From e93441dbdd4ba36294ff25ebb12c17558f48cc14 Mon Sep 17 00:00:00 2001
From: "alasdair.hunter" <alasdair.hunter@bsc.es>
Date: Thu, 20 Apr 2017 17:15:47 +0200
Subject: [PATCH 1/3] Minor bugfix

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

diff --git a/R/Corr.R b/R/Corr.R
index 10858c29..4654db2c 100644
--- a/R/Corr.R
+++ b/R/Corr.R
@@ -149,8 +149,8 @@ Corr <- function(var_exp, var_obs, posloop = 1, poscor = 2, compROW = NULL,
     }
   }
   if (pval && (method == "pearson")) {
-    t <- CORR * sqrt((eno - 2) / (1 - (CORR ^ 2)))
-    p_val <- 1 - pt(t, eno - 2)
+    t <-sqrt(CORR * CORR * (eno - 2) / (1 - (CORR ^ 2)))
+    p_val <- pt(t, eno - 2, lower.tail = FALSE)
   } 
   if (conf && (method == "pearson")) {
     conf_low <- (1 - siglev) / 2
-- 
GitLab


From 5b5d7199e31e374aca4b6cc3b3e79b2d37bceabf Mon Sep 17 00:00:00 2001
From: Nicolau Manubens <nicolau.manubens@ic3.cat>
Date: Fri, 21 Apr 2017 11:51:57 +0200
Subject: [PATCH 2/3] Fix in PlotLayout for custom dimension orderings. Fixes
 #189.

---
 R/PlotLayout.R | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/R/PlotLayout.R b/R/PlotLayout.R
index a3f67e56..7d5eee1e 100644
--- a/R/PlotLayout.R
+++ b/R/PlotLayout.R
@@ -432,8 +432,13 @@ PlotLayout <- function(fun, plot_dims, var, ..., special_args = NULL,
       }
       plot_number <<- plot_number + 1
     } else {
+      if (is.character(plot_dims[[array_number]])) {
+        plot_dim_indices <- which(names(dim(x)) %in% plot_dims[[array_number]])
+      } else {
+        plot_dim_indices <- plot_dims[[array_number]]
+      }
       # For each of the arrays provided in that array
-      apply(x, (1:length(dim(x)))[1:(length(dim(x)) - length(plot_dims[[array_number]]))], 
+      apply(x, (1:length(dim(x)))[-plot_dim_indices], 
             function(y) {
         # Do the plot
         fun_args <- c(list(y, toptitle = titles[plot_number]), list(...), 
-- 
GitLab


From 8991ba0a9c9d871f36c395f862f40bdbe678fae8 Mon Sep 17 00:00:00 2001
From: Nicolau Manubens <nicolau.manubens@ic3.cat>
Date: Mon, 15 May 2017 17:30:45 +0200
Subject: [PATCH 3/3] Fixed bug when loading files with generic grids. Fixes
 #192.

---
 R/Load.R  | 13 +++++++++----
 R/Utils.R | 19 +++++++++++++------
 2 files changed, 22 insertions(+), 10 deletions(-)

diff --git a/R/Load.R b/R/Load.R
index 96b696a8..190872f3 100644
--- a/R/Load.R
+++ b/R/Load.R
@@ -268,14 +268,19 @@ Load <- function(var, exp = NULL, obs = NULL, sdates, nmember = NULL,
   # grid
   if (!is.null(grid)) {
     if (is.character(grid)) {
-      supported_grids <- list('r[0-9]{1,}x[0-9]{1,}', 't[0-9]{1,}grid')
-      grid_matches <- unlist(lapply(lapply(supported_grids, regexpr, grid), .IsFullMatch, grid))
-      if (sum(grid_matches) < 1) {
-        stop("The specified grid in the parameter 'grid' is incorrect. Must be one of r<NX>x<NY> or t<RES>grid.")
+      if (grid == 'none') {
+        grid <- NULL
+      } else {
+        supported_grids <- list('r[0-9]{1,}x[0-9]{1,}', 't[0-9]{1,}grid')
+        grid_matches <- unlist(lapply(lapply(supported_grids, regexpr, grid), .IsFullMatch, grid))
+        if (sum(grid_matches) < 1) {
+          stop("The specified grid in the parameter 'grid' is incorrect. Must be one of r<NX>x<NY> or t<RES>grid.")
+        }
       }
     } else {
       stop("Error: parameter 'grid' should be a character string, if specified.")
     }
+    }
   }
 
   # maskmod
diff --git a/R/Utils.R b/R/Utils.R
index ec154153..c748a508 100644
--- a/R/Utils.R
+++ b/R/Utils.R
@@ -220,6 +220,9 @@
         # Here we read the grid type and its number of longitudes and latitudes
         file_info <- system(paste('cdo -s griddes', filein, '2> /dev/null'), intern = TRUE)
         grids_positions <- grep('# gridID', file_info)
+        if (length(grids_positions) < 1) {
+          stop("The grid should be defined in the files.")
+        }
         grids_first_lines <- grids_positions + 2
         grids_last_lines <- c((grids_positions - 2)[-1], length(file_info))
         grids_info <- as.list(1:length(grids_positions))
@@ -239,12 +242,14 @@
                   } else {
                     NA
                   }
-          if ((nlons == length(lon)) && 
-              (nlats == length(lat))) {
-            TRUE
-          } else {
-            FALSE
+          result <- FALSE
+          if (!any(is.na(c(nlons, nlats)))) {
+            if ((nlons == length(lon)) && 
+                (nlats == length(lat))) {
+              result <- TRUE
+            }
           }
+          result
         }))
         grids_matches <- grids_matches[which(grids_types %in% c('gaussian', 'lonlat'))]
         grids_info <- grids_info[which(grids_types %in% c('gaussian', 'lonlat'))]
@@ -261,8 +266,10 @@
           } else {
             stop("Error: Load() can't disambiguate: More than one lonlat/gaussian grids with the same size as the requested variable defined in ", filename)
           }
-        } else {
+        } else if (sum(grids_matches) == 1) {
           grid_type <- grids_types[which(grids_matches)]
+        } else {
+          stop("Unexpected error.")
         }
         grid_lons <- length(lon)
         grid_lats <- length(lat)
-- 
GitLab