@@ -532,7 +537,7 @@ VizScorecard <- function(data, sign = NULL, row_dim = 'region',
     # Remove temporary scorecard table
     unlink(paste0(fileout, '_tmpScorecard*.png'))
   }
-  if (plot_legend == FALSE) {
+  if (drawleg == FALSE) {
     save_kable(table_html, file = fileout)
   } 
 }
-- 
GitLab


From b2991f51d966829406211ab8250e101dbbcc7769 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 30 Apr 2025 16:25:55 +0200
Subject: [PATCH 57/72] Change 'plotfile' for 'fileout' in R/VizPDFsOLE.R

---
 R/VizPDFsOLE.R | 23 ++++++++++++++---------
 1 file changed, 14 insertions(+), 9 deletions(-)

diff --git a/R/VizPDFsOLE.R b/R/VizPDFsOLE.R
index 5ae68e3..280f3b0 100644
--- a/R/VizPDFsOLE.R
+++ b/R/VizPDFsOLE.R
@@ -18,8 +18,9 @@
 #'  legend ("bottom", "top", "right" or "left")(Default 'bottom'). 
 #'@param legendSize (optional) A numeric value for setting the size of the 
 #'  legend text. (Default 1.0). 
-#'@param plotfile (optional) A filename where the plot will be saved. 
+#'@param fileout (optional) A filename where the plot will be saved. 
 #'  (Default: the plot is not saved).
+#'@param plotfile Deprecated. Use 'fileout' instead
 #'@param width (optional) A numeric value indicating the plot width in 
 #'  units ("in", "cm", or "mm"). (Default width = 30). 
 #'@param height (optional) A numeric value indicating the plot height. 
@@ -44,11 +45,11 @@
 #'}
 #'@import ggplot2 stats
 VizPDFsOLE <- function(pdf_1, pdf_2, nsigma = 3, legendPos = 'bottom', 
-                       legendSize = 1.0, plotfile = NULL, width = 30, 
-                       height = 15, units = "cm", dpi = 300) {
+                       legendSize = 1.0, fileout = NULL, plotfile = NULL,
+                       width = 30, height = 15, units = "cm", dpi = 300) {
   y <- type <- NULL
 
-  if(!is.null(plotfile)){
+  if(!is.null(fileout)){
     if (!is.numeric(dpi)) {
       stop("Parameter 'dpi' must be numeric.")
     }
@@ -84,8 +85,12 @@ VizPDFsOLE <- function(pdf_1, pdf_2, nsigma = 3, legendPos = 'bottom',
               "only the first element will be used.")
       width <- width[1]
     }
-    if (!is.character(plotfile)) {
-      stop("Parameter 'plotfile' must be a character string ",
+    if (missing(fileout) && !missing(plotfile)) {
+      warning("The parameter 'plotfile' is deprecated. Use 'fileout' instead.")
+      fileout <- plotfile
+    }
+    if (!is.character(fileout)) {
+      stop("Parameter 'fileout' must be a character string ",
            "indicating the path and name of output png file.")
     }
   }
@@ -229,10 +234,10 @@ VizPDFsOLE <- function(pdf_1, pdf_2, nsigma = 3, legendPos = 'bottom',
   
  
   #-----------------------------------------------------------------------------
-  # Save to plotfile if needed, and return plot
+  # Save to fileout if needed, and return plot
   #-----------------------------------------------------------------------------
-  if (!is.null(plotfile)) {
-    ggsave(plotfile, g, width = width, height = height, units = units, dpi = dpi)
+  if (!is.null(fileout)) {
+    ggsave(fileout, g, width = width, height = height, units = units, dpi = dpi)
   }
   return(g)
 }
-- 
GitLab


From 1cd33f6430d0634c725e3c9cb5806fb10b783843 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 30 Apr 2025 17:17:23 +0200
Subject: [PATCH 58/72] Update tests/testthat/test-VizScorecard.R

---
 tests/testthat/test-VizScorecard.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/testthat/test-VizScorecard.R b/tests/testthat/test-VizScorecard.R
index 4c185e7..5247314 100644
--- a/tests/testthat/test-VizScorecard.R
+++ b/tests/testthat/test-VizScorecard.R
@@ -22,7 +22,7 @@ test_that("1. Test input", {
   )
   # check sign
   expect_error(
-    VizScorecard(data = data, sign = 1, plot_legend = TRUE),
+    VizScorecard(data = data, sign = 1, drawleg = TRUE),
     "Parameter 'sign' must be a boolean array or NULL."
   )
   expect_error(
@@ -146,10 +146,10 @@ test_that("1. Test input", {
     paste0("Parameter 'palette' must be provided when 'legend_breaks' exceed ", 
            "the length of 11.")
   )
-  # Check plot_legend
+  # Check drawleg
   expect_error(
-    VizScorecard(data, plot_legend = 'a'),
-    "Parameter 'plot_legend' must be a logical value."
+    VizScorecard(data, drawleg = 'a'),
+    "Parameter 'drawleg' must be a logical value."
   )
   # Check label_scale
   expect_error(
@@ -297,7 +297,7 @@ test_that("1. Test input", {
 #              col_title = 'Start date', 
 #              table_title = "Temperature of ECMWF System 5", 
 #              table_subtitle = "(Ref: ERA5 1994-2016)",
-#              plot_legend = TRUE),
+#              drawleg = TRUE),
 #     name = 'VizScorecard_1a.png' 
 #   )
 # })
\ No newline at end of file
-- 
GitLab


From f78c6b8a21a8ca963a6ad79f9f9186bf644c0b77 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Tue, 6 May 2025 16:13:38 +0200
Subject: [PATCH 59/72] Update test-VizForecastPDF.R and test-VizPDFsOLE.R

---
 tests/testthat/test-VizForecastPDF.R |  2 +-
 tests/testthat/test-VizPDFsOLE.R     | 38 ++++++++++++++--------------
 2 files changed, 20 insertions(+), 20 deletions(-)

diff --git a/tests/testthat/test-VizForecastPDF.R b/tests/testthat/test-VizForecastPDF.R
index 5857f57..8f5bc32 100644
--- a/tests/testthat/test-VizForecastPDF.R
+++ b/tests/testthat/test-VizForecastPDF.R
@@ -35,7 +35,7 @@ fcsts <- data.frame(fcst1 = rnorm(10), fcst2 = rnorm(10, 0.5, 1.2))
 
 save_fun <- function(...) {
   path <- tempfile(fileext = ".png")
-  do.call(VizForecastPDF, list(..., plotfile = path))
+  do.call(VizForecastPDF, list(..., fileout = path))
   path
 }
 
diff --git a/tests/testthat/test-VizPDFsOLE.R b/tests/testthat/test-VizPDFsOLE.R
index 19e3af2..03da292 100644
--- a/tests/testthat/test-VizPDFsOLE.R
+++ b/tests/testthat/test-VizPDFsOLE.R
@@ -8,61 +8,61 @@ test_that("Sanity checks", {
   attr(pdf_2, "name") <- "NAO2"
   dim(pdf_2) <-  c(statistic = 2)
 
-  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, plotfile = "plot.png", 
+  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, fileout = "plot.png", 
                                        width = 30, height = 15, 
                                        units = "cm", dpi = '300') , 
               "Parameter 'dpi' must be numeric.")
   
-  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, plotfile = "plot.png", 
+  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, fileout = "plot.png", 
                            width = 30, height = 15, 
                            units = 20, dpi = 300) , 
                "Parameter 'units' must be character")
   
-  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, plotfile = "plot.png", 
+  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, fileout = "plot.png", 
                            width = 30, height = 15, 
                            units = "dm", dpi = 300) , 
                "Parameter 'units' must be equal to 'in', 'cm' or 'mm'.")
   
-  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, plotfile = "plot.png", 
+  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, fileout = "plot.png", 
                            width = 30, height = '15', 
                            units = "cm", dpi = 300) , 
                "Parameter 'height' must be numeric.")
   
-  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, plotfile = "plot.png", 
+  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, fileout = "plot.png", 
                            width = list(30), height = 15, 
                            units = "cm", dpi = 300) , 
                "Parameter 'width' must be numeric.")
   
-  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, plotfile = 0, 
+  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, fileout = 0, 
                            width = 30, height = 15, 
                            units = "cm", dpi = 300) , 
-               paste0("Parameter 'plotfile' must be a character string ",
+               paste0("Parameter 'fileout' must be a character string ",
                     "indicating the path and name of output png file."))
   
-  expect_error(VizPDFsOLE(pdf_1, pdf_2, legendPos = 1, plotfile = NULL, 
+  expect_error(VizPDFsOLE(pdf_1, pdf_2, legendPos = 1, fileout = NULL, 
                            width = 30, height = 15, 
                            units = "cm", dpi = 300) , 
                "Parameter 'legendPos' must be character")
   
   expect_error(VizPDFsOLE(pdf_1, pdf_2, legendPos = 'arriba', 
-                           plotfile = "plot.png", 
+                           fileout = "plot.png", 
                            width = 30, height = 15, 
                            units = "cm", dpi = 300) , 
                "Parameter 'legendPos' must be equal to 'bottom', 'top', 'right' or 'left'.")
   
-  expect_error(VizPDFsOLE(pdf_1, pdf_2, legendSize = '3', plotfile = NULL, 
+  expect_error(VizPDFsOLE(pdf_1, pdf_2, legendSize = '3', fileout = NULL, 
                            width = 30, height = 15, 
                            units = "cm", dpi = 300) , 
                "Parameter 'legendSize' must be numeric.")
   
-  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = '3', plotfile = NULL, 
+  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = '3', fileout = NULL, 
                            width = 30, height = 15, 
                            units = "cm", dpi = 300) , 
                "Parameter 'nsigma' must be numeric.")
   
   pdf_1 <- list(1.1,0.6)
   attr(pdf_1, "name") <- "NAO1"
-  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, plotfile = NULL, 
+  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, fileout = NULL, 
                            width = 30, height = 15, 
                            units = "cm", dpi = 300) , 
                "Parameter 'pdf_1' must be an array.")
@@ -70,7 +70,7 @@ test_that("Sanity checks", {
   pdf_1 <- c('1.1','0.6')
   attr(pdf_1, "name") <- "NAO1"
   dim(pdf_1) <-  c(statistic = 2)
-  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, plotfile = NULL, 
+  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, fileout = NULL, 
                            width = 30, height = 15, 
                            units = "cm", dpi = 300) , 
                "Parameter 'pdf_1' must be a numeric array.")
@@ -78,7 +78,7 @@ test_that("Sanity checks", {
   pdf_1 <- c(1.1,0.6)
   attr(pdf_1, "name") <- "NAO1"
   dim(pdf_1) <-  c(2)
-  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, plotfile = NULL, 
+  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, fileout = NULL, 
                            width = 30, height = 15, 
                            units = "cm", dpi = 300) , 
                paste0("Parameters 'pdf_1' and 'pdf_2' ",
@@ -87,7 +87,7 @@ test_that("Sanity checks", {
   pdf_1 <- c(1.1,0.6)
   attr(pdf_1, "name") <- "NAO1"
   dim(pdf_1) <-  c(statisti = 2)
-  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, plotfile = NULL, 
+  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, fileout = NULL, 
                            width = 30, height = 15, 
                            units = "cm", dpi = 300) , 
                "Parameter 'pdf_1' must have dimension 'statistic'.")
@@ -95,7 +95,7 @@ test_that("Sanity checks", {
   pdf_1 <- c(1.1,0.6)
   attr(pdf_1, "name") <- "NAO1"
   dim(pdf_1) <-  c(statistic = 2, model = 1)
-  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, plotfile = NULL, 
+  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, fileout = NULL, 
                            width = 30, height = 15, 
                            units = "cm", dpi = 300) , 
                "Parameter 'pdf_1' must have only dimension 'statistic'.")
@@ -103,7 +103,7 @@ test_that("Sanity checks", {
   pdf_1 <- c(1.1, 0.6, 0.2)
   attr(pdf_1, "name") <- "NAO1"
   dim(pdf_1) <-  c(statistic = 3)
-  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, plotfile = NULL, 
+  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, fileout = NULL, 
                            width = 30, height = 15, 
                            units = "cm", dpi = 300) , 
                paste0("Length of dimension 'statistic'",
@@ -112,7 +112,7 @@ test_that("Sanity checks", {
   pdf_1 <- c(1.1, 0.6)
   attr(pdf_1, "name") <- 12
   dim(pdf_1) <-  c(statistic = 2)
-  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, plotfile = NULL, 
+  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, fileout = NULL, 
                            width = 30, height = 15, 
                            units = "cm", dpi = 300) , 
                paste0("The 'name' attribute of parameter 'pdf_1' must be a character ",
@@ -125,7 +125,7 @@ test_that("Sanity checks", {
   attr(pdf_2, "name") <- 12
   dim(pdf_2) <-  c(statistic = 2)
   
-  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, plotfile = NULL, 
+  expect_error(VizPDFsOLE(pdf_1, pdf_2, nsigma = 3, fileout = NULL, 
                            width = 30, height = 15, 
                            units = "cm", dpi = 300) , 
                paste0("The 'name' attribute of parameter 'pdf_2' must be a character ",
-- 
GitLab


From 54b5bec28346a961a2936a2191d123a8cc3307fd Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Tue, 6 May 2025 16:17:11 +0200
Subject: [PATCH 60/72] Update man files

---
 man/ColorBarDiscrete.Rd        | 31 +++++++++++++++++++++++--------
 man/Viz2VarsVsLTime.Rd         | 16 +++++++++++-----
 man/VizACC.Rd                  |  9 ++++++---
 man/VizAno.Rd                  |  7 +++++--
 man/VizClim.Rd                 | 14 ++++++++++----
 man/VizCombinedMap.Rd          | 10 ++++++----
 man/VizForecastPDF.Rd          | 12 +++++++++---
 man/VizPDFsOLE.Rd              |  5 ++++-
 man/VizScorecard.Rd            |  7 +++++--
 man/VizTriangles4Categories.Rd |  7 +++++--
 man/VizWeeklyClim.Rd           |  7 +++++--
 11 files changed, 89 insertions(+), 36 deletions(-)

diff --git a/man/ColorBarDiscrete.Rd b/man/ColorBarDiscrete.Rd
index fccc06d..06bc118 100644
--- a/man/ColorBarDiscrete.Rd
+++ b/man/ColorBarDiscrete.Rd
@@ -17,12 +17,17 @@ ColorBarDiscrete(
   draw_separators = TRUE,
   labels = NULL,
   bar_extra_labels = NULL,
+  extra_labels = NULL,
   title = NULL,
   title_scale = 1,
-  label_scale = 1,
-  tick_scale = 1,
-  extra_margin = rep(0, 4),
+  bar_label_scale = 1,
+  label_scale = NULL,
+  bar_tick_scale = 1,
+  tick_scale = NULL,
+  bar_extra_margin = rep(0, 4),
+  extra_margin = NULL,
   bar_label_digits = 4,
+  label_digits = NULL,
   ...
 )
 }
@@ -100,22 +105,30 @@ same length as 'cols'.}
 the colour bar. The number of provided decimals will be conserved. 
 Disregarded if 'plot = FALSE'.}
 
+\item{extra_labels}{Deprecated. Use 'bar_extra_labels' instead.}
+
 \item{title}{Title to draw on top of the colour bar, most commonly with the 
 units of the represented field in the neighbour figures. Empty by default.}
 
 \item{title_scale}{Scale factor for the 'title' of the colour bar. 
 Takes 1 by default.}
 
-\item{label_scale}{Scale factor for the labels of the colour bar. 
+\item{bar_label_scale}{Scale factor for the labels of the colour bar. 
 Takes 1 by default.}
 
-\item{tick_scale}{Scale factor for the length of the ticks of the labels 
+\item{label_scale}{Deprecated. Use 'bar_label_scale' instead.}
+
+\item{bar_tick_scale}{Scale factor for the length of the ticks of the labels 
 along the colour bar. Takes 1 by default.}
 
-\item{extra_margin}{Extra margins to be added around the colour bar, 
+\item{tick_scale}{Deprecated. Use 'bar_tick_scale' instead.}
+
+\item{bar_extra_margin}{Extra margins to be added around the colour bar, 
 in the format c(y1, x1, y2, x2). The units are margin lines. Takes 
 rep(0, 4) by default.}
 
+\item{extra_margin}{Deprecated. Use 'bar_extra_margin' instead.}
+
 \item{bar_label_digits}{Number of significant digits to be displayed in the 
 labels of the colour bar, usually to avoid too many decimal digits 
 overflowing the figure region. This does not have effect over the labels 
@@ -128,6 +141,8 @@ provided in 'bar_extra_labels'. Takes 4 by default.}
  lwd mai mex mfcol mfrow mfg mkh oma omd omi page pch pin plt pty smo srt 
  tck tcl usr xaxp xaxs xaxt xlog xpd yaxp yaxs yaxt ylbias ylog.\cr For more 
 information about the parameters see `par`.}
+
+\item{label_digits.}{Deprecated. Use 'bar_label_digits' instead.}
 }
 \value{
 \item{brks}{
@@ -154,7 +169,7 @@ belongs to.\cr\cr
 \examples{
 cb <- ColorBarDiscrete(
  brks = 0:4, cols = c("green1", "green2", "green3", "green4"),
- vertical = FALSE, labels = paste0('lev ', 1:4), label_scale = 1.5, 
- extra_margin = c(0.5, 2, 0.5, 2), plot = FALSE)
+ vertical = FALSE, labels = paste0('lev ', 1:4), bar_label_scale = 1.5, 
+ bar_extra_margin = c(0.5, 2, 0.5, 2), plot = FALSE)
 
 }
diff --git a/man/Viz2VarsVsLTime.Rd b/man/Viz2VarsVsLTime.Rd
index 8b47618..0317331 100644
--- a/man/Viz2VarsVsLTime.Rd
+++ b/man/Viz2VarsVsLTime.Rd
@@ -17,9 +17,11 @@ Viz2VarsVsLTime(
   listvars = c("var1", "var2"),
   biglab = FALSE,
   hlines = NULL,
-  leg = TRUE,
+  drawleg = TRUE,
+  leg = NULL,
   siglev = FALSE,
-  sizetit = 1,
+  title_scale = 1,
+  sizetit = NULL,
   show_conf = TRUE,
   fileout = NULL,
   width = 8,
@@ -55,14 +57,18 @@ Viz2VarsVsLTime(
 \item{hlines}{c(a, b, ...) Add horizontal black lines at Y-positions a, b, 
 ... The default value is NULL.}
 
-\item{leg}{TRUE/FALSE if legend should be added or not to the plot. 
+\item{drawleg}{TRUE/FALSE if legend should be added or not to the plot. 
 Default = TRUE.}
 
+\item{leg}{Deprecated. Use 'drawleg' instead.}
+
 \item{siglev}{TRUE/FALSE if significance level should replace confidence 
 interval.\cr 
 Default = FALSE.}
 
-\item{sizetit}{Multiplicative factor to change title size, optional.}
+\item{title_scale}{Multiplicative factor to change title size, optional.}
+
+\item{sizetit}{Deprecated. Use 'title_scale' instead.}
 
 \item{show_conf}{TRUE/FALSE to show/not confidence intervals for input 
 variables.}
@@ -117,7 +123,7 @@ input_rms[, 2, ] <- rms_ano$rms[, 1, 1, ]
 input_rms[, 3, ] <- rms_ano$conf.upper[, 1, 1, ]
 esviz:::Viz2VarsVsLTime(input_cor, input_rms,
                toptitle = "Time correlation and RMSE with ERA5",
-               ytitle = "K", sizetit = 0.7,
+               ytitle = "K", title_scale = 0.7,
                monini = 11, freq = 1, limits = c(-1, 5),
                listexp = c('SEAS5'), listvars = c('Corr', 'RMSE'),
                fileout = NULL)
diff --git a/man/VizACC.Rd b/man/VizACC.Rd
index 51ff6e6..410ef2a 100644
--- a/man/VizACC.Rd
+++ b/man/VizACC.Rd
@@ -8,7 +8,8 @@ VizACC(
   ACC,
   sdates,
   toptitle = "",
-  sizetit = 1,
+  title_scale = 1,
+  sizetit = NULL,
   ytitle = "",
   limits = NULL,
   legends = NULL,
@@ -37,7 +38,9 @@ interval and the 95\% significance level.}
 
 \item{toptitle}{A character string of the main title, optional.}
 
-\item{sizetit}{A multiplicative factor to scale title size, optional.}
+\item{title_scale}{A multiplicative factor to scale title size, optional.}
+
+\item{sizetit}{Deprecated. Use 'title_scale' instead.}
 
 \item{ytitle}{A character string of the title of Y-axis for each experiment:
 c('', ''), optional.}
@@ -110,7 +113,7 @@ input_acc[, , , , 4] <- acc$p.val
 sdates <- paste0(2000:2005, '1101')
 esviz:::VizACC(input_acc, sdates, 
       toptitle = "Spatial anomaly corr. coeff. with ERA5",
-      ytitle = "K", sizetit = 0.7, freq = 12,
+      ytitle = "K", title_scale = 0.7, freq = 12,
       legends = 'SEAS5', fileout = NULL)
  }
 }
diff --git a/man/VizAno.Rd b/man/VizAno.Rd
index 36f2773..817d0a3 100644
--- a/man/VizAno.Rd
+++ b/man/VizAno.Rd
@@ -20,7 +20,8 @@ VizAno(
   linezero = FALSE,
   points = FALSE,
   vlines = NULL,
-  sizetit = 1,
+  title_scale = 1,
+  sizetit = NULL,
   fileout = NULL,
   width = 8,
   height = 5,
@@ -69,7 +70,9 @@ Default = FALSE.}
 
 \item{vlines}{List of x location where to add vertical black lines, optional.}
 
-\item{sizetit}{Multiplicative factor to scale title size, optional.}
+\item{title_scale}{Multiplicative factor to scale title size, optional.}
+
+\item{sizetit}{Deprecated. Use 'title_scale' instead.}
 
 \item{fileout}{Name of the output file for each experiment: c('',''). 
 Extensions allowed: eps/ps, jpeg, png, pdf, bmp and tiff. If filenames 
diff --git a/man/VizClim.Rd b/man/VizClim.Rd
index b207aaa..5ed33f7 100644
--- a/man/VizClim.Rd
+++ b/man/VizClim.Rd
@@ -15,8 +15,10 @@ VizClim(
   listexp = c("exp1", "exp2", "exp3"),
   listobs = c("obs1", "obs2", "obs3"),
   biglab = FALSE,
-  leg = TRUE,
-  sizetit = 1,
+  drawleg = TRUE,
+  leg = NULL,
+  title_scale = 1,
+  sizetit = NULL,
   fileout = NULL,
   width = 8,
   height = 5,
@@ -49,9 +51,13 @@ c(nobs, nmemb, nltime) or c(nobs, nltime)}
 
 \item{biglab}{TRUE/FALSE for presentation/paper plot. Default = FALSE.}
 
-\item{leg}{TRUE/FALSE to plot the legend or not.}
+\item{drawleg}{TRUE/FALSE to plot the legend or not. Default = TRUE.}
 
-\item{sizetit}{Multiplicative factor to scale title size, optional.}
+\item{leg}{Deprecated. Use 'drawleg' instead.}
+
+\item{title_scale}{Multiplicative factor to scale title size, optional.}
+
+\item{sizetit}{Deprecated. Use 'title_scale' instead.}
 
 \item{fileout}{Name of output file. Extensions allowed: eps/ps, jpeg, png, 
 pdf, bmp and tiff. The default value is NULL, which the figure is shown
diff --git a/man/VizCombinedMap.Rd b/man/VizCombinedMap.Rd
index a9e9654..0e44027 100644
--- a/man/VizCombinedMap.Rd
+++ b/man/VizCombinedMap.Rd
@@ -25,6 +25,7 @@ VizCombinedMap(
   bar_titles = NULL,
   bar_label_scale = 1,
   cex_bar_titles = 1.5,
+  margin_scale = NULL,
   plot_margin = NULL,
   bar_extra_margin = c(2, 0, 2, 0),
   fileout = NULL,
@@ -117,10 +118,11 @@ be shown on top of each of the colour bars.}
 \item{cex_bar_titles}{Scale factor for the sizes of the bar titles. Takes 1.5 
 by default.}
 
-\item{plot_margin}{Numeric vector of length 4 for the margin sizes in the 
-following order: bottom, left, top, and right. If not specified, use the 
-default of par("mar"), c(5.1, 4.1, 4.1, 2.1). Used as 'margin_scale' in 
-VizEquiMap.}
+\item{margin_scale}{Numeric vector of length 4 for the margin sizes in the 
+following order: bottom, left, top, and right. If not specified (NULL), the 
+default of par("mar"), c(5.1, 4.1, 4.1, 2.1), is used. Default is NULL.}
+
+\item{plot_margin}{Deprecated. Use 'margin_scale' instead.}
 
 \item{bar_extra_margin}{A numeric vector of 4 indicating the extra margins to
 be added around the color bar, in the format c(y1, x1, y2, x2). The units 
diff --git a/man/VizForecastPDF.Rd b/man/VizForecastPDF.Rd
index cec38a5..37d671f 100644
--- a/man/VizForecastPDF.Rd
+++ b/man/VizForecastPDF.Rd
@@ -9,8 +9,10 @@ VizForecastPDF(
   tercile.limits,
   extreme.limits = NULL,
   obs = NULL,
+  fileout = NULL,
   plotfile = NULL,
-  title = "Set a title",
+  toptitle = "Set a title",
+  title = NULL,
   var.name = "Varname (units)",
   fcst.names = NULL,
   add.ensmemb = c("above", "below", "no"),
@@ -41,10 +43,14 @@ forecast panels. (Default: extreme categories are not shown).}
 panel or a single value that will be reused for all forecast panels. 
 (Default: observation is not shown).}
 
-\item{plotfile}{(optional) A filename (pdf, png...) where the plot will be 
+\item{fileout}{(optional) A filename (pdf, png...) where the plot will be 
 saved. (Default: the plot is not saved).}
 
-\item{title}{A string with the plot title.}
+\item{plotfile}{Deprecated. Use 'fileout' instead.}
+
+\item{toptitle}{A string with the plot title.}
+
+\item{title}{Deprecated. Use 'toptitle' instead.}
 
 \item{var.name}{A string with the variable name and units.}
 
diff --git a/man/VizPDFsOLE.Rd b/man/VizPDFsOLE.Rd
index 726d06f..b790f39 100644
--- a/man/VizPDFsOLE.Rd
+++ b/man/VizPDFsOLE.Rd
@@ -11,6 +11,7 @@ VizPDFsOLE(
   nsigma = 3,
   legendPos = "bottom",
   legendSize = 1,
+  fileout = NULL,
   plotfile = NULL,
   width = 30,
   height = 15,
@@ -36,9 +37,11 @@ legend ("bottom", "top", "right" or "left")(Default 'bottom').}
 \item{legendSize}{(optional) A numeric value for setting the size of the 
 legend text. (Default 1.0).}
 
-\item{plotfile}{(optional) A filename where the plot will be saved. 
+\item{fileout}{(optional) A filename where the plot will be saved. 
 (Default: the plot is not saved).}
 
+\item{plotfile}{Deprecated. Use 'fileout' instead}
+
 \item{width}{(optional) A numeric value indicating the plot width in 
 units ("in", "cm", or "mm"). (Default width = 30).}
 
diff --git a/man/VizScorecard.Rd b/man/VizScorecard.Rd
index 838314a..2b29c11 100644
--- a/man/VizScorecard.Rd
+++ b/man/VizScorecard.Rd
@@ -22,7 +22,8 @@ VizScorecard(
   table_title = NULL,
   table_subtitle = NULL,
   legend_breaks = NULL,
-  plot_legend = TRUE,
+  drawleg = TRUE,
+  plot_legend = NULL,
   label_scale = 1.4,
   legend_width = NULL,
   legend_height = 50,
@@ -93,9 +94,11 @@ be given as input if the 'legend_dims' require different breaks. This
 parameter is required even if the legend is not plotted, to define the 
 colors in the scorecard table. It is set as NULL by default.}
 
-\item{plot_legend}{A logical value to determine if the legend is plotted. It 
+\item{drawleg}{A logical value to determine if the legend is plotted. It 
 is set as TRUE by default.}
 
+\item{plot_legend}{Deprecated. Use 'drawleg' instead.}
+
 \item{label_scale}{A numeric value to define the size of the legend labels. 
 It is set as 1.4 by default.}
 
diff --git a/man/VizTriangles4Categories.Rd b/man/VizTriangles4Categories.Rd
index b28c1a0..866b0cd 100644
--- a/man/VizTriangles4Categories.Rd
+++ b/man/VizTriangles4Categories.Rd
@@ -19,7 +19,8 @@ VizTriangles4Categories(
   xtitle = NULL,
   ylabels = NULL,
   ytitle = NULL,
-  legend = TRUE,
+  drawleg = TRUE,
+  legend = NULL,
   lab_legend = NULL,
   cex_leg = 1,
   col_leg = "black",
@@ -73,9 +74,11 @@ length of the row of parameter 'data' as default.}
 
 \item{ytitle}{A string of title of the y-axis. Set NULL as default.}
 
-\item{legend}{A logical value to decide to draw the color bar legend or not. 
+\item{drawleg}{A logical value to decide to draw the color bar legend or not. 
 Set TRUE as default.}
 
+\item{legend}{Deprecated. Use 'drawleg' instead.}
+
 \item{lab_legend}{A vector of labels indicating what is represented in each 
 category (i.e. triangle). Set the sequence from 1 to the length of 
 the categories (2 or 4).}
diff --git a/man/VizWeeklyClim.Rd b/man/VizWeeklyClim.Rd
index bba0005..c97e3f0 100644
--- a/man/VizWeeklyClim.Rd
+++ b/man/VizWeeklyClim.Rd
@@ -13,6 +13,7 @@ VizWeeklyClim(
   time_dim = "time",
   sdate_dim = "sdate",
   ylim = NULL,
+  toptitle = NULL,
   title = NULL,
   subtitle = NULL,
   ytitle = NULL,
@@ -66,7 +67,9 @@ The default value is 'sdate'.}
 Use NA to refer to the existing minimum or maximum. For more information, 
 see 'ggplot2' documentation of 'scale_y_continuous' parameter.}
 
-\item{title}{The text for the top title of the plot. It is NULL by default.}
+\item{toptitle}{The text for the top title of the plot. It is NULL by default.}
+
+\item{title}{Deprecated. Use 'toptitle' instead.}
 
 \item{subtitle}{The text for the subtitle of the plot. It is NULL bu default.}
 
@@ -113,7 +116,7 @@ data <- array(rnorm(49*20*3, 274), dim = c(time = 49, sdate = 20, member = 3))
 VizWeeklyClim(data = data, first_date = '2002-08-09', 
              last_date = '2002-09-15', ref_period = 2010:2019, 
              data_years = 2000:2019, time_dim = 'time', sdate_dim = 'sdate',
-             title = "Observed weekly means and climatology", 
+             toptitle = "Observed weekly means and climatology", 
              subtitle = "Target years: 2010 to 2019", 
              ytitle = paste0('tas', " (", "deg.C", ")"))
 
-- 
GitLab


From 66362d858de176b4f32a9a946364d70789a073e5 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Tue, 6 May 2025 16:52:12 +0200
Subject: [PATCH 61/72] fix typo in R/ColorBarDiscrete.R

---
 R/ColorBarDiscrete.R    | 2 +-
 man/ColorBarDiscrete.Rd | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/ColorBarDiscrete.R b/R/ColorBarDiscrete.R
index f44c0e0..302f52c 100644
--- a/R/ColorBarDiscrete.R
+++ b/R/ColorBarDiscrete.R
@@ -92,7 +92,7 @@
 #'  labels of the colour bar, usually to avoid too many decimal digits 
 #'  overflowing the figure region. This does not have effect over the labels 
 #'  provided in 'bar_extra_labels'. Takes 4 by default.
-#'@param label_digits. Deprecated. Use 'bar_label_digits' instead.
+#'@param label_digits Deprecated. Use 'bar_label_digits' instead.
 #'@param ... Arguments to be passed to the method. Only accepts the following 
 #'  graphical parameters:\cr adj ann ask bg bty cex.lab cex.main cex.sub cin 
 #'  col.axis col.lab col.main col.sub cra crt csi cxy err family fg fig fin 
diff --git a/man/ColorBarDiscrete.Rd b/man/ColorBarDiscrete.Rd
index 06bc118..3809bfd 100644
--- a/man/ColorBarDiscrete.Rd
+++ b/man/ColorBarDiscrete.Rd
@@ -134,6 +134,8 @@ labels of the colour bar, usually to avoid too many decimal digits
 overflowing the figure region. This does not have effect over the labels 
 provided in 'bar_extra_labels'. Takes 4 by default.}
 
+\item{label_digits}{Deprecated. Use 'bar_label_digits' instead.}
+
 \item{...}{Arguments to be passed to the method. Only accepts the following 
  graphical parameters:\cr adj ann ask bg bty cex.lab cex.main cex.sub cin 
  col.axis col.lab col.main col.sub cra crt csi cxy err family fg fig fin 
@@ -141,8 +143,6 @@ provided in 'bar_extra_labels'. Takes 4 by default.}
  lwd mai mex mfcol mfrow mfg mkh oma omd omi page pch pin plt pty smo srt 
  tck tcl usr xaxp xaxs xaxt xlog xpd yaxp yaxs yaxt ylbias ylog.\cr For more 
 information about the parameters see `par`.}
-
-\item{label_digits.}{Deprecated. Use 'bar_label_digits' instead.}
 }
 \value{
 \item{brks}{
-- 
GitLab


From 4ec0f9486e78676c925dfa68a2885d0d544c210f Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Tue, 6 May 2025 17:03:25 +0200
Subject: [PATCH 62/72] bugfix in 'bar_extra_margin' check in
 R/ColorBarDiscrete.R

---
 R/ColorBarDiscrete.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/ColorBarDiscrete.R b/R/ColorBarDiscrete.R
index 302f52c..3d7b572 100644
--- a/R/ColorBarDiscrete.R
+++ b/R/ColorBarDiscrete.R
@@ -365,7 +365,7 @@ ColorBarDiscrete <- function(brks = NULL, cols = NULL, vertical = TRUE,
     warning("The parameter 'extra_margin' is deprecated. Use 'bar_extra_margin' instead.")
     bar_extra_margin <- extra_margin
   }
-  if (!is.numeric(bar_extra_margin) || length(extra_margin) != 4) {
+  if (!is.numeric(bar_extra_margin) || length(bar_extra_margin) != 4) {
     stop("Parameter 'bar_extra_margin' must be a numeric vector of length 4.")
   }
 
-- 
GitLab


From ae01ec699870950166a8057535aaca95e85c1f25 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 14 May 2025 12:34:38 +0200
Subject: [PATCH 63/72] Update DESCRIPTION and NAMESPACE files

---
 DESCRIPTION | 15 ++++++++++-----
 NAMESPACE   |  1 +
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index e4d4332..f97e8a3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -5,10 +5,15 @@ Authors@R: c(
     person("BSC-CNS", role = c("aut", "cph")),
     person("An-Chi", "Ho", , "an.ho@bsc.es", role = c("aut", "cre")),
     person("Eva", "Rifà", , "eva.rifarovira@bsc.es", role = "ctb"))
-Description: This package is an R plotting package for climate science and services. 
-    It includes several functions to plot different kinds of maps, time series, 
-    scorecards, etc. Some functions are origined from packages "s2dv" and "CSTools" 
-    but with more consistent and integrated functinalities.
+    person("Victòria", "Agudetse", , "victoria.agudetse@bsc.es", role = "ctb")
+    person("Ariadna", "Batalla", , "ariadna.batalla@bsc.es", role = ("ctb", "cre"))
+    person("Núria", "Pérez-Zanón", , "nuria.perez@bsc.es, role = "ctb")
+    person("Nadia", "Milders", "Carlotta", "nadia.milders@bsc.es", role = "ctb")
+    person("Verónica", "Torralba", , "veronica.torralba@bsc.es", role = "ctb")
+Description: An R plotting package for climate science and services. Provides a 
+    set of functions for visualizing climate data, including maps, time series, 
+    scorecards and other diagnostics. Some functions are adapted from the "s2dv"
+    and "CSTools" packages, with more consistent and integrated functinalities.
 Depends:
     R (>= 3.6.0)
 Imports:
@@ -43,6 +48,6 @@ URL: https://earth.bsc.es/gitlab/es/esviz/
 BugReports: https://earth.bsc.es/gitlab/es/esviz/-/issues
 SystemRequirements: GDAL (>= 2.0.1), GEOS (>= 3.4.0), PROJ (>= 4.8.0)
 Encoding: UTF-8
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Config/testthat/edition: 3
 LazyData: true
diff --git a/NAMESPACE b/NAMESPACE
index 254964c..b821438 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -4,6 +4,7 @@ export(ClimColors)
 export(ClimPalette)
 export(ColorBarContinuous)
 export(ColorBarDiscrete)
+export(Hatching)
 export(ShapeToMask)
 export(VizCombinedMap)
 export(VizEquiMap)
-- 
GitLab


From a45134016ce8dbf1039587d967fcc87f42c121ce Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Wed, 14 May 2025 12:48:04 +0200
Subject: [PATCH 64/72] DESCRIPTION typo fix

---
 DESCRIPTION | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f97e8a3..f90e502 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,13 +3,13 @@ Title: Plotting Functions for Climate Science and Services
 Version: 0.0.1
 Authors@R: c(
     person("BSC-CNS", role = c("aut", "cph")),
-    person("An-Chi", "Ho", , "an.ho@bsc.es", role = c("aut", "cre")),
-    person("Eva", "Rifà", , "eva.rifarovira@bsc.es", role = "ctb"))
-    person("Victòria", "Agudetse", , "victoria.agudetse@bsc.es", role = "ctb")
-    person("Ariadna", "Batalla", , "ariadna.batalla@bsc.es", role = ("ctb", "cre"))
-    person("Núria", "Pérez-Zanón", , "nuria.perez@bsc.es, role = "ctb")
-    person("Nadia", "Milders", "Carlotta", "nadia.milders@bsc.es", role = "ctb")
-    person("Verónica", "Torralba", , "veronica.torralba@bsc.es", role = "ctb")
+    person("An-Chi", "Ho", , "an.ho@bsc.es", role = "aut"),
+    person("Eva", "Rifà", , "eva.rifarovira@bsc.es", role = "ctb"),
+    person("Victòria", "Agudetse", , "victoria.agudetse@bsc.es", role = "ctb"),
+    person("Ariadna", "Batalla", , "ariadna.batalla@bsc.es", role = c("ctb", "cre")),
+    person("Núria", "Pérez-Zanón", , "nuria.perez@bsc.es", role = "ctb"),
+    person("Nadia", "Milders", , "nadia.milders@bsc.es", role = "ctb"),
+    person("Verónica", "Torralba", , "veronica.torralba@bsc.es", role = "ctb"))
 Description: An R plotting package for climate science and services. Provides a 
     set of functions for visualizing climate data, including maps, time series, 
     scorecards and other diagnostics. Some functions are adapted from the "s2dv"
-- 
GitLab


From bb048da5900f159a8759a51f0100033d025d2629 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 16 May 2025 12:25:44 +0200
Subject: [PATCH 65/72] Revert commit that changed 'plot_legend' for 'drawleg'
 in R/VizScorecard.R

---
 R/VizScorecard.R | 19 +++++++------------
 1 file changed, 7 insertions(+), 12 deletions(-)

diff --git a/R/VizScorecard.R b/R/VizScorecard.R
index a4a89fe..ab2e415 100644
--- a/R/VizScorecard.R
+++ b/R/VizScorecard.R
@@ -45,9 +45,8 @@
 #'  be given as input if the 'legend_dims' require different breaks. This  
 #'  parameter is required even if the legend is not plotted, to define the 
 #'  colors in the scorecard table. It is set as NULL by default.
-#'@param drawleg A logical value to determine if the legend is plotted. It 
+#'@param plot_legend A logical value to determine if the legend is plotted. It 
 #'  is set as TRUE by default.
-#'@param plot_legend Deprecated. Use 'drawleg' instead.
 #'@param label_scale A numeric value to define the size of the legend labels. 
 #'  It is set as 1.4 by default.
 #'@param legend_width A numeric value to define the width of the legend bars. By 
@@ -118,7 +117,7 @@ VizScorecard <- function(data, sign = NULL, row_dim = 'region',
                          row_title = NULL, subrow_title = NULL, 
                          col_title = NULL, table_title = NULL, 
                          table_subtitle = NULL, legend_breaks = NULL, 
-                         drawleg = TRUE, plot_legend = NULL, label_scale = 1.4, 
+                         plot_legend = TRUE, label_scale = 1.4, 
                          legend_width = NULL, legend_height = 50, 
                          palette = NULL, colorunder = NULL, colorsup = NULL,
                          round_decimal = 2, font_size = 1.1,
@@ -269,13 +268,9 @@ VizScorecard <- function(data, sign = NULL, row_dim = 'region',
   } else {
     stop("Parameter 'legend_breaks' must be a numeric vector, a list or NULL.")
   }
-  # Check drawleg
-  if (missing(drawleg) && !missing(plot_legend)) {
-    warning("The parameter 'plot_legend' is deprecated. Use 'drawleg' instead.")
-    drawleg <- plot_legend
-  }
-  if (!inherits(drawleg, 'logical')) {
-    stop("Parameter 'drawleg' must be a logical value.")
+  # Check plot_legend
+  if (!inherits(plot_legend, 'logical')) {
+    stop("Parameter 'plot_legend' must be a logical value.")
   }
   # Check label_scale
   if (any(!is.numeric(label_scale), length(label_scale) != 1)) {
@@ -513,7 +508,7 @@ VizScorecard <- function(data, sign = NULL, row_dim = 'region',
                 column_spec(n_columns, border_right = "2px solid black") %>%
                 row_spec(seq(from = 0, to = n_subrow_names * n_row_names, by = n_subrow_names), 
                          extra_css = "border-bottom: 2px solid black", hline_after = TRUE)
-  if (drawleg == TRUE) {
+  if (plot_legend == TRUE) {
     # Save the scorecard (without legend)
     save_kable(table_html, file = paste0(fileout, '_tmpScorecard.png'), vheight = 1)
     
@@ -537,7 +532,7 @@ VizScorecard <- function(data, sign = NULL, row_dim = 'region',
     # Remove temporary scorecard table
     unlink(paste0(fileout, '_tmpScorecard*.png'))
   }
-  if (drawleg == FALSE) {
+  if (plot_legend == FALSE) {
     save_kable(table_html, file = fileout)
   } 
 }
-- 
GitLab


From 6250b918508d6f0ef888af0c77336505b6cc357d Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 16 May 2025 12:42:51 +0200
Subject: [PATCH 66/72] Add 'col_title' definition to R/VizScorecard.R
 documentation

---
 R/VizScorecard.R | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/R/VizScorecard.R b/R/VizScorecard.R
index ab2e415..85b06f4 100644
--- a/R/VizScorecard.R
+++ b/R/VizScorecard.R
@@ -35,6 +35,8 @@
 #'  as NULL by default.
 #'@param subrow_title A character string for the title of the sub-row names. It 
 #'  is set as NULL by default.
+#'@param col_title A character string for the title of the column names. It is 
+#'  set as NULL by default.
 #'@param table_title A character string for the title of the plot. It is set as 
 #'  NULL by default.
 #'@param table_subtitle A character string for the sub-title of the plot. It is 
-- 
GitLab


From a0b8b39efbfc2382073ca56dc84dfd323e4845f3 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 16 May 2025 13:00:46 +0200
Subject: [PATCH 67/72] Reverse 'drawleg' commit
 tests/testthat/test-VizScorecard.R

---
 tests/testthat/test-VizScorecard.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/testthat/test-VizScorecard.R b/tests/testthat/test-VizScorecard.R
index 5247314..4c185e7 100644
--- a/tests/testthat/test-VizScorecard.R
+++ b/tests/testthat/test-VizScorecard.R
@@ -22,7 +22,7 @@ test_that("1. Test input", {
   )
   # check sign
   expect_error(
-    VizScorecard(data = data, sign = 1, drawleg = TRUE),
+    VizScorecard(data = data, sign = 1, plot_legend = TRUE),
     "Parameter 'sign' must be a boolean array or NULL."
   )
   expect_error(
@@ -146,10 +146,10 @@ test_that("1. Test input", {
     paste0("Parameter 'palette' must be provided when 'legend_breaks' exceed ", 
            "the length of 11.")
   )
-  # Check drawleg
+  # Check plot_legend
   expect_error(
-    VizScorecard(data, drawleg = 'a'),
-    "Parameter 'drawleg' must be a logical value."
+    VizScorecard(data, plot_legend = 'a'),
+    "Parameter 'plot_legend' must be a logical value."
   )
   # Check label_scale
   expect_error(
@@ -297,7 +297,7 @@ test_that("1. Test input", {
 #              col_title = 'Start date', 
 #              table_title = "Temperature of ECMWF System 5", 
 #              table_subtitle = "(Ref: ERA5 1994-2016)",
-#              drawleg = TRUE),
+#              plot_legend = TRUE),
 #     name = 'VizScorecard_1a.png' 
 #   )
 # })
\ No newline at end of file
-- 
GitLab


From 6f9faa2a11b4a5e2d3a1ddf257ee70b0fc660c2f Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 16 May 2025 15:14:23 +0200
Subject: [PATCH 68/72] Update parameters in vignettes [1-4]

---
 vignettes/map_proj_equi.Rmd     | 8 ++++----
 vignettes/map_proj_robinson.Rmd | 2 +-
 2 files changed, 5 insertions(+), 5 deletions(-)

diff --git a/vignettes/map_proj_equi.Rmd b/vignettes/map_proj_equi.Rmd
index 9bef222..4d8ba19 100644
--- a/vignettes/map_proj_equi.Rmd
+++ b/vignettes/map_proj_equi.Rmd
@@ -18,7 +18,7 @@ In this vignette, we will go through the functions that plot the maps with equid
 `VizEquiMap()`, `VizAnimateMap()`, `VizLayout()`.
 
 Some traits of these plotting functions:
- - Expect a data matrix in the parameter `var` of dimensions 
+ - Expect a data matrix in the parameter `data` of dimensions 
 `c(n. of latitudes, n. of longitudes)`, `lat` with a vector with the latitudes 
 of the centers of the grid cells and `lon`, a vector with the longitudes. 
  - The N colors to paint the grid cells with (via `cols`) as well as the N +
@@ -201,7 +201,7 @@ In the following example, we plot the ensemble-mean climatology at each forecast
 
 ```r
 VizLayout(fun = VizEquiMap, plot_dims = c('lat', 'lon'),
-          var = exp_clim, lon = lons, lat = lats,
+          data = exp_clim, lon = lons, lat = lats,
           units = 'K', title_scale = 0.8,
           toptitle = "SEAS5 tas climatology (1997-2016)",
            titles = paste0("ftime ", seq_len(dim(exp_clim)[1]), ": ", 
@@ -235,12 +235,12 @@ args <- list(
        units = 'K', units_scale = 2),
        list(), list(),
        list(monini = 11, freq = 12, ytitle = "K/year",  limits = c(-0.02, 0.1), 
-            listexp = c('SEAS5', 'Meteo-France System 7'), sizetit = 0.5, leg = F)
+            listexp = c('SEAS5', 'Meteo-France System 7'), title_scale = 0.5, leg = F)
 )
 
 VizLayout(fun = c('VizEquiMap', 'plot', 'plot', 'VizVsLTime'),
           plot_dims = list(c('lat', 'lon'), 1, 1, 1:3),
-          var = list(exp_clim, array(1:10), array(10:1), input_trend),
+          data = list(exp_clim, array(1:10), array(10:1), input_trend),
           special_args = args, drawleg = 'E',
           brks = brks, cols = cols, 
           col_inf = col_inf, col_sup = col_sup, triangle_ends = c(T, T),
diff --git a/vignettes/map_proj_robinson.Rmd b/vignettes/map_proj_robinson.Rmd
index 6db8f21..a63b997 100644
--- a/vignettes/map_proj_robinson.Rmd
+++ b/vignettes/map_proj_robinson.Rmd
@@ -61,7 +61,7 @@ The plot style can be either "point" or "polygen", which is more time-consuming.
 ```r
 VizRobinson(rmsss$rmsss[1, , ], lon = lons, lat = lats,
             target_proj = "ESRI:54030",
-            dots = !rmsss$sign[1, , ], dots_size = 0.7,
+            dots = !rmsss$sign[1, , ], dot_size = 0.7,
             brks = brks, cols = cols, col_inf = col_inf, 
             style = 'point', drawleg = 'bar',
             toptitle = "RMSSS SEAS5-ERA5 monthly tas anomaly Nov 2011-2016", 
-- 
GitLab


From d030673b94fc19c8e03cb5d36c5b3fdbb1e458a8 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 30 May 2025 11:04:11 +0200
Subject: [PATCH 69/72] Update parameters in vignettes [5-8]

---
 vignettes/map_proj_stereo.Rmd             |  2 +-
 vignettes/multimodel_skill_assessment.Rmd |  6 ++---
 vignettes/time_series.Rmd                 | 28 +++++++++++------------
 3 files changed, 18 insertions(+), 18 deletions(-)

diff --git a/vignettes/map_proj_stereo.Rmd b/vignettes/map_proj_stereo.Rmd
index 5100da4..d654e56 100644
--- a/vignettes/map_proj_stereo.Rmd
+++ b/vignettes/map_proj_stereo.Rmd
@@ -123,7 +123,7 @@ VizAnimateMap(exp1_clim, equi = FALSE,
               filled.continents = FALSE, monini = 11,
               toptitle = "SEAS5 tas climatology (Nov. 2011-2016), North Pole",
               brks = brks, cols = cols, col_sup = col_sup, triangle_ends = c(F, T), 
-              units = "K", sizetit = 0.5,
+              units = "K", title_scale = 0.5,
               fileout = 'map_stereo_anim_clim_exp1_np.gif')
 
 ```
diff --git a/vignettes/multimodel_skill_assessment.Rmd b/vignettes/multimodel_skill_assessment.Rmd
index e0b16e0..fa0e0c0 100644
--- a/vignettes/multimodel_skill_assessment.Rmd
+++ b/vignettes/multimodel_skill_assessment.Rmd
@@ -195,7 +195,7 @@ To obtain a spatial plot with a scale from -1 to 1 value of correlation for the
 ```r
 VizCombinedMap(AnomDJF$data$corr[,1,1,,], lon = Lon, lat = Lat, map_select_fun = max,
                display_range = c(0, 1), map_dim = 'nexp',
-               legend_scale = 0.5, brks = 11,
+               bar_label_scale = 0.5, brks = 11,
                cols = list(c('white', 'black'),
                            c('white', 'darkblue'),
                            c('white', 'darkred'),
@@ -225,7 +225,7 @@ The following lines are necessary to obtain the plot which visualizes the best m
 ```r
 VizCombinedMap(AnomDJF$data$rms[,1,1,,], lon = Lon, lat = Lat, map_select_fun = min,
                display_range = c(0, ceiling(max(abs(AnomDJF$data$rms)))), map_dim = 'nexp',
-               legend_scale = 0.5, brks = 11,
+               bar_label_scale = 0.5, brks = 11,
                cols = list(c('black', 'white'),
                            c('darkblue', 'white'),
                            c('darkred', 'white'),
@@ -253,7 +253,7 @@ VizCombinedMap(AnomDJF$data$rmsss[,1,1,,], lon = Lon, lat = Lat,
                map_select_fun = function(x) {x[which.min(abs(x - 1))]},
                display_range = c(0, 
                                  ceiling(max(abs(AnomDJF$data$rmsss)))), map_dim = 'nexp',
-               legend_scale = 0.5, brks = 11,
+               bar_label_scale = 0.5, brks = 11,
                cols = list(c('white', 'black'),
                            c('white', 'darkblue'),
                            c('white', 'darkred'),
diff --git a/vignettes/time_series.Rmd b/vignettes/time_series.Rmd
index e6d6a0c..9ec0b84 100644
--- a/vignettes/time_series.Rmd
+++ b/vignettes/time_series.Rmd
@@ -35,7 +35,7 @@ parameter `freq`.
 file name of which you have to provide to the `fileout` parameter. Can plot in
 a presentation oriented style or in a paper oriented style, adjustable with the
 parameter `biglab`.
- - Can plot a legend automatically, adjustable via the parameters `leg`, 
+ - Can plot a legend automatically, adjustable via the parameters `drawleg`, 
 `listexp` and `listobs`/`listvar` in `VizVsLTime()`, `Viz2VarVsLtime()` and 
 `VizClim()` or via the parameter `legends` in `VizAno()` and `VizACC()`.
  - Accept any additional parameters via the parameter `...` to be sent to 
@@ -213,8 +213,8 @@ input_reg[1, 4, ] <- reg_ano$regression[1, ]
 
 VizVsLTime(input_reg,
            toptitle = "Regression of System5c3s and Meteo-France System 7, Europe",
-           ytitle = "K/year", sizetit = 0.7,
-           monini = 11, freq = 1, leg = FALSE,
+           ytitle = "K/year", title_scale = 0.7,
+           monini = 11, freq = 1, drawleg = FALSE,
            fileout = 'ts_regression_exp1_exp2.png')
 ```
 <img src="./Figures/ts_regression_exp1_exp2.png" width="600" />
@@ -237,7 +237,7 @@ names(spr_stats) <- names(spread)
 for (i_plot in seq_len(length(spread))) {
   inputs <- list(spread[[i_plot]], 
                  toptitle = paste0(spr_stats[i_plot], " across members and start dates, Europe"),
-                 ytitle = "K", sizetit = 0.7,
+                 ytitle = "K", title_scale = 0.7,
                  monini = 11, freq = 1,
                  listexp = c('SEAS5', 'Meteo-France System 7'),
                  fileout = paste0('ts_', names(spr_stats)[i_plot], '_exp1_exp2.png'))
@@ -271,7 +271,7 @@ input_cor[, 4, ] <- corr_ano$p.val[, 1, ]
 
 VizVsLTime(input_cor,
            toptitle = "Time correlation with ERA5, over Europe",
-           ytitle = "K", sizetit = 0.7,
+           ytitle = "K", title_scale = 0.7,
            monini = 11, freq = 1,
            listexp = c('SEAS5', 'Meteo-France System 7'),
            fileout = 'ts_corr_exp1_exp2_obs.png')
@@ -290,7 +290,7 @@ input_rms[, 3, ] <- rms_ano$conf.upper[, 1, ]
 
 VizVsLTime(input_rms,
            toptitle = "RMSE against ERA5, over Europe",
-           ytitle = "K", sizetit = 0.7,
+           ytitle = "K", title_scale = 0.7,
            monini = 11, freq = 1,
            listexp = c('SEAS5', 'Meteo-France System 7'),
            fileout = 'ts_rms_exp1_exp2_obs.png')
@@ -308,7 +308,7 @@ input_rmsss[, 1, 4, ] <- rmsss$p.val
 
 VizVsLTime(input_rmsss,
            toptitle = "RMSSS against ERA5 , Europe",
-           ytitle = "K", sizetit = 0.7,
+           ytitle = "K", title_scale = 0.7,
            monini = 11, freq = 1, siglev = TRUE,
            listexp = c('SEAS5', 'Meteo-France System 7'),
            fileout = 'ts_rmsss_exp1_exp2_obs.png')
@@ -332,8 +332,8 @@ input_ratio_rms[1, 4, ] <- ratio_rms$p.val
 
 VizVsLTime(input_ratio_rms,
             toptitle = "RMSE Ratio of SEAS5 and Meteo-France System 7 against ERA5, Europe",
-            ytitle = "K", sizetit = 0.6,
-            monini = 11, freq = 1, siglev = TRUE, leg = FALSE,
+            ytitle = "K", title_scale = 0.6,
+            monini = 11, freq = 1, siglev = TRUE, drawleg = FALSE,
             fileout = 'ts_ratiorms_exp1_exp2_obs.png')
 ```
 <img src="./Figures/ts_ratiorms_exp1_exp2_obs.png" width="600" />
@@ -354,7 +354,7 @@ input_ratio_sdrms[, 1, 4, ] <- ratio_sdrms$p.val
 VizVsLTime(input_ratio_sdrms,
            toptitle = "S. dev. over members and s. dates / RMSE, 
            Europe",
-           ytitle = "K", sizetit = 0.7,
+           ytitle = "K", title_scale = 0.7,
            monini = 11, freq = 1, siglev = TRUE,
            listexp = c('SEAS5', 'Meteo-France System 7'),
            fileout = 'ts_ratiosdrms_exp1_exp2_obs.png')
@@ -382,7 +382,7 @@ input_ratio_sdrms[1, , 4, ] <- ratio_sdrms$p.val
 
 VizVsLTime(input_ratio_sdrms,
            toptitle = "S. dev. over members and s. dates / RMSE, Europe",
-           ytitle = "K", sizetit = 0.7,
+           ytitle = "K", title_scale = 0.7,
            monini = 11, freq = 1, siglev = TRUE,
            listexp = c('SEAS5'),
            listobs = c('ERA5', 'ERA5 with random turbulance'),
@@ -403,7 +403,7 @@ input_eno[, 2, ] <- eno
 
 VizVsLTime(input_eno,
             toptitle = "Effective n. of independent data, Europe",
-            sizetit = 0.7,
+            title_scale = 0.7,
             monini = 11, freq = 1, siglev = FALSE, show_conf = FALSE,
             listexp = c('SEAS5', 'Meteo-France System 7'),
             fileout = 'ts_eno_exp1_exp2.png')
@@ -428,7 +428,7 @@ We put correlation and RMS from the previous sections in one plot.
 ```r
 Viz2VarsVsLTime(input_cor[, 1:3, ], input_rms,
                 toptitle = "Time correlation and RMSE with ERA5, Europe",
-                ytitle = "K", sizetit = 0.7,
+                ytitle = "K", title_scale = 0.7,
                 monini = 11, freq = 1, limits = c(-0.8, 2.2),
                 listexp = c('SEAS5', 'Meteo-France System 7'),
                 listvars = c('Corr', 'RMSE'),
@@ -480,7 +480,7 @@ input_acc[, , , , 4] <- acc$p.val
 
 VizACC(input_acc, sdates, 
        toptitle = "Spatial anomaly corr. coeff. with ERA5 over Europe",
-       ytitle = "K", sizetit = 0.7, freq = 1, limits = c(-0.8, 1.6),
+       ytitle = "K", title_scale = 0.7, freq = 1, limits = c(-0.8, 1.6),
        legends = c('SEAS5', 'Meteo-France System 7'),
        fileout = 'ts_acc_exp1_exp2_obs.png')
 ```
-- 
GitLab


From 7a2820befc586ef85b71419b80c674fec418afe8 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Tue, 10 Jun 2025 12:44:28 +0200
Subject: [PATCH 70/72] More parameter standarization updates

---
 R/VizCombinedMap.R                  |  4 +-
 R/VizEquiMap.R                      | 67 +++++++++++-----------
 R/VizForecastPDF.R                  |  8 ++-
 man/VizCombinedMap.Rd               |  4 +-
 man/VizEquiMap.Rd                   | 86 ++++++++++++++---------------
 man/VizForecastPDF.Rd               | 40 +++++++++++---
 man/VizScorecard.Rd                 | 10 ++--
 tests/testthat/test-VizWeeklyClim.R |  2 +-
 8 files changed, 124 insertions(+), 97 deletions(-)

diff --git a/R/VizCombinedMap.R b/R/VizCombinedMap.R
index 4f176a4..79e91a1 100644
--- a/R/VizCombinedMap.R
+++ b/R/VizCombinedMap.R
@@ -76,9 +76,9 @@
 #'@param fileout File where to save the plot. If not specified (default) a 
 #'  graphics device will pop up. Extensions allowed: eps/ps, jpeg, png, pdf, bmp 
 #'  and tiff
-#'@param width File width, in the units specified in the parameter size_units 
+#'@param width File width, in the units specified in the parameter 'size_units' 
 #'  (inches by default). Takes 8 by default.
-#'@param height File height, in the units specified in the parameter size_units 
+#'@param height File height, in the units specified in the parameter 'size_units' 
 #'  (inches by default). Takes 5 by default.
 #'@param size_units Units of the size of the device (file or window) to plot in. 
 #'  Inches ('in') by default. See ?Devices and the creator function of the 
diff --git a/R/VizEquiMap.R b/R/VizEquiMap.R
index 8b305f2..a905818 100644
--- a/R/VizEquiMap.R
+++ b/R/VizEquiMap.R
@@ -185,6 +185,31 @@
 #'@param vertical TRUE/FALSE for vertical/horizontal colour bar. Default is 
 #'  FALSE. Parameters 'width' and 'height' might need to be modified to
 #'  accommodate the vertical colour bar.
+#'@param include_lower_boundary Logical value indicating whether to include
+#'  the minimum value of the field. Takes TRUE by default.
+#'@param include_upper_boundary Logical value indicating whether to include
+#'  the maximum value of the field. Takes TRUE by default.
+#'@param hatching_mask Logical or binary (0/1) array with two named dimensions:
+#' c(latitude, longitude). Hatching is applied to grid cells where
+#' 'hatching_mask' is TRUE (or 1). Arrays with dimensions c(longitude, latitude)
+#' are also accepted, but the resulting hatching may appear transposed. To
+#' ensure correct alignment with the map, provide 'data'. The function will
+#' compare the dimension order of 'hatching_mask' and 'data', and automatically
+#' transpose 'hatching_mask' if the latitude and longitude dimensions appear to
+#' be reversed.
+#'@param hatching_density The density of shading lines, in lines per inch. A
+#'  zero value of density means no shading nor filling, whereas negative values
+#'  and NA suppress shading (and so allow color filling). NULL means that no
+#'  shading lines are drawn. Default is 10.
+#'@param hatching_angle The slope of shading lines, given as an angle in degrees
+#'  (counter-clockwise). Default is 45.
+#'@param hatching_color Color of the hatching lines. Default is
+#'  \code{"#252525"}.
+#'@param hatching_lwd The line width, a positive number. The interpretation is
+#'  device-specific, and some devices do not implement line widths less than
+#'  one. Default is 0.5.
+#'@param hatching_cross A logical value indicating crosshatching. If TRUE, adds
+#'  a second set of lines in the opposite angle. Default is FALSE.
 #'@param boxlim Limits of a box to be added to the plot, in degrees: 
 #'  c(x1, y1, x2, y2). A list with multiple box specifications can also be 
 #'  provided.
@@ -204,40 +229,15 @@
 #'@param fileout File where to save the plot. If not specified (default) a 
 #'  graphics device will pop up. Extensions allowed: eps/ps, jpeg, png, pdf, 
 #'  bmp and tiff.
-#'@param width File width, in the units specified in the parameter size_units 
+#'@param width File width, in the units specified in the parameter 'size_units' 
 #'  (inches by default). Takes 8 by default.
 #'@param height File height, in the units specified in the parameter 
-#'  size_units (inches by default). Takes 5 by default.
+#'  'size_units' (inches by default). Takes 5 by default.
 #'@param size_units Units of the size of the device (file or window) to plot 
 #'  in. Inches ('in') by default. See ?Devices and the creator function of 
 #'  the corresponding device.
 #'@param res Resolution of the device (file or window) to plot in. See 
 #'  ?Devices and the creator function of the corresponding device.
-#'@param include_lower_boundary Logical value indicating whether to include
-#'  the minimum value of the field. Takes TRUE by default.
-#'@param include_upper_boundary Logical value indicating whether to include
-#'  the maximum value of the field. Takes TRUE by default.
-#'@param hatching_mask Logical or binary (0/1) array with two named dimensions:
-#' c(latitude, longitude). Hatching is applied to grid cells where
-#' 'hatching_mask' is TRUE (or 1). Arrays with dimensions c(longitude, latitude)
-#' are also accepted, but the resulting hatching may appear transposed. To
-#' ensure correct alignment with the map, provide 'data'. The function will
-#' compare the dimension order of 'hatching_mask' and 'data', and automatically
-#' transpose 'hatching_mask' if the latitude and longitude dimensions appear to
-#' be reversed.
-#'@param hatching_density The density of shading lines, in lines per inch. A
-#'  zero value of density means no shading nor filling, whereas negative values
-#'  and NA suppress shading (and so allow color filling). NULL means that no
-#'  shading lines are drawn. Default is 10.
-#'@param hatching_angle The slope of shading lines, given as an angle in degrees
-#'  (counter-clockwise). Default is 45.
-#'@param hatching_color Color of the hatching lines. Default is
-#'  \code{"#252525"}.
-#'@param hatching_lwd The line width, a positive number. The interpretation is
-#'  device-specific, and some devices do not implement line widths less than
-#'  one. Default is 0.5.
-#'@param hatching_cross A logical value indicating crosshatching. If TRUE, adds
-#'  a second set of lines in the opposite angle. Default is FALSE.
 #'@param \dots Arguments to be passed to the method. Only accepts the following 
 #'  graphical parameters:\cr
 #'  adj ann ask bg bty cex.sub cin col.axis col.lab col.main col.sub cra crt 
@@ -309,16 +309,17 @@ VizEquiMap <- function(data, lon, lat, varu = NULL, varv = NULL,
                        draw_separators = FALSE, triangle_ends_scale = 1, 
                        bar_label_digits = 4, bar_label_scale = 1, 
                        units_scale = 1, bar_tick_scale = 1, 
-                       bar_extra_margin = rep(0, 4),
+                       bar_extra_margin = rep(0, 4), 
+                       include_lower_boundary = TRUE,
+                       include_upper_boundary = TRUE, hatching_mask = NULL,
+                       hatching_density = 10, hatching_angle = 45,
+                       hatching_color = "#252525", hatching_lwd = 0.5,
+                       hatching_cross = FALSE,
                        boxlim = NULL, boxcol = 'purple2', boxlwd = 5, 
                        margin_scale = rep(1, 4), title_scale = 1, 
                        caption_size = 0.8, numbfig = NULL, fileout = NULL, 
                        width = 8, height = 5, size_units = 'in', 
-                       res = 100, include_lower_boundary = TRUE,
-                       include_upper_boundary = TRUE, hatching_mask = NULL,
-                       hatching_density = 10, hatching_angle = 45,
-                       hatching_color = "#252525", hatching_lwd = 0.5,
-                       hatching_cross = FALSE, var = NULL, ...) {
+                       res = 100, var = NULL, ...) {
   # Process the user graphical parameters that may be passed in the call
   ## Graphical parameters to exclude
   excludedArgs <- c("cex", "cex.axis", "cex.lab", "cex.main", "col", "din", "fig", "fin", "lab", "las", "lty", "lwd", "mai", "mar", "mgp", "new", "oma", "ps", "tck")
diff --git a/R/VizForecastPDF.R b/R/VizForecastPDF.R
index e7c35d3..9f30162 100644
--- a/R/VizForecastPDF.R
+++ b/R/VizForecastPDF.R
@@ -40,7 +40,11 @@
 #'  \code{'hydro'} for yellow/gray/blue (suitable for precipitation and 
 #'  inflows) or the \code{"vitigeoss"} color set.
 #'@param memb_dim A character string indicating the name of the member 
-#'  dimension.
+#'  dimension
+#'@param width File width, in the units specified in the parameter size_units 
+#'  (inches by default). Takes 8 by default.
+#'@param height File height, in the units specified in the parameter 
+#'  size_units (inches by default). Takes 5 by default.
 #'@param fileout (optional) A filename (pdf, png...) where the plot will be 
 #'  saved. (Default: the plot is not saved).
 #'@param plotfile Deprecated. Use 'fileout' instead.
@@ -75,7 +79,7 @@ VizForecastPDF <- function(fcst, tercile.limits, extreme.limits = NULL,
                            add.ensmemb = c("above", "below", "no"), 
                            color.set = c("ggplot", "s2s4e", "hydro", "vitigeoss"), 
                            memb_dim = 'member', 
-                           height = 5, width = 6, res = 300, fileout = NULL,
+                           width = 6, height = 5, res = 300, fileout = NULL,
                            plotfile = NULL) {
   value <- init <- extremes <- x <- ymin <- ymax <- tercile <- NULL
   y <- xend <- yend <- yjitter <- MLT <- lab.pos <- NULL
diff --git a/man/VizCombinedMap.Rd b/man/VizCombinedMap.Rd
index 0e44027..d6278fe 100644
--- a/man/VizCombinedMap.Rd
+++ b/man/VizCombinedMap.Rd
@@ -132,10 +132,10 @@ are margin lines. The default values are c(2, 0, 2, 0).}
 graphics device will pop up. Extensions allowed: eps/ps, jpeg, png, pdf, bmp 
 and tiff}
 
-\item{width}{File width, in the units specified in the parameter size_units 
+\item{width}{File width, in the units specified in the parameter 'size_units' 
 (inches by default). Takes 8 by default.}
 
-\item{height}{File height, in the units specified in the parameter size_units 
+\item{height}{File height, in the units specified in the parameter 'size_units' 
 (inches by default). Takes 5 by default.}
 
 \item{size_units}{Units of the size of the device (file or window) to plot in. 
diff --git a/man/VizEquiMap.Rd b/man/VizEquiMap.Rd
index 397fc1c..90f44eb 100644
--- a/man/VizEquiMap.Rd
+++ b/man/VizEquiMap.Rd
@@ -75,6 +75,14 @@ VizEquiMap(
   units_scale = 1,
   bar_tick_scale = 1,
   bar_extra_margin = rep(0, 4),
+  include_lower_boundary = TRUE,
+  include_upper_boundary = TRUE,
+  hatching_mask = NULL,
+  hatching_density = 10,
+  hatching_angle = 45,
+  hatching_color = "#252525",
+  hatching_lwd = 0.5,
+  hatching_cross = FALSE,
   boxlim = NULL,
   boxcol = "purple2",
   boxlwd = 5,
@@ -87,14 +95,6 @@ VizEquiMap(
   height = 5,
   size_units = "in",
   res = 100,
-  include_lower_boundary = TRUE,
-  include_upper_boundary = TRUE,
-  hatching_mask = NULL,
-  hatching_density = 10,
-  hatching_angle = 45,
-  hatching_color = "#252525",
-  hatching_lwd = 0.5,
-  hatching_cross = FALSE,
   var = NULL,
   ...
 )
@@ -331,6 +331,39 @@ parameters to control the visual aspect of the drawn colour bar
 parameters to control the visual aspect of the drawn colour bar (3/3). 
 See ?ColorBar for a full explanation.}
 
+\item{include_lower_boundary}{Logical value indicating whether to include
+the minimum value of the field. Takes TRUE by default.}
+
+\item{include_upper_boundary}{Logical value indicating whether to include
+the maximum value of the field. Takes TRUE by default.}
+
+\item{hatching_mask}{Logical or binary (0/1) array with two named dimensions:
+c(latitude, longitude). Hatching is applied to grid cells where
+'hatching_mask' is TRUE (or 1). Arrays with dimensions c(longitude, latitude)
+are also accepted, but the resulting hatching may appear transposed. To
+ensure correct alignment with the map, provide 'data'. The function will
+compare the dimension order of 'hatching_mask' and 'data', and automatically
+transpose 'hatching_mask' if the latitude and longitude dimensions appear to
+be reversed.}
+
+\item{hatching_density}{The density of shading lines, in lines per inch. A
+zero value of density means no shading nor filling, whereas negative values
+and NA suppress shading (and so allow color filling). NULL means that no
+shading lines are drawn. Default is 10.}
+
+\item{hatching_angle}{The slope of shading lines, given as an angle in degrees
+(counter-clockwise). Default is 45.}
+
+\item{hatching_color}{Color of the hatching lines. Default is
+\code{"#252525"}.}
+
+\item{hatching_lwd}{The line width, a positive number. The interpretation is
+device-specific, and some devices do not implement line widths less than
+one. Default is 0.5.}
+
+\item{hatching_cross}{A logical value indicating crosshatching. If TRUE, adds
+a second set of lines in the opposite angle. Default is FALSE.}
+
 \item{boxlim}{Limits of a box to be added to the plot, in degrees: 
 c(x1, y1, x2, y2). A list with multiple box specifications can also be 
 provided.}
@@ -358,11 +391,11 @@ axe labels, ticks, thinner lines, ... Defaults to 1.}
 graphics device will pop up. Extensions allowed: eps/ps, jpeg, png, pdf, 
 bmp and tiff.}
 
-\item{width}{File width, in the units specified in the parameter size_units 
+\item{width}{File width, in the units specified in the parameter 'size_units' 
 (inches by default). Takes 8 by default.}
 
 \item{height}{File height, in the units specified in the parameter 
-size_units (inches by default). Takes 5 by default.}
+'size_units' (inches by default). Takes 5 by default.}
 
 \item{size_units}{Units of the size of the device (file or window) to plot 
 in. Inches ('in') by default. See ?Devices and the creator function of 
@@ -371,39 +404,6 @@ the corresponding device.}
 \item{res}{Resolution of the device (file or window) to plot in. See 
 ?Devices and the creator function of the corresponding device.}
 
-\item{include_lower_boundary}{Logical value indicating whether to include
-the minimum value of the field. Takes TRUE by default.}
-
-\item{include_upper_boundary}{Logical value indicating whether to include
-the maximum value of the field. Takes TRUE by default.}
-
-\item{hatching_mask}{Logical or binary (0/1) array with two named dimensions:
-c(latitude, longitude). Hatching is applied to grid cells where
-'hatching_mask' is TRUE (or 1). Arrays with dimensions c(longitude, latitude)
-are also accepted, but the resulting hatching may appear transposed. To
-ensure correct alignment with the map, provide 'data'. The function will
-compare the dimension order of 'hatching_mask' and 'data', and automatically
-transpose 'hatching_mask' if the latitude and longitude dimensions appear to
-be reversed.}
-
-\item{hatching_density}{The density of shading lines, in lines per inch. A
-zero value of density means no shading nor filling, whereas negative values
-and NA suppress shading (and so allow color filling). NULL means that no
-shading lines are drawn. Default is 10.}
-
-\item{hatching_angle}{The slope of shading lines, given as an angle in degrees
-(counter-clockwise). Default is 45.}
-
-\item{hatching_color}{Color of the hatching lines. Default is
-\code{"#252525"}.}
-
-\item{hatching_lwd}{The line width, a positive number. The interpretation is
-device-specific, and some devices do not implement line widths less than
-one. Default is 0.5.}
-
-\item{hatching_cross}{A logical value indicating crosshatching. If TRUE, adds
-a second set of lines in the opposite angle. Default is FALSE.}
-
 \item{var}{Deprecated. Use 'data' instead.}
 
 \item{\dots}{Arguments to be passed to the method. Only accepts the following 
diff --git a/man/VizForecastPDF.Rd b/man/VizForecastPDF.Rd
index 37d671f..a0d0560 100644
--- a/man/VizForecastPDF.Rd
+++ b/man/VizForecastPDF.Rd
@@ -9,15 +9,31 @@ VizForecastPDF(
   tercile.limits,
   extreme.limits = NULL,
   obs = NULL,
-  fileout = NULL,
-  plotfile = NULL,
   toptitle = "Set a title",
   title = NULL,
   var.name = "Varname (units)",
+  title.legend = "Probability of terciles",
+  ensemble.legend = "Ensemble members",
+  obs.title = "Observations",
+  title.extremes = "Probability of extremes",
+  strings.extremes = c("Below p10", "Above p90"),
+  strings.legend = c("Below normal", "Near normal", "Above normal"),
+  strings.obs = NULL,
+  xlab.title = "Probability density",
+  title.cex = 1,
+  labs.cex = 1,
   fcst.names = NULL,
+  fcst.names.cex = 1,
+  obs.lines = TRUE,
+  obs.size = 3,
   add.ensmemb = c("above", "below", "no"),
   color.set = c("ggplot", "s2s4e", "hydro", "vitigeoss"),
-  memb_dim = "member"
+  memb_dim = "member",
+  width = 6,
+  height = 5,
+  res = 300,
+  fileout = NULL,
+  plotfile = NULL
 )
 }
 \arguments{
@@ -43,11 +59,6 @@ forecast panels. (Default: extreme categories are not shown).}
 panel or a single value that will be reused for all forecast panels. 
 (Default: observation is not shown).}
 
-\item{fileout}{(optional) A filename (pdf, png...) where the plot will be 
-saved. (Default: the plot is not saved).}
-
-\item{plotfile}{Deprecated. Use 'fileout' instead.}
-
 \item{toptitle}{A string with the plot title.}
 
 \item{title}{Deprecated. Use 'toptitle' instead.}
@@ -66,7 +77,18 @@ or \code{'below'} the pdf, or not (\code{'no'}).}
 inflows) or the \code{"vitigeoss"} color set.}
 
 \item{memb_dim}{A character string indicating the name of the member 
-dimension.}
+dimension}
+
+\item{width}{File width, in the units specified in the parameter size_units 
+(inches by default). Takes 8 by default.}
+
+\item{height}{File height, in the units specified in the parameter 
+size_units (inches by default). Takes 5 by default.}
+
+\item{fileout}{(optional) A filename (pdf, png...) where the plot will be 
+saved. (Default: the plot is not saved).}
+
+\item{plotfile}{Deprecated. Use 'fileout' instead.}
 }
 \value{
 A ggplot object containing the plot.
diff --git a/man/VizScorecard.Rd b/man/VizScorecard.Rd
index 2b29c11..1fef634 100644
--- a/man/VizScorecard.Rd
+++ b/man/VizScorecard.Rd
@@ -22,8 +22,7 @@ VizScorecard(
   table_title = NULL,
   table_subtitle = NULL,
   legend_breaks = NULL,
-  drawleg = TRUE,
-  plot_legend = NULL,
+  plot_legend = TRUE,
   label_scale = 1.4,
   legend_width = NULL,
   legend_height = 50,
@@ -81,6 +80,9 @@ as NULL by default.}
 \item{subrow_title}{A character string for the title of the sub-row names. It 
 is set as NULL by default.}
 
+\item{col_title}{A character string for the title of the column names. It is 
+set as NULL by default.}
+
 \item{table_title}{A character string for the title of the plot. It is set as 
 NULL by default.}
 
@@ -94,11 +96,9 @@ be given as input if the 'legend_dims' require different breaks. This
 parameter is required even if the legend is not plotted, to define the 
 colors in the scorecard table. It is set as NULL by default.}
 
-\item{drawleg}{A logical value to determine if the legend is plotted. It 
+\item{plot_legend}{A logical value to determine if the legend is plotted. It 
 is set as TRUE by default.}
 
-\item{plot_legend}{Deprecated. Use 'drawleg' instead.}
-
 \item{label_scale}{A numeric value to define the size of the legend labels. 
 It is set as 1.4 by default.}
 
diff --git a/tests/testthat/test-VizWeeklyClim.R b/tests/testthat/test-VizWeeklyClim.R
index 2edbdb0..fe8a030 100644
--- a/tests/testthat/test-VizWeeklyClim.R
+++ b/tests/testthat/test-VizWeeklyClim.R
@@ -152,7 +152,7 @@ test_that("2. Output", {
     save_fun(data = data, first_date = '2002-08-09', 
              last_date = '2002-09-15', ref_period = 2010:2019, 
              data_years = 2000:2019, time_dim = 'time', sdate_dim = 'sdate',
-             title = "Observed weekly means and climatology", 
+             toptitle = "Observed weekly means and climatology", 
              subtitle = "Target years: 2010 to 2019", 
              ytitle = paste0('tas', " (", "deg.C", ")")),
     name = 'VizWeeklyClim_1a.png' 
-- 
GitLab


From ad199d1d98b30e0e651b21b7b6851127d2c9d870 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Tue, 10 Jun 2025 15:03:55 +0200
Subject: [PATCH 71/72] Add  description in R/VizForecastPDF.R documentation

---
 R/VizForecastPDF.R | 22 ++++++++++------------
 1 file changed, 10 insertions(+), 12 deletions(-)

diff --git a/R/VizForecastPDF.R b/R/VizForecastPDF.R
index 9f30162..14802fc 100644
--- a/R/VizForecastPDF.R
+++ b/R/VizForecastPDF.R
@@ -40,7 +40,7 @@
 #'  \code{'hydro'} for yellow/gray/blue (suitable for precipitation and 
 #'  inflows) or the \code{"vitigeoss"} color set.
 #'@param memb_dim A character string indicating the name of the member 
-#'  dimension
+#'  dimension.
 #'@param width File width, in the units specified in the parameter size_units 
 #'  (inches by default). Takes 8 by default.
 #'@param height File height, in the units specified in the parameter 
@@ -48,8 +48,11 @@
 #'@param fileout (optional) A filename (pdf, png...) where the plot will be 
 #'  saved. (Default: the plot is not saved).
 #'@param plotfile Deprecated. Use 'fileout' instead.
-#'
+#'@param res Resolution of the device (file or window) to plot in. See 
+#'  ?Devices and the creator function of the corresponding device.
+#'  
 #'@return A ggplot object containing the plot.
+#'
 #'@examples
 #'fcsts <- data.frame(fcst1 = rnorm(10), fcst2 = rnorm(10, 0.5, 1.2))
 #'VizForecastPDF(fcsts,c(-1,1))
@@ -69,18 +72,13 @@ VizForecastPDF <- function(fcst, tercile.limits, extreme.limits = NULL,
                            strings.extremes = c('Below p10', 'Above p90'),
                            strings.legend = c('Below normal', 'Near normal', 'Above normal'),
                            strings.obs = NULL,
-                           xlab.title = 'Probability density',
-                           title.cex = 1, 
-                           labs.cex = 1,
-                           fcst.names = NULL,
-                           fcst.names.cex = 1,
-                           obs.lines = TRUE,
-                           obs.size = 3,
+                           xlab.title = 'Probability density', title.cex = 1, 
+                           labs.cex = 1, fcst.names = NULL, fcst.names.cex = 1,
+                           obs.lines = TRUE, obs.size = 3,
                            add.ensmemb = c("above", "below", "no"), 
                            color.set = c("ggplot", "s2s4e", "hydro", "vitigeoss"), 
-                           memb_dim = 'member', 
-                           width = 6, height = 5, res = 300, fileout = NULL,
-                           plotfile = NULL) {
+                           memb_dim = 'member', width = 6, height = 5, 
+                           fileout = NULL, plotfile = NULL, res = 300) {
   value <- init <- extremes <- x <- ymin <- ymax <- tercile <- NULL
   y <- xend <- yend <- yjitter <- MLT <- lab.pos <- NULL
   ggColorHue <- function(n) {
-- 
GitLab


From f1f6cc8b69857916076951d75ca4f65eb2211c5e Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Mon, 16 Jun 2025 12:59:20 +0200
Subject: [PATCH 72/72] Add missing descriptions in R/VizForecastPDF.R

---
 R/VizForecastPDF.R | 53 ++++++++++++++++++++++++++++++++++------------
 1 file changed, 40 insertions(+), 13 deletions(-)

diff --git a/R/VizForecastPDF.R b/R/VizForecastPDF.R
index 14802fc..c91c0ab 100644
--- a/R/VizForecastPDF.R
+++ b/R/VizForecastPDF.R
@@ -28,12 +28,39 @@
 #'@param obs (optional) A vector providing the observed values for each forecast 
 #'  panel or a single value that will be reused for all forecast panels. 
 #'  (Default: observation is not shown).
-#'@param toptitle A string with the plot title.
+#'@param toptitle A string with the plot main title.
 #'@param title Deprecated. Use 'toptitle' instead.
 #'@param var.name A string with the variable name and units.
-#'@param fcst.names (optional) An array of strings with the titles of each 
-#'  individual forecast.
-#'@param add.ensmemb Either to add the ensemble members \code{'above'} (default) 
+#'@param title.legend A string with the title of the legend showing the 
+#'  probabilistic categories. By default, it is set to "Probability of terciles".
+#'@param strings.legend A vector of strings with the name of the probabilistic 
+#'  categories. By default, it is set to c("Below normal", "Near normal", 
+#'  "Above normal").
+#'@param ensemble.legend A string with the title of the legend showing the 
+#'  ensemble members. By default, it is set to "Ensemble members".
+#'@param obs.title A string with the title of the legend showing the 
+#'  observations ('obs'). By default, it is set to "Observations".
+#'@param strings.obs A vector of strings with the name of the observations, 
+#'  which correspond to the values of 'obs'. By default, it is set to NULL.
+#'@param title.extremes A string with the title of the legend showing the 
+#'  extreme categories. By default, it is set to "Probability of extremes".
+#'@param strings.extremes A vector of strings with the name of the extreme 
+#'  categories. By default, it is set to c("Below p10", "Above p90").
+#'@param xlab.title A string with the title of the x-axis. By default, it is set
+#'  to "Probability density".
+#'@param fcst.names (optional) A string or vector of strings with the titles of 
+#'  each individual forecast panel.
+#'@param title.cex A number with the size of 'toptitle'. By default, it is set 
+#'  to 1.
+#'@param labs.cex A number with the size of the labels in the axes. By default, 
+#'  it is set to 1.
+#'@param fcst.names.cex A number with the size of the 'fcst.names'. By default, 
+#'  it is set to 1.
+#'@param obs.lines A logical value indicating whether to draw horizontal lines 
+#'  at the height of the observations. The default value is TRUE.
+#'@param obs.size A number with the size of the observation dots. By default, it
+#' is set to 3.
+#'@param add.ensmemb Either to add the ensemble members \code{'above'} (default)
 #'  or \code{'below'} the pdf, or not (\code{'no'}).
 #'@param color.set A selection of predefined color sets: use \code{'ggplot'} 
 #'  (default) for blue/green/red, \code{'s2s4e'} for blue/grey/orange, 
@@ -65,19 +92,19 @@
 VizForecastPDF <- function(fcst, tercile.limits, extreme.limits = NULL, 
                            obs = NULL, toptitle = "Set a title", title = NULL,
                            var.name = "Varname (units)", 
-                           title.legend = 'Probability of terciles', 
-                           ensemble.legend = 'Ensemble members', 
-                           obs.title = 'Observations',
-                           title.extremes = 'Probability of extremes', 
-                           strings.extremes = c('Below p10', 'Above p90'),
-                           strings.legend = c('Below normal', 'Near normal', 'Above normal'),
+                           title.legend = "Probability of terciles", 
+                           strings.legend = c("Below normal", "Near normal", "Above normal"),
+                           ensemble.legend = "Ensemble members", 
+                           obs.title = "Observations",
                            strings.obs = NULL,
-                           xlab.title = 'Probability density', title.cex = 1, 
-                           labs.cex = 1, fcst.names = NULL, fcst.names.cex = 1,
+                           title.extremes = "Probability of extremes", 
+                           strings.extremes = c("Below p10", "Above p90"),
+                           xlab.title = "Probability density", fcst.names = NULL,
+                           title.cex = 1, labs.cex = 1,  fcst.names.cex = 1,
                            obs.lines = TRUE, obs.size = 3,
                            add.ensmemb = c("above", "below", "no"), 
                            color.set = c("ggplot", "s2s4e", "hydro", "vitigeoss"), 
-                           memb_dim = 'member', width = 6, height = 5, 
+                           memb_dim = "member", width = 6, height = 5, 
                            fileout = NULL, plotfile = NULL, res = 300) {
   value <- init <- extremes <- x <- ymin <- ymax <- tercile <- NULL
   y <- xend <- yend <- yjitter <- MLT <- lab.pos <- NULL
-- 
GitLab