From 0b36ea1ed72d13e0b0da6e4d0e610ccb40e52ade Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Wed, 10 Jan 2024 12:59:22 +0100
Subject: [PATCH 1/6] Add new function CST_ChangeDimNames()

---
 R/CST_ChangeDimNames.R | 74 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 74 insertions(+)
 create mode 100644 R/CST_ChangeDimNames.R

diff --git a/R/CST_ChangeDimNames.R b/R/CST_ChangeDimNames.R
new file mode 100644
index 00000000..503b67aa
--- /dev/null
+++ b/R/CST_ChangeDimNames.R
@@ -0,0 +1,74 @@
+#'Change the name of one or more dimensions for an object of class s2dv_cube
+#'
+#'Change the names of the dimensions specified in 'original_names' to the names
+#'in 'new_names'. The coordinate names and the dimensions of any attributes
+#'are also modified accordingly. 
+#' 
+#'@author Agudetse Roures Victoria, \email{victoria.agudetse@bsc.es}
+#'
+#'@param data An object of class \code{s2dv_cube} whose dimension names
+#'  should be changed.
+#'@param original_names A single character string or a vector indicating the 
+#'  dimensions to be renamed.
+#'@param new_names A single character string or a vector indicating the new
+#'  dimension names, in the same order as the dimensions in 'original_names'. 
+#'
+#'@return An object of class \code{s2dv_cube} with similar data, coordinates and 
+#'attributes as the \code{data} input, but with modified dimension names.
+#'
+#'@examples
+#'#Example with sample data:
+#'# Check original dimensions and coordinates
+#'lonlat_temp$exp$dims
+#'names(lonlat_temp$exp$coords)
+#'dim(lonlat_temp$exp$attrs$Dates)
+#'# Change 'dataset' to 'dat' and 'ftime' to 'time'
+#'exp <- CST_ChangeDimNames(lonlat_temp$exp,
+#'                          original_names = c("dataset", "ftime"),
+#'                          new_names = c("dat", "time"))
+#'# Check new dimensions and coordinates
+#'exp$dims
+#'names(exp$coords)
+#'dim(lonlat_temp$exp$attrs$Dates)
+#' 
+#'@export
+CST_ChangeDimNames <- function(data, original_names, new_names) {
+  if (!inherits(data, "s2dv_cube")) {
+    stop("Parameter 'data' must be an object of class 's2dv_cube'")
+  }
+  if (!(length(original_names) == length(new_names))) {
+    stop("The number of dimension names in 'new_names' must be the same
+         as in 'original_names'")
+  }
+  if (!all(original_names %in% names(data$dims))) {
+    stop("Some of the dimensions in 'original_names' could not be found in
+         'data'")
+  }
+  for (index in 1:length(original_names)) {
+    original_name <- original_names[index]
+    new_name <- new_names[index]
+    # Step 1: Change dims and data
+    names(data$dims)[which(names(data$dims) == original_name)] <- new_name
+    dim(data$data) <- data$dims
+    # Step 2: Change coords
+    names(data$coords)[which(names(data$coords) == original_name)] <- new_name
+    # Step 3: Change attrs
+    # 3.1 - Dates
+    if (original_name %in% names(dim(data$attrs$Dates))) {
+      names(dim(data$attrs$Dates))[which(names(dim(data$attrs$Dates)) 
+                                         == original_name)] <- new_name
+    }
+    # 3.2 - Variable metadata
+    if (original_name %in% names(data$attrs$Variable$metadata)) {
+      names(data$attrs$Variable$metadata)[which(names(data$attrs$Variable$metadata) 
+                                                == original_name)] <- new_name
+    }
+    # 3.3 - Source files
+    if (original_name %in% names(dim(data$attrs$source_files))) {
+      names(dim(data$attrs$source_files))[which(names(dim(data$attrs$source_files))
+                                                == original_name)] <- new_name
+    }
+  }
+  return(data)
+}
+
-- 
GitLab


From 16d762d1d3f2c4fcfca3564e9f1a557db651fd33 Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Wed, 10 Jan 2024 13:23:28 +0100
Subject: [PATCH 2/6] Update DESCRIPTION, fix example

---
 DESCRIPTION            | 2 +-
 R/CST_ChangeDimNames.R | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 3af5dcb1..4e41770d 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -90,5 +90,5 @@ VignetteBuilder: knitr
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 Config/testthat/edition: 3
diff --git a/R/CST_ChangeDimNames.R b/R/CST_ChangeDimNames.R
index 503b67aa..a36f42a3 100644
--- a/R/CST_ChangeDimNames.R
+++ b/R/CST_ChangeDimNames.R
@@ -29,7 +29,7 @@
 #'# Check new dimensions and coordinates
 #'exp$dims
 #'names(exp$coords)
-#'dim(lonlat_temp$exp$attrs$Dates)
+#'dim(exp$attrs$Dates)
 #' 
 #'@export
 CST_ChangeDimNames <- function(data, original_names, new_names) {
-- 
GitLab


From 897035a01258146107b3d1df330e23d31d3478b3 Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Wed, 10 Jan 2024 17:00:06 +0100
Subject: [PATCH 3/6] Improve efficiency, add modification of attributes, add
 dots to error messages

---
 R/CST_ChangeDimNames.R | 21 ++++++++++++++++-----
 1 file changed, 16 insertions(+), 5 deletions(-)

diff --git a/R/CST_ChangeDimNames.R b/R/CST_ChangeDimNames.R
index a36f42a3..99347b00 100644
--- a/R/CST_ChangeDimNames.R
+++ b/R/CST_ChangeDimNames.R
@@ -34,22 +34,26 @@
 #'@export
 CST_ChangeDimNames <- function(data, original_names, new_names) {
   if (!inherits(data, "s2dv_cube")) {
-    stop("Parameter 'data' must be an object of class 's2dv_cube'")
+    stop("Parameter 'data' must be an object of class 's2dv_cube'.")
   }
   if (!(length(original_names) == length(new_names))) {
     stop("The number of dimension names in 'new_names' must be the same
-         as in 'original_names'")
+         as in 'original_names'.")
   }
   if (!all(original_names %in% names(data$dims))) {
     stop("Some of the dimensions in 'original_names' could not be found in
-         'data'")
+         'data'.")
   }
   for (index in 1:length(original_names)) {
     original_name <- original_names[index]
     new_name <- new_names[index]
-    # Step 1: Change dims and data
+    # Step 1: Change dims
     names(data$dims)[which(names(data$dims) == original_name)] <- new_name
-    dim(data$data) <- data$dims
+    # dim(data$data) <- data$dims
+    # ## TODO: Improve code
+    # if !(is.null(attributes(data$data)$dimensions)) {
+    #   attributes(data$data)$dimensions <- names(data$dims)
+    # }
     # Step 2: Change coords
     names(data$coords)[which(names(data$coords) == original_name)] <- new_name
     # Step 3: Change attrs
@@ -69,6 +73,13 @@ CST_ChangeDimNames <- function(data, original_names, new_names) {
                                                 == original_name)] <- new_name
     }
   }
+  # Change data dimnames after renaming all dimensions
+  dim(data$data) <- data$dims
+  if (!is.null(attributes(data$data)$dimensions)) {
+    attributes(data$data)$dimensions <- names(data$dims)
+  }
+  # Change $Dates 'dim' attribute
+  attr(attributes(data$attrs$Dates)$dim, "names") <- names(dim(data$attrs$Dates))
   return(data)
 }
 
-- 
GitLab


From d66509df44d3d45458cda54be862a78a6641361a Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Wed, 10 Jan 2024 17:00:48 +0100
Subject: [PATCH 4/6] update function

---
 R/CST_ChangeDimNames.R | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/R/CST_ChangeDimNames.R b/R/CST_ChangeDimNames.R
index 99347b00..876f5183 100644
--- a/R/CST_ChangeDimNames.R
+++ b/R/CST_ChangeDimNames.R
@@ -49,11 +49,6 @@ CST_ChangeDimNames <- function(data, original_names, new_names) {
     new_name <- new_names[index]
     # Step 1: Change dims
     names(data$dims)[which(names(data$dims) == original_name)] <- new_name
-    # dim(data$data) <- data$dims
-    # ## TODO: Improve code
-    # if !(is.null(attributes(data$data)$dimensions)) {
-    #   attributes(data$data)$dimensions <- names(data$dims)
-    # }
     # Step 2: Change coords
     names(data$coords)[which(names(data$coords) == original_name)] <- new_name
     # Step 3: Change attrs
-- 
GitLab


From 93544eb67d98e1b4e88ec2db319b56df23a7f247 Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Wed, 10 Jan 2024 17:03:22 +0100
Subject: [PATCH 5/6] Add checks for 'original_names' and 'new_names'
 parameters

---
 R/CST_ChangeDimNames.R | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/R/CST_ChangeDimNames.R b/R/CST_ChangeDimNames.R
index 876f5183..1c79890e 100644
--- a/R/CST_ChangeDimNames.R
+++ b/R/CST_ChangeDimNames.R
@@ -36,6 +36,15 @@ CST_ChangeDimNames <- function(data, original_names, new_names) {
   if (!inherits(data, "s2dv_cube")) {
     stop("Parameter 'data' must be an object of class 's2dv_cube'.")
   }
+  if (!is.character(original_names)) {
+    stop("Parameter 'original_names' must be a character string or a
+         vector of character strings.")
+  }
+  if (!is.character(new_names)) {
+    stop("Parameter 'new_names' must be a character string or a
+         vector of character strings.")
+  }
+
   if (!(length(original_names) == length(new_names))) {
     stop("The number of dimension names in 'new_names' must be the same
          as in 'original_names'.")
-- 
GitLab


From 90894e1a2171e0bcbf01c6bc97bf8c2a1098de0f Mon Sep 17 00:00:00 2001
From: Eva Rifa <eva.rifarovira@bsc.es>
Date: Thu, 11 Jan 2024 09:24:43 +0100
Subject: [PATCH 6/6] Add unit test, add few style spaces and update NAMESPACE.

---
 NAMESPACE                                |  1 +
 R/CST_ChangeDimNames.R                   | 18 ++---
 man/CST_ChangeDimNames.Rd                | 46 ++++++++++++
 tests/testthat/test-CST_ChangeDimNames.R | 95 ++++++++++++++++++++++++
 4 files changed, 151 insertions(+), 9 deletions(-)
 create mode 100644 man/CST_ChangeDimNames.Rd
 create mode 100644 tests/testthat/test-CST_ChangeDimNames.R

diff --git a/NAMESPACE b/NAMESPACE
index 012f76cf..a03e7c8b 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -19,6 +19,7 @@ export(CST_BEI_Weighting)
 export(CST_BiasCorrection)
 export(CST_Calibration)
 export(CST_CategoricalEnsCombination)
+export(CST_ChangeDimNames)
 export(CST_DynBiasCorrection)
 export(CST_EnsClustering)
 export(CST_InsertDim)
diff --git a/R/CST_ChangeDimNames.R b/R/CST_ChangeDimNames.R
index 1c79890e..433039b6 100644
--- a/R/CST_ChangeDimNames.R
+++ b/R/CST_ChangeDimNames.R
@@ -17,7 +17,7 @@
 #'attributes as the \code{data} input, but with modified dimension names.
 #'
 #'@examples
-#'#Example with sample data:
+#'# Example with sample data:
 #'# Check original dimensions and coordinates
 #'lonlat_temp$exp$dims
 #'names(lonlat_temp$exp$coords)
@@ -37,21 +37,21 @@ CST_ChangeDimNames <- function(data, original_names, new_names) {
     stop("Parameter 'data' must be an object of class 's2dv_cube'.")
   }
   if (!is.character(original_names)) {
-    stop("Parameter 'original_names' must be a character string or a
-         vector of character strings.")
+    stop("Parameter 'original_names' must be a character string or a ",
+         "vector of character strings.")
   }
   if (!is.character(new_names)) {
-    stop("Parameter 'new_names' must be a character string or a
-         vector of character strings.")
+    stop("Parameter 'new_names' must be a character string or a ",
+         "vector of character strings.")
   }
 
   if (!(length(original_names) == length(new_names))) {
-    stop("The number of dimension names in 'new_names' must be the same
-         as in 'original_names'.")
+    stop("The number of dimension names in 'new_names' must be the same ",
+         "as in 'original_names'.")
   }
   if (!all(original_names %in% names(data$dims))) {
-    stop("Some of the dimensions in 'original_names' could not be found in
-         'data'.")
+    stop("Some of the dimensions in 'original_names' could not be found in ",
+         "'data'.")
   }
   for (index in 1:length(original_names)) {
     original_name <- original_names[index]
diff --git a/man/CST_ChangeDimNames.Rd b/man/CST_ChangeDimNames.Rd
new file mode 100644
index 00000000..86806be0
--- /dev/null
+++ b/man/CST_ChangeDimNames.Rd
@@ -0,0 +1,46 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/CST_ChangeDimNames.R
+\name{CST_ChangeDimNames}
+\alias{CST_ChangeDimNames}
+\title{Change the name of one or more dimensions for an object of class s2dv_cube}
+\usage{
+CST_ChangeDimNames(data, original_names, new_names)
+}
+\arguments{
+\item{data}{An object of class \code{s2dv_cube} whose dimension names
+should be changed.}
+
+\item{original_names}{A single character string or a vector indicating the 
+dimensions to be renamed.}
+
+\item{new_names}{A single character string or a vector indicating the new
+dimension names, in the same order as the dimensions in 'original_names'.}
+}
+\value{
+An object of class \code{s2dv_cube} with similar data, coordinates and 
+attributes as the \code{data} input, but with modified dimension names.
+}
+\description{
+Change the names of the dimensions specified in 'original_names' to the names
+in 'new_names'. The coordinate names and the dimensions of any attributes
+are also modified accordingly.
+}
+\examples{
+# Example with sample data:
+# Check original dimensions and coordinates
+lonlat_temp$exp$dims
+names(lonlat_temp$exp$coords)
+dim(lonlat_temp$exp$attrs$Dates)
+# Change 'dataset' to 'dat' and 'ftime' to 'time'
+exp <- CST_ChangeDimNames(lonlat_temp$exp,
+                         original_names = c("dataset", "ftime"),
+                         new_names = c("dat", "time"))
+# Check new dimensions and coordinates
+exp$dims
+names(exp$coords)
+dim(exp$attrs$Dates)
+
+}
+\author{
+Agudetse Roures Victoria, \email{victoria.agudetse@bsc.es}
+}
diff --git a/tests/testthat/test-CST_ChangeDimNames.R b/tests/testthat/test-CST_ChangeDimNames.R
new file mode 100644
index 00000000..ceef7375
--- /dev/null
+++ b/tests/testthat/test-CST_ChangeDimNames.R
@@ -0,0 +1,95 @@
+##############################################
+test_that("1. Input checks", {
+  expect_error(
+    CST_ChangeDimNames(1),
+    "Parameter 'data' must be an object of class 's2dv_cube'."
+  )
+  expect_error(
+    CST_ChangeDimNames(lonlat_prec_st, 1, 'bbb'),
+    paste0("Parameter 'original_names' must be a character string or a ", 
+           "vector of character strings.")
+  )
+  expect_error(
+    CST_ChangeDimNames(lonlat_prec_st, 'aaa', 1),
+    paste0("Parameter 'new_names' must be a character string or a ",
+           "vector of character strings.")
+  )
+  expect_error(
+    CST_ChangeDimNames(lonlat_prec_st, 'aaa', c('aaa', 'bbb')),
+    paste0("The number of dimension names in 'new_names' must be the same ",
+           "as in 'original_names'.")
+  )
+  expect_error(
+    CST_ChangeDimNames(lonlat_prec_st, 'aaa', 'bbb'),
+    paste0("Some of the dimensions in 'original_names' could not be found in ",
+           "'data'.")
+  )
+})
+##############################################
+test_that("2. Output checks", {
+  exp <- CST_ChangeDimNames(lonlat_temp_st$exp,
+                            original_names = c("lon", 'ftime', 'sdate'),
+                            new_names = c("lons", 'ftimes', 'sdates'))
+  # dims
+  expect_equal(
+    dim(exp$data),
+    c(dataset = 1, var = 1, member = 15, sdates = 6, ftimes = 3, lat = 22, lons = 53)
+  )
+  expect_equal(
+    exp$dims,
+    dim(exp$data)
+  )
+  expect_equal(
+    as.vector(exp$data),
+    as.vector(lonlat_temp_st$exp$data)
+  )
+  # coords
+  expect_equal(
+    names(exp$coords),
+    c("dataset", "var", "member", "sdates", "ftimes", "lat", "lons")
+  )
+  # dim Dates
+  expect_equal(
+    dim(exp$attrs$Dates),
+    c(sdates = 6, ftimes = 3)
+  )
+  # variable metadata
+  expect_equal(
+    names(exp$attrs$Variable$metadata),
+    c("lat", "lons", "ftimes", "tas" )
+  )
+  # source_files
+  expect_equal(
+    dim(exp$attrs$source_files),
+    c(dataset = 1, var = 1, sdates = 6)
+  )
+  # Dates 'dim' attribute
+  dat <- CST_ChangeDimNames(lonlat_prec,
+                            original_names = c("lon", 'ftime', 'sdate', 'member'),
+                            new_names = c("lons", 'ftimes', 'sdates', 'members')) 
+  expect_equal(
+    as.vector(lonlat_prec$data),
+    as.vector(dat$data)
+  )
+  expect_equal(
+    attributes(dat$attrs$Dates)$dim,
+    c(ftimes = 31, sdates = 3)
+  )
+  expect_equal(
+    attributes(exp$attrs$Dates)$dim,
+    c(sdates = 6, ftimes = 3)
+  )
+  expect_equal(
+    as.vector(dat$attrs$Dates),
+    as.vector(lonlat_prec$attrs$Dates)
+  )
+  # attribute dimensions
+  expect_equal(
+    attributes(dat$data)$dimensions,
+    names(dim(dat$data))
+  )
+  expect_equal(
+    attributes(exp$data)$dimensions,
+    NULL
+  )
+})
\ No newline at end of file
-- 
GitLab