From 1d7802fe02bfe8f6b75d2d9df94b868b65fd6436 Mon Sep 17 00:00:00 2001
From: Eva Rifa <eva.rifarovira@bsc.es>
Date: Wed, 15 Feb 2023 17:15:47 +0100
Subject: [PATCH] Add Apply in WeightedMean, added checks, corrected
 documentation, code format, improved atomic function

---
 NAMESPACE                           |   1 -
 R/WeightedMean.R                    | 257 ++++++++++++++++-----------
 man/WeightedMean.Rd                 |  72 +++++---
 tests/testthat/test-WeightedCells.R |   3 +-
 tests/testthat/test-WeightedMean.R  | 259 +++++++++++++++++++++++-----
 5 files changed, 426 insertions(+), 166 deletions(-)

diff --git a/NAMESPACE b/NAMESPACE
index e3226a5..47ee4dc 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -20,5 +20,4 @@ export(WeightedMean)
 import(PCICt)
 import(climdex.pcic)
 import(multiApply)
-importFrom(plyr,aaply)
 importFrom(stats,quantile)
diff --git a/R/WeightedMean.R b/R/WeightedMean.R
index 393f56f..ffcd273 100644
--- a/R/WeightedMean.R
+++ b/R/WeightedMean.R
@@ -1,101 +1,173 @@
 #'Calculate spatial area-weighted average of multidimensional arrays
 #'
+#'This function computes a spatial area-weighted average of n-dimensional arrays 
+#'being possible to select a region and to add a mask to be applied when 
+#'computing the average.
 #'
-#'This function computes a spatial area-weighted average of n-dimensional arrays being possible to select a region and to add a mask to be applied when computing the average.
+#'@param data A numeric array with named dimensions, representing the data to be
+#'  applied the weights. It should have at least the latitude dimension and it 
+#'  can have more other dimensions.
+#'@param lon A numeric vector of longitude locations of the cell centers of the 
+#'  grid of \code{data}. This vector must be of the same length as the longitude 
+#'  dimension in the parameter \code{data} (in degrees).
+#'@param lat A numeric vector of latitude locations of the cell centers of the 
+#'  grid of \code{data}. This vector must be of the same length as the latitude 
+#'  dimension in the parameter \code{data} (in degrees). 
+#'@param region A vector of length four indicating the minimum longitude, the 
+#'  maximum longitude, the minimum latitude and the maximum latitude of the 
+#'  region to be averaged.
+#'@param mask A matrix with the same spatial dimensions of \code{data}. It can 
+#'  contain either a) TRUE where the value at that position is to be accounted 
+#'  for and FALSE where not, or b) numeric values, where those greater or equal 
+#'  to 0.5 are to be accounted for, and those smaller are not. Attention: if the 
+#'  longitude and latitude dimensions of the data and mask coincide in length, 
+#'  the user must ensure the dimensions of the mask are in the same order as the 
+#'  dimensions in the array provided in the parameter \code{data}.
+#'@param londim A character string indicating the name of the longitudinal
+#'  dimension. The default value is 'lon'.
+#'@param latdim A character string indicating the name of the latitudinal
+#'  dimension. The default value is 'lat'.
+#'@param na.rm A logical value indicating whether missing values should be 
+#'  stripped before the computation proceeds, by default it is set to TRUE.
+#'@param ncores An integer indicating the number of cores to use for parallel 
+#'  computation. The default value is NULL.
 #'
-#'@param data An array with minimum two dimensions of latitude and longitude.
-#'@param lon Numeric vector of longitude locations of the cell centers of the grid of \code{data}. This vector must be the same length as the longitude dimension in the parameter \code{data}.
-#'@param lat Numeric vector of latitude locations of the cell centers of the grid of \code{data}. This vector must be the same length as the latitude dimension in the parameter \code{data}. 
-#'@param region A vector of length four indicating the minimum longitude, the maximum longitude, the minimum latitude and the maximum latitude of the region to be averaged.
-#'@param mask A matrix with the same spatial dimensions of \code{data}. It can contain either a) TRUE where the value at that position is to be accounted for and FALSE where not, or b) numeric values, where those greater or equal to 0.5 are to be accounted for, and those smaller are not. Attention: if the longitude and latitude dimensions of the data and mask coincide in length, the user must ensure the dimensions of the mask are in the same order as the dimensions in the array provided in the parameter \code{data}.
-#'@param londim An integer number indicating the position of the longitude dimension in the \code{data} object.
-#'@param latdim An integer number indicating the position of the latitude dimension in the \code{data} object.
+#'@return An array, matrix or vector containig the area-weighted average with 
+#'the same dimensions as \code{data}, except for the spatial longitude and 
+#'latitude dimensions, which disappear. 
 #'
-#'@return An array, matrix or vector containig the area-weighted average with the same dimensions as \code{data}, except for the spatial longitude and latitude dimensions, which disappear.
-#'
-#'@importFrom plyr aaply
 #'@examples
-#'##Example synthetic data 1:
+#'# Example 1:
 #'data <- 1:(2 * 3 * 4 * 5)
 #'dim(data) <- c(lon = 2, lat = 3, time = 4, model = 5)
 #'lat <- c(1, 10, 20)
 #'lon <- c(1, 10)
-#'
-#'a <- WeightedMean(data = data, lon = lon, lat = lat, region = NULL, 
-#'                  mask = NULL, londim = 1, latdim = 2)
-#'str(a)
+#'a <- WeightedMean(data = data, lon = lon, lat = lat, region = NULL)
 #'
 #'mask <- c(0, 1, 0, 1, 0, 1)
 #'dim(mask) <- c(lon = 2, lat = 3)
-#'a <- WeightedMean(data = data, lon = lon, lat = lat, region = NULL, 
-#'                  mask = mask, londim = 1, latdim = 2)
-#'str(a)
+#'a <- WeightedMean(data = data, lon = lon, lat = lat, mask = mask)
 #'
 #'region <- c(1, 10, 1, 10)
 #'a <- WeightedMean(data = data, lon = lon, lat = lat, region = region, 
-#'                  mask = mask, londim = 1, latdim = 2)
-#'str(a)
+#'                  mask = mask)
 #'
-#'##Example synthetic data:
+#'# Example 2:
 #'data <- 1:(2 * 3 * 4)
-#'dim(data) <- c(lon = 2, lat = 3, time=4)
+#'dim(data) <- c(lon = 2, lat = 3, time = 4)
 #'lat <- c(1, 10, 20)
 #'lon <- c(1, 10)
-#'
-#'a <- WeightedMean(data = data, lon = lon, lat = lat, region = NULL,
-#'                  mask = NULL, londim = 1, latdim = 2)
-#'str(a)
+#'a <- WeightedMean(data = data, lon = lon, lat = lat)
+#' 
+#'@import multiApply
 #'@export
-WeightedMean <- function(data, lon, lat, region = NULL, mask = NULL, londim = NULL, latdim = NULL){
-  if (is.null(data) | is.null(lon) | is.null(lat)) {
-    stop("Parameter 'data', 'lon' and 'lat' cannot be NULL.")
+WeightedMean <- function(data, lon, lat, region = NULL, mask = NULL, 
+                         londim = 'lon', latdim = 'lat', na.rm = TRUE, 
+                         ncores = NULL) {
+  # Check inputs
+  # data
+  if (is.null(data)) {
+    stop("Parameter 'data' cannot be NULL.")
   }
-  if (!is.numeric(data) | !is.numeric(lon)| !is.numeric(lat)) {
-    stop("Parameter 'data', 'lon' and 'lat' must be a numeric.")
+  if (!is.array(data)) {
+    stop("Parameter 'data' must be a numeric array.")
   }
-  if (length(dim(data)) < 2) {
-    stop("Parameter 'data' needs to have dimensions lon and lat.")
+  dim_names <- names(dim(data))
+  if (is.null(dim_names)) {
+    stop("Parameter 'data' must have dimension names.")
   }
-  if (!is.null(dim(lat)) | !is.null(dim(lon))) {
-    stop("Parameter 'lon' and lat' need to be a vector.")
+  # lon, lat
+  if (is.null(lon) | is.null(lat)) {
+    stop("Parameters 'lon' and 'lat' cannot be NULL.")
   }
-  dim_names <- names(dim(data))
-  dims <- 1 : length(dim(data))
-  if (is.null(londim)) {
-    if (!is.null(dim_names)) {
-      londim <- which(dim_names == 'lon')
-    }
-    if(is.null(londim)) {
-      londim <- which(dim(data) == length(lon))
-    }
-    if (length(londim) == 0)  {
-      stop("No longitudinal dimension provided in parameter 'londim' nor as attribute of parameter 'data'.")
-    }
+  if (!is.numeric(lon) | !is.numeric(lat)) {
+    stop("Parameters 'lon' and 'lat' must be numeric.")
   }
-  if (is.null(latdim)) {
-    if (!is.null(dim_names)) {
-      latdim <- which(dim_names == 'lat')
+  if (!is.null(dim(lon)) | !is.null(dim(lat))) {
+    if (length(dim(lon)) == 1 & length(dim(lat)) == 1) {
+      lon <- as.vector(lon)
+      lat <- as.vector(lat)
+    } else {
+      stop("Parameters 'lon' and 'lat' need to be a vector.")
     }
-    if (is.null(latdim)) {
-      latdim <- which(dim(data) == length(lat))
-    }  
-    if (length(latdim) == 0) {
-        stop("No latitudinal dimension provided in parameter 'latdim' nor as attribute of parameter 'data'.")
+  }
+  # londim
+  if (is.numeric(londim)) {
+    warning("Numeric 'londim' is deprecated, use dimension names instead. The ", 
+            "corresponding dimension name will be assigned.")
+    londim <- dim_names[londim]
+  }
+  if (!is.character(londim)) {
+    stop("Parameter 'londim' must be a character string.")
+  }
+  if (length(londim) > 1) {
+    warning("Parameter 'londim' must be of length 1. Only the first value ", 
+            "will be used.")
+    londim <- londim[1]
+  }
+  if (!londim %in% names(dim(data))) {
+    stop("Parameter 'londim' is not found in 'data'.")
+  }
+  if (dim(data)[londim] != length(lon)) {
+    stop(paste0("The longitudinal dimension of parameter 'data' must be of the ", 
+                "same length as parameter 'lon'."))
+  }
+  # latdim
+  if (is.numeric(latdim)) {
+    warning("Numeric 'latdim' is deprecated, use dimension names instead. The ", 
+            "corresponding dimension name will be assigned.")
+    latdim <- dim_names[latdim]
+  }
+  if (!is.character(latdim)) {
+    stop("Parameter 'latdim' must be a character string.")
+  }
+  if (length(latdim) > 1) {
+    warning("Parameter 'latdim' must be of length 1. Only the first value ", 
+            "will be used.")
+    latdim <- latdim[1]
+  }
+  if (!latdim %in% names(dim(data))) {
+    stop("Parameter 'latdim' is not found in 'data'.")
+  }
+  if (dim(data)[latdim] != length(lat)) {
+    stop(paste0("The latitudinal dimension of parameter 'data' must be of the ", 
+                "same length as parameter 'lat'."))
+  }
+  lon_pos <- which(dim_names == londim)
+  lat_pos <- which(dim_names == latdim)
+  # region
+  if (!is.null(region)) {
+    if (length(region) != 4) {
+      stop(paste0("The region argument has to be of length four indicating ", 
+                  "the minimum longitude, the maximum longitude, the minimum ", 
+                  "latitude and the maximum latitude of the region to be averaged."))
     }
   }
-  if (londim == latdim) {
-    stop("Parameter 'londim' and 'latdim' cannot be equal.")
+  # mask
+  if (!is.null(mask)) {
+    if (!all(dim(data)[which(names(dim(data)) %in% c(londim, latdim))] %in% 
+             dim(mask)[which(names(dim(mask)) %in% c(londim, latdim))])) {
+      stop("Parameter 'mask' must have the same spatial dimensions of data.")
+    }
   }
-  if (dim(data)[londim] != length(lon)){
-    stop("The longitudinal dimension of parameter 'data' must be the same length of parameter 'lon'.")
+  # na.rm
+  if (!is.logical(na.rm) | length(na.rm) > 1) {
+    stop("Parameter 'na.rm' must be one logical value.")
   }
-  if (dim(data)[latdim] != length(lat)){
-    stop("The latitudinal dimension of parameter 'data' must be the same length of parameter 'lat'.")
+  # ncores
+  if (!is.null(ncores)) {
+    if (!is.numeric(ncores) | length(ncores) > 1) {
+      stop("Parameter 'ncores' must be either NULL or a positive integer.")
+    } else if (ncores %% 1 != 0 | ncores <= 0) {
+      stop("Parameter 'ncores' must be a positive integer.")
+    }
   }
+
   nlon <- length(lon)
   nlat <- length(lat)
   if (!is.null(region)) {
-    aux <- SelBox(data, lon = lon, lat = lat, region = region, londim = londim, latdim = latdim, mask = mask)
+    aux <- SelBox(data, lon = lon, lat = lat, region = region, londim = lon_pos, 
+                  latdim = lat_pos, mask = mask)
     data <- aux$data
     lon <- aux$lon
     lat <- aux$lat
@@ -103,24 +175,8 @@ WeightedMean <- function(data, lon, lat, region = NULL, mask = NULL, londim = NU
       mask <- aux$mask
     }
   }
-  if (length(dim(data)) > 2) {
-    wtmean <- aaply(data, .margins = dims[c(-londim, -latdim)], 
-                          .fun = .WeightedMean, lon, lat, mask, .drop = FALSE)
-    dim(wtmean) <- dim(data)[-c(latdim,londim)]
-  } else {
-    wtmean <- .WeightedMean(data, lon = lon, lat = lat, mask = mask)
-  }
-  if(length(dim(data)) > 3) {
-    if (is.null(dim_names)) {
-      dim_names <- paste0("dim", 1:length(dim(data)))
-    }
-    names(dim(wtmean)) = dim_names[-c(londim, latdim)]
-  } else {
-    attributes(wtmean) <- NULL
-  }
-  wtmean
-}
-.WeightedMean <- function(data, lon, lat, mask) {
+
+  # Compute the weights
   cosphi <- t(array(cos(lat * pi / 180), dim = c(length(lat), length(lon))))
   nblat <- length(lat)
   nblon <- length(lon)
@@ -131,23 +187,32 @@ WeightedMean <- function(data, lon, lat, region = NULL, mask = NULL, londim = NU
   dlat <- c(dlat, dlat[1])
   dlat <- t(array(dlat, dim = c(nblat, nblon)))
   weight <- (dlon * dlat * cosphi) 
-  if ((is.null(mask) == FALSE) && all(dim(data) != dim(mask))) {
-    stop("The provided parameter 'mask' must have the same size as the parameter 'data'.")
-  }
-  if ((nblat == dim(data)[1]) && (nblon == dim(data)[2])) {
-    data <- t(data)
-    if (!is.null(mask)) {
-      mask <- t(mask)
-    }
-  } 
-  if ((nblon != dim(data)[1]) || (nblat != dim(data)[2])) {
-    stop("The parameter 'data' needs to have at least two dimensions of 'lon' and 'lat'.")
+
+  if (is.null(mask)) {
+    res <- Apply(data = list(data), 
+                 target_dims = c(londim, latdim), 
+                 fun = .WeightedMean,
+                 mask = NULL, 
+                 weight = weight, 
+                 na.rm = na.rm, 
+                 ncores = ncores)$output1
+  } else {
+    res <- Apply(data = list(data, mask), 
+                 target_dims = c(londim, latdim), 
+                 fun = .WeightedMean,
+                 weight = weight, 
+                 na.rm = na.rm, 
+                 ncores = ncores)$output1
   }
-  if(!is.null(mask)) {
+  return(res)
+}
+
+.WeightedMean <- function(data, mask = NULL, weight, na.rm = TRUE) {
+  if (!is.null(mask)) {
     data[mask < 0.5] <- NA
   }
   weight[is.na(data)] <- NA
-  coeff <- sum(weight, na.rm = TRUE)
-  mean <- sum(weight * data, na.rm = TRUE) / coeff
-  output <- mean
+  coeff <- sum(weight, na.rm = na.rm)
+  mean <- sum(weight * data, na.rm = na.rm) / coeff
+  return(mean)
 }
diff --git a/man/WeightedMean.Rd b/man/WeightedMean.Rd
index ac3411c..ad59157 100644
--- a/man/WeightedMean.Rd
+++ b/man/WeightedMean.Rd
@@ -10,60 +10,80 @@ WeightedMean(
   lat,
   region = NULL,
   mask = NULL,
-  londim = NULL,
-  latdim = NULL
+  londim = "lon",
+  latdim = "lat",
+  na.rm = TRUE,
+  ncores = NULL
 )
 }
 \arguments{
-\item{data}{An array with minimum two dimensions of latitude and longitude.}
+\item{data}{A numeric array with named dimensions, representing the data to be
+applied the weights. It should have at least the latitude dimension and it 
+can have more other dimensions.}
 
-\item{lon}{Numeric vector of longitude locations of the cell centers of the grid of \code{data}. This vector must be the same length as the longitude dimension in the parameter \code{data}.}
+\item{lon}{A numeric vector of longitude locations of the cell centers of the 
+grid of \code{data}. This vector must be of the same length as the longitude 
+dimension in the parameter \code{data} (in degrees).}
 
-\item{lat}{Numeric vector of latitude locations of the cell centers of the grid of \code{data}. This vector must be the same length as the latitude dimension in the parameter \code{data}.}
+\item{lat}{A numeric vector of latitude locations of the cell centers of the 
+grid of \code{data}. This vector must be of the same length as the latitude 
+dimension in the parameter \code{data} (in degrees).}
 
-\item{region}{A vector of length four indicating the minimum longitude, the maximum longitude, the minimum latitude and the maximum latitude of the region to be averaged.}
+\item{region}{A vector of length four indicating the minimum longitude, the 
+maximum longitude, the minimum latitude and the maximum latitude of the 
+region to be averaged.}
 
-\item{mask}{A matrix with the same spatial dimensions of \code{data}. It can contain either a) TRUE where the value at that position is to be accounted for and FALSE where not, or b) numeric values, where those greater or equal to 0.5 are to be accounted for, and those smaller are not. Attention: if the longitude and latitude dimensions of the data and mask coincide in length, the user must ensure the dimensions of the mask are in the same order as the dimensions in the array provided in the parameter \code{data}.}
+\item{mask}{A matrix with the same spatial dimensions of \code{data}. It can 
+contain either a) TRUE where the value at that position is to be accounted 
+for and FALSE where not, or b) numeric values, where those greater or equal 
+to 0.5 are to be accounted for, and those smaller are not. Attention: if the 
+longitude and latitude dimensions of the data and mask coincide in length, 
+the user must ensure the dimensions of the mask are in the same order as the 
+dimensions in the array provided in the parameter \code{data}.}
 
-\item{londim}{An integer number indicating the position of the longitude dimension in the \code{data} object.}
+\item{londim}{A character string indicating the name of the longitudinal
+dimension. The default value is 'lon'.}
 
-\item{latdim}{An integer number indicating the position of the latitude dimension in the \code{data} object.}
+\item{latdim}{A character string indicating the name of the latitudinal
+dimension. The default value is 'lat'.}
+
+\item{na.rm}{A logical value indicating whether missing values should be 
+stripped before the computation proceeds, by default it is set to TRUE.}
+
+\item{ncores}{An integer indicating the number of cores to use for parallel 
+computation. The default value is NULL.}
 }
 \value{
-An array, matrix or vector containig the area-weighted average with the same dimensions as \code{data}, except for the spatial longitude and latitude dimensions, which disappear.
+An array, matrix or vector containig the area-weighted average with 
+the same dimensions as \code{data}, except for the spatial longitude and 
+latitude dimensions, which disappear.
 }
 \description{
-This function computes a spatial area-weighted average of n-dimensional arrays being possible to select a region and to add a mask to be applied when computing the average.
+This function computes a spatial area-weighted average of n-dimensional arrays 
+being possible to select a region and to add a mask to be applied when 
+computing the average.
 }
 \examples{
-##Example synthetic data 1:
+# Example 1:
 data <- 1:(2 * 3 * 4 * 5)
 dim(data) <- c(lon = 2, lat = 3, time = 4, model = 5)
 lat <- c(1, 10, 20)
 lon <- c(1, 10)
-
-a <- WeightedMean(data = data, lon = lon, lat = lat, region = NULL, 
-                 mask = NULL, londim = 1, latdim = 2)
-str(a)
+a <- WeightedMean(data = data, lon = lon, lat = lat, region = NULL)
 
 mask <- c(0, 1, 0, 1, 0, 1)
 dim(mask) <- c(lon = 2, lat = 3)
-a <- WeightedMean(data = data, lon = lon, lat = lat, region = NULL, 
-                 mask = mask, londim = 1, latdim = 2)
-str(a)
+a <- WeightedMean(data = data, lon = lon, lat = lat, mask = mask)
 
 region <- c(1, 10, 1, 10)
 a <- WeightedMean(data = data, lon = lon, lat = lat, region = region, 
-                 mask = mask, londim = 1, latdim = 2)
-str(a)
+                 mask = mask)
 
-##Example synthetic data:
+# Example 2:
 data <- 1:(2 * 3 * 4)
-dim(data) <- c(lon = 2, lat = 3, time=4)
+dim(data) <- c(lon = 2, lat = 3, time = 4)
 lat <- c(1, 10, 20)
 lon <- c(1, 10)
+a <- WeightedMean(data = data, lon = lon, lat = lat)
 
-a <- WeightedMean(data = data, lon = lon, lat = lat, region = NULL,
-                 mask = NULL, londim = 1, latdim = 2)
-str(a)
 }
diff --git a/tests/testthat/test-WeightedCells.R b/tests/testthat/test-WeightedCells.R
index dcf171d..a5e9dd1 100644
--- a/tests/testthat/test-WeightedCells.R
+++ b/tests/testthat/test-WeightedCells.R
@@ -1,4 +1,4 @@
-context("s2dv::WeightedCells tests")
+context("ClimProjDiags::WeightedCells tests")
 
 ##############################################
 
@@ -66,7 +66,6 @@ test_that("1. Input checks", {
     WeightedCells(data1, lat1, ncores = 1.5),
     "Parameter 'ncores' must be either NULL or a positive integer."
   )
-
 })
 
 ##############################################
diff --git a/tests/testthat/test-WeightedMean.R b/tests/testthat/test-WeightedMean.R
index 2c5a231..24144db 100644
--- a/tests/testthat/test-WeightedMean.R
+++ b/tests/testthat/test-WeightedMean.R
@@ -1,4 +1,7 @@
-context("WeightedMean tests")
+context("ClimProjDiags::WeightedMean tests")
+
+##############################################
+
 set.seed(1)
 dat1 <- array(rnorm(10000), dim = c(lat = 50, lon = 100))
 lat1 <- seq(-90, 90, length.out = 50)
@@ -19,53 +22,227 @@ dat4 <- array(rnorm(10000), dim = c(lat = 180, lon = 360, sdate = 2, time = 1))
 lat4 <- seq(-89.5, 89.5, length.out = 180)
 lon4 <- seq(-179.5, 179.5, length.out = 360)
 
+set.seed(2)
+mask <- array(rnorm(180*360), dim = c(lat = 180, lon = 360))
+region <- c(1, 55, 2, 67)
+
+dat5 <- dat4
+dat5[1,1,1,1] <- NA
+
+##############################################
+
+test_that("1. Input checks", {
+  # data, lon, lat
+  expect_error(
+    WeightedMean(c(), lon = 1:10, lat = 1:10),
+    "Parameter 'data' cannot be NULL."
+  )
+  expect_error(
+    WeightedMean(1:10, lon = 1:10, lat = 1:10),
+    "Parameter 'data' must be a numeric array."
+  )
+  expect_error(
+    WeightedMean(array(1:10), lon = 1:10, lat = 1:10),
+    "Parameter 'data' must have dimension names."
+  )
+  # lon, lat
+  expect_error(
+    WeightedMean(array(1:10, dim = c(lon = 10)), lon = NULL, lat = 1:10),
+    "Parameters 'lon' and 'lat' cannot be NULL."
+  )
+  expect_error(
+    WeightedMean(array(1:10, dim = c(lon = 10)), lon = 'a', lat = 1:10),
+    "Parameters 'lon' and 'lat' must be numeric."
+  )
+  expect_error(
+    WeightedMean(array(1:10, dim = c(lon = 10)), 
+                 lon = 1:10, lat = array(1:10, dim = c(lon = 10, lat = 1))),
+    "Parameters 'lon' and 'lat' need to be a vector."
+  )
+  # londim
+  expect_warning(
+    WeightedMean(array(1:10, dim = c(lon = 10, lat = 1)), 
+                 lon = 1:10, lat = 1, londim = 1, latdim = 2),
+    "Numeric 'londim' is deprecated, use dimension names instead. The ", 
+    "corresponding dimension name will be assigned."
+  )
+  expect_error(
+    WeightedMean(array(1:10, dim = c(lon = 10, lat = 1)), 
+                 lon = 1:10, lat = 1, londim = list(1,2), latdim = 2),
+    "Parameter 'londim' must be a character string."
+  )
+  expect_warning(
+    WeightedMean(array(1:10, dim = c(lon = 10, lat = 1)), 
+                 lon = 1:10, lat = 1, londim = c('lon', 'lat'), latdim = 'lat'),
+    "Parameter 'londim' must be of length 1. Only the first value ", 
+    "will be used."
+  )
+  expect_error(
+    WeightedMean(array(1:10, dim = c(lons = 10, lat = 1)), 
+                 lon = 1:10, lat = 1, londim = 'lon', latdim = 'lat'),
+    "Parameter 'londim' is not found in 'data'."
+  )
+  expect_error(
+    WeightedMean(array(1:10, dim = c(lon = 10, lat = 1)), 
+                 lon = 1:11, lat = 1, londim = 'lon', latdim = 'lat'),
+    paste0("The longitudinal dimension of parameter 'data' must be of the ", 
+           "same length as parameter 'lon'.")
+  )
+  # latdim
+  expect_warning(
+    WeightedMean(array(1:10, dim = c(lon = 10, lat = 1)), 
+                 lon = 1:10, lat = 1, latdim = 2),
+    "Numeric 'latdim' is deprecated, use dimension names instead. The ", 
+    "corresponding dimension name will be assigned."
+  )
+  expect_error(
+    WeightedMean(array(1:10, dim = c(lon = 10, lat = 1)), 
+                 lon = 1:10, lat = 1, latdim = list(1,2)),
+    "Parameter 'latdim' must be a character string."
+  )
+  expect_warning(
+    WeightedMean(array(1:10, dim = c(lon = 10, lat = 1)), 
+                 lon = 1:10, lat = 1, latdim = c('lat', 'lon')),
+    "Parameter 'latdim' must be of length 1. Only the first value ", 
+    "will be used."
+  )
+  expect_error(
+    WeightedMean(array(1:10, dim = c(lon = 10, lats = 1)), 
+                 lon = 1:10, lat = 1, londim = 'lon', latdim = 'lat'),
+    "Parameter 'latdim' is not found in 'data'."
+  )
+  expect_error(
+    WeightedMean(array(1:10, dim = c(lon = 10, lat = 1)), 
+                 lon = 1:10, lat = 1:2, londim = 'lon', latdim = 'lat'),
+    paste0("The latitudinal dimension of parameter 'data' must be of the ", 
+           "same length as parameter 'lat'.")
+  )
+  # region
+  expect_error(
+    WeightedMean(dat1, lat = lat1, lon = lon1, region = 1:3),
+    paste0("The region argument has to be of length four indicating ", 
+           "the minimum longitude, the maximum longitude, the minimum ", 
+           "latitude and the maximum latitude of the region to be averaged.")
+  )
+  # mask
+  expect_error(
+    WeightedMean(dat1, lat = lat1, lon = lon1, mask = 1:3),
+    "Parameter 'mask' must have the same spatial dimensions of data."
+  )
+  # na.rm
+  expect_error(
+    WeightedMean(dat1, lat = lat1, lon = lon1, na.rm = 1:3),
+    "Parameter 'na.rm' must be one logical value."
+  )
+  # ncores
+  expect_error(
+    WeightedMean(dat1, lat = lat1, lon = lon1, ncores = 'a'),
+    "Parameter 'ncores' must be either NULL or a positive integer."
+  )
+  expect_error(
+    WeightedMean(dat1, lat = lat1, lon = lon1, ncores = 1.5),
+    "Parameter 'ncores' must be a positive integer."
+  )
+})
+
+##############################################
+test_that("2. Output test: dat1", {
+  expect_equal(
+    dim(WeightedMean(dat1, lat = lat1, lon = lon1)),
+    NULL
+  )
+  expect_equal(
+    as.vector(WeightedMean(dat1, lat = lat1, lon = lon1)),
+    -0.009785971,
+    tolerance = 0.0001
+  )
+})
+
+##############################################
 
-test_that("dat1", {
-expect_equal(
-dim(WeightedMean(dat1, lat = lat1, lon = lon1)),
-NULL
-)
-expect_equal(
-as.vector(WeightedMean(dat1, lat = lat1, lon = lon1)),
--0.009785971,
-tolerance = 0.0001
-)
+test_that("3. Output test: dat2", {
+  expect_equal(
+    dim(WeightedMean(dat2, lat = lat2, lon = lon2)),
+    c(sdate = 2)
+  )
+  expect_equal(
+    as.vector(WeightedMean(dat2, lat = lat2, lon = lon2)),
+    c(-0.005799676, -0.007599831),
+    tolerance = 0.0001
+  )
 })
 
-test_that("dat2", {
-expect_equal(
-dim(WeightedMean(dat2, lat = lat2, lon = lon2)),
-NULL
-)
-expect_equal(
-as.vector(WeightedMean(dat2, lat = lat2, lon = lon2)),
-c(-0.005799676, -0.007599831),
-tolerance = 0.0001
-)
+test_that("4. Output test: dat3", {
+  expect_equal(
+    dim(WeightedMean(dat3, lat = lat3, lon = lon3)),
+    c(sdate = 2)
+  )
+  expect_equal(
+    as.vector(WeightedMean(dat3, lat = lat3, lon = lon3)),
+    c(-0.0253997, 0.0132251),
+    tolerance = 0.0001
+  )
+})
+
+##############################################
+
+test_that("5. Output test: dat4", {
+  expect_equal(
+    dim(WeightedMean(dat4, lat = lat4, lon = lon4)),
+    c(sdate = 2, time = 1)
+  )
+  expect_equal(
+    as.vector(WeightedMean(dat4, lat = lat4, lon = lon4)),
+    c(-0.005799676, -0.007599831),
+    tolerance = 0.0001
+  )
+  expect_equal(
+    dim(WeightedMean(dat4, lat = lat4, lon = lon4, mask = mask, region = region)),
+    c(sdate = 2, time = 1)
+  )
+  expect_equal(
+    as.vector(WeightedMean(dat4, lat = lat4, lon = lon4, 
+                           mask = mask, region = region)),
+    c( 0.03610427, 0.02197599),
+    tolerance = 0.0001
+  )
 })
 
-test_that("dat3", {
-expect_equal(
-dim(WeightedMean(dat3, lat = lat3, lon = lon3)),
-NULL
-)
-expect_equal(
-as.vector(WeightedMean(dat3, lat = lat3, lon = lon3)),
-c(-0.0253997, 0.0132251),
-tolerance = 0.0001
-)
+##############################################
 
+test_that("6. Output test: dat4 (mask, region, ncores)", {
+  expect_equal(
+    dim(WeightedMean(dat4, lat = lat4, lon = lon4, mask = mask, region = region)),
+    c(sdate = 2, time = 1)
+  )
+  expect_equal(
+    as.vector(WeightedMean(dat4, lat = lat4, lon = lon4, mask = mask, 
+                           region = region, ncores = 1)),
+    c( 0.03610427, 0.02197599),
+    tolerance = 0.0001
+  )
 })
 
+##############################################
 
-test_that("dat4", {
-expect_equal(
-dim(WeightedMean(dat4, lat = lat4, lon = lon4)),
-c(sdate = 2, time = 1)
-)
-expect_equal(
-as.vector(WeightedMean(dat4, lat = lat4, lon = lon4)),
-c(-0.005799676, -0.007599831),
-tolerance = 0.0001
-)
+test_that("7. Output test: dat5", {
+  expect_equal(
+    dim(WeightedMean(dat5, lat = lat4, lon = lon4, na.rm = FALSE)),
+    c(sdate = 2, time = 1)
+  )
+  expect_equal(
+    as.vector(WeightedMean(dat5, lat = lat4, lon = lon4, na.rm = FALSE)),
+    c(NA, -0.007599831),
+    tolerance = 0.0001
+  )
+  expect_equal(
+    as.vector(WeightedMean(dat5, lat = lat4, lon = lon4, na.rm = TRUE)),
+    as.vector(WeightedMean(dat4, lat = lat4, lon = lon4, na.rm = TRUE)),
+    tolerance = 0.0001
+  )
+  expect_equal(
+    as.vector(WeightedMean(dat4, lat = lat4, lon = lon4, na.rm = FALSE)),
+    c(-0.005799676, -0.007599831),
+    tolerance = 0.0001
+  )
 })
-- 
GitLab