From 20ad5bc298512dc122cfe84930b15c534c6b9dbe Mon Sep 17 00:00:00 2001
From: allabres <alba.llabres@bsc.es>
Date: Fri, 23 Aug 2024 14:48:44 +0200
Subject: [PATCH 01/14] solved issue dates parameter

---
 R/PeriodStandardization.R | 1 +
 1 file changed, 1 insertion(+)

diff --git a/R/PeriodStandardization.R b/R/PeriodStandardization.R
index 6ab707e..93a77dd 100644
--- a/R/PeriodStandardization.R
+++ b/R/PeriodStandardization.R
@@ -108,6 +108,7 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear',
     }
   }
   res <- PeriodStandardization(data = data$data, data_cor = data_cor$data, 
+                               dates = data$attrs$Dates,
                                time_dim = time_dim, leadtime_dim = leadtime_dim, 
                                memb_dim = memb_dim, 
                                ref_period = ref_period,
-- 
GitLab


From 743dae5c85d8651471f5044012941ce53c3ccf40 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 30 Aug 2024 13:01:02 +0200
Subject: [PATCH 02/14] Fix grammatical errors in documentation and warning

---
 R/PeriodStandardization.R | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/R/PeriodStandardization.R b/R/PeriodStandardization.R
index 93a77dd..b71270f 100644
--- a/R/PeriodStandardization.R
+++ b/R/PeriodStandardization.R
@@ -12,12 +12,12 @@
 #'coordinates and therefore, the result will be filled with NA for the 
 #'specific coordinates. When NAs are not removed, if the length of the data for 
 #'a computational step is smaller than 4, there will not be enough data for 
-#'standarize and the result will be also filled with NAs for that coordinates. 
+#'standardization and the result will be also filled with NAs for those coordinates. 
 #'About the distribution used to fit the data, there are only two possibilities: 
-#''log-logistic' and 'Gamma'. The 'Gamma' method only works when only 
-#'precipitation is provided and other variables are 0 because it is positive 
+#''log-logistic' and 'Gamma'. The 'Gamma' method works only when precipitation 
+#'is the sole variable provided, and all other variables are 0 because it is positive 
 #'defined (SPI indicator). When only 'data' is provided ('data_cor' is NULL) the 
-#'standardization is computed with cross validation. This function is build to 
+#'standardization is computed with cross validation. This function is built to 
 #'be compatible with other tools in that work with 's2dv_cube' object 
 #'class. The input data must be this object class. If you don't work with 
 #''s2dv_cube', see PeriodStandardization. For more information on the SPEI 
@@ -338,7 +338,7 @@ PeriodStandardization <- function(data, data_cor = NULL, dates = NULL,
               "will not be used.")
       ref_period <- NULL
     } else if (!all(unlist(ref_period) %in% years_dates)) {
-      warning("Parameter 'ref_period' contain years outside the dates. ", 
+      warning("Parameter 'ref_period' contains years outside the dates. ", 
               "It will not be used.")
       ref_period <- NULL
     } else {
-- 
GitLab


From 939eba075bef67c0dc912dd6ac088678482bdf32 Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 30 Aug 2024 13:12:31 +0200
Subject: [PATCH 03/14] Fix warning in test-PeriodStandardization.R

---
 tests/testthat/test-PeriodStandardization.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/testthat/test-PeriodStandardization.R b/tests/testthat/test-PeriodStandardization.R
index 7673db2..1e816c0 100644
--- a/tests/testthat/test-PeriodStandardization.R
+++ b/tests/testthat/test-PeriodStandardization.R
@@ -130,7 +130,7 @@ test_that("1. Initial checks PeriodStandardization", {
   expect_warning(
     PeriodStandardization(data = dat1, ref_period = list(2020, 2021), 
                           dates = dates1),
-    paste0("Parameter 'ref_period' contain years outside the dates. ", 
+    paste0("Parameter 'ref_period' contains years outside the dates. ", 
            "It will not be used.")
   )
   # handle_infinity
-- 
GitLab


From cc19ae17e948949b36f25755f38036535a173f5d Mon Sep 17 00:00:00 2001
From: ARIADNA BATALLA FERRES <ariadna.batalla@bsc.es>
Date: Fri, 30 Aug 2024 13:29:36 +0200
Subject: [PATCH 04/14] Update man/CST_PeriodStandardization.Rd

---
 man/CST_PeriodStandardization.Rd | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/man/CST_PeriodStandardization.Rd b/man/CST_PeriodStandardization.Rd
index fe0dd3b..95f6474 100644
--- a/man/CST_PeriodStandardization.Rd
+++ b/man/CST_PeriodStandardization.Rd
@@ -105,12 +105,12 @@ parameter 'na.rm', the standardization cannot be carried out for those
 coordinates and therefore, the result will be filled with NA for the 
 specific coordinates. When NAs are not removed, if the length of the data for 
 a computational step is smaller than 4, there will not be enough data for 
-standarize and the result will be also filled with NAs for that coordinates. 
+standardization and the result will be also filled with NAs for those coordinates. 
 About the distribution used to fit the data, there are only two possibilities: 
-'log-logistic' and 'Gamma'. The 'Gamma' method only works when only 
-precipitation is provided and other variables are 0 because it is positive 
+'log-logistic' and 'Gamma'. The 'Gamma' method works only when precipitation 
+is the sole variable provided, and all other variables are 0 because it is positive 
 defined (SPI indicator). When only 'data' is provided ('data_cor' is NULL) the 
-standardization is computed with cross validation. This function is build to 
+standardization is computed with cross validation. This function is built to 
 be compatible with other tools in that work with 's2dv_cube' object 
 class. The input data must be this object class. If you don't work with 
 's2dv_cube', see PeriodStandardization. For more information on the SPEI 
-- 
GitLab


From f9234b3a3e233f739127bedacb02bc7d33238676 Mon Sep 17 00:00:00 2001
From: tkariyat <theertha.kariyathan@bsc.es>
Date: Wed, 16 Oct 2024 10:12:26 +0200
Subject: [PATCH 05/14] CST_PeriodPET(): Add longname and other variable
 metadata

---
 R/PeriodPET.R | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/R/PeriodPET.R b/R/PeriodPET.R
index 27d6eca..02ddb5f 100644
--- a/R/PeriodPET.R
+++ b/R/PeriodPET.R
@@ -91,8 +91,12 @@ CST_PeriodPET <- function(data, pet_method = 'hargreaves',
   source_files <- lapply(data, function(x) {x$attrs$source_files})
   coords <- data[[1]]$coords
   Dates <- data[[1]]$attrs$Dates
+  
   metadata <- data[[1]]$attrs$Variable$metadata
-  metadata_names <- intersect(names(dim(res)), names(metadata))
+  metadata[["PET"]]$longname <- "Potential evapotranspiration"
+  metadata[["PET"]]$units <- "mm"
+
+  metadata_names <- c(intersect(names(dim(res)), names(metadata)), "PET")
   suppressWarnings(
     res <- s2dv_cube(data = res, coords = coords, 
                      varName = paste0('PET'), 
@@ -383,4 +387,4 @@ PeriodPET <- function(data, dates, lat, pet_method = 'hargreaves',
     pet <- array(pet[which(mask_dates == 1)], dim = dims)
   }
   return(pet)
-}
\ No newline at end of file
+}
-- 
GitLab


From 62ba9194542b096dc4e477026f46be82617f3d37 Mon Sep 17 00:00:00 2001
From: tkariyat <theertha.kariyathan@bsc.es>
Date: Thu, 9 Jan 2025 15:53:51 +0100
Subject: [PATCH 06/14] Add contribute.md

---
 CONTRIBUTING.md                             | 66 +++++++++++++++++++++
 R/PeriodStandardization.R                   | 12 +++-
 tests/testthat/test-PeriodStandardization.R | 19 +++++-
 3 files changed, 92 insertions(+), 5 deletions(-)
 create mode 100644 CONTRIBUTING.md

diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
new file mode 100644
index 0000000..3faa54d
--- /dev/null
+++ b/CONTRIBUTING.md
@@ -0,0 +1,66 @@
+### Questions and bug reports
+
+If you have questions about the usage of a function or would like to report a bug, please follow these steps:
+
+1. Use the search function in GitLab to see if a similar problem has already been reported and/or solved.
+
+2. Rather than including a long script, try to run your code in small blocks to narrow down where the problem is coming from as much as possible.
+
+3. Open an issue tagging the maintainers (@tkariyat), and include a descriptive title and a piece of code to reproduce your problem (if applicable).
+
+### How to contribute
+
+If you would like to add a bugfix, an enhancement or a new functions, follow these steps:
+
+1. Open an issue to ask for help or describe a feature to be integrated
+
+2. Agree with the maintainers (@tkariyat) on the requirements
+
+3. Create a new branch from master with a meaningful name
+
+4. Once the development is finished, open a merge request to merge the branch on master
+
+*Note: Remember to work with multidimensional arrays with named dimensions when possible and use multiApply (https://earth.bsc.es/gitlab/ces/multiApply)*
+
+### Adding a function
+
+To add a new function in this R package, follow these considerations:
+
+* Each function exposed to the users should be in its own separate file in the R folder
+* The name of the function should match the name of the file (e.g.: `Function()` included in file **Function.R**
+* The documentation should be in roxygen2 format as a header of the function
+* Once the function and the documentation are finished, run the command `devtools::document()` in your R terminal to automatically generate the **Function.Rd** file
+* When doing the development, please use an R version between R/4.1.2 and R/4.3.x 
+
+### Style guide
+
+* Use `<-` for variable assignment
+* Include spaces between operators (e.g. `+`, `-`, `&`), before `{`, and after `for`, `if`, `while`, `,` and `)`.
+* When possible, maximum line length should be 100 characters (soft limit of 80 characters).
+* Number of indentation spaces is 2, using tabs for indentation is forbidden.
+* Double quotes are recommended for strings. When writing quotes within quoted text, use double quotes outside and single quotes inside. E.g.: `“Parameter 'na.rm' is missing.”`
+* Self-explanatory names are preferred for variables. Try to be consistent with the variable naming style. Generally: avoid special characters (except underscores) and reserved words (ex: if, for, else, …)
+* Remember to include short comments to make the code easier to understand. Comments should be in their own line and they should start with `#` followed by a space. Comments that start with `##` and a space are for details not needed to understand the general procedure but useful to make note of more technical aspects of the code.
+
+#### Examples:
+
+```r
+# Proper spacing, indentation spaces and text quotes:
+NewFunction <- function(text = "default", uppercase = TRUE) {
+  # Check uppercase parameter
+  if (!is.logical(uppercase)) {
+    stop("Parameter 'uppercase' should be TRUE or FALSE.")
+  }
+  # Only transform text if needed
+  if (uppercase && is.character(text)) {
+    text <- toupper(text)
+  }
+  return(text)
+}
+
+# How to format line breaks to avoid long lines:
+my_strings <- list(one = "one",
+                   two = "two",
+                   three = "three",
+                   four = "four")
+```
diff --git a/R/PeriodStandardization.R b/R/PeriodStandardization.R
index b71270f..00ebc71 100644
--- a/R/PeriodStandardization.R
+++ b/R/PeriodStandardization.R
@@ -125,7 +125,10 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear',
 
   if (is.null(data_cor)) {
     data$data <- std
-    data$attrs$Variable$varName <- paste0(data$attrs$Variable$varName, ' standardized')
+    data_longname <- data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname
+    if (!is.null(data_longname)) {
+      data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname <- paste(data_longname, 'standardized')
+    }
     if (return_params) {
       return(list(spei = data, params = params))
     } else {
@@ -133,7 +136,10 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear',
     }
   } else {
     data_cor$data <- std
-    data_cor$attrs$Variable$varName <- paste0(data_cor$attrs$Variable$varName, ' standardized')
+    data_cor_longname <- data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname
+    if (!is.null(data_cor_longname)) {
+      data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname <- paste(data_cor_longname, 'standardized')
+    }
     data_cor$attrs$Datasets <- c(data_cor$attrs$Datasets, data$attrs$Datasets)
     data_cor$attrs$source_files <- c(data_cor$attrs$source_files, data$attrs$source_files)
     return(data_cor)
@@ -644,4 +650,4 @@ PeriodStandardization <- function(data, data_cor = NULL, dates = NULL,
   } else {
     return(NA)
   }
-}
\ No newline at end of file
+}
diff --git a/tests/testthat/test-PeriodStandardization.R b/tests/testthat/test-PeriodStandardization.R
index 1e816c0..4def61d 100644
--- a/tests/testthat/test-PeriodStandardization.R
+++ b/tests/testthat/test-PeriodStandardization.R
@@ -38,7 +38,15 @@ dims3 <- c(syear = 6, time = 2, lat = 2, ensemble = 25)
 set.seed(1)
 dat3 <- array(abs(rnorm(600, 21.19, 25.64)), dim = dims)
 
-
+# dat4
+test <- NULL
+test$data <- array(rnorm(600, -204.1, 78.1), dim = dims)
+test$dims <- dims
+test$coords <- setNames(as.list(as.numeric(test$dims)), names(test$dims))
+test$attrs <- list(Variable = list(varName = 'prlr',
+                                   metadata = list(units = "m s-1", 
+                                                   longname = "Total precipitation")))
+class(test) <- 's2dv_cube'
 ##############################################
 
 test_that("1. Initial checks CST_PeriodStandardization", {
@@ -152,11 +160,18 @@ test_that("1. Initial checks PeriodStandardization", {
 
 test_that("2. Output checks", {
   # CST_PeriodStandardization
+  prlr <- CST_PeriodStandardization(data = test)
+  expect_equal(
+    names(prlr),
+    c("data", "dims", "coords", "attrs")
+  )
+  
   SPEI_s2dv_cube <- CST_PeriodStandardization(data = cube1)
   expect_equal(
     names(SPEI_s2dv_cube),
-    c('data', 'attrs')
+    c('data')
   )
+  
   # PeriodStandardization
   SPEI <- PeriodStandardization(data = dat1)
   expect_equal(
-- 
GitLab


From d144517e56acb7d36c08038c0363dca9222c10a6 Mon Sep 17 00:00:00 2001
From: THEERTHA KARIYATHAN <tkariyat@bscearth421.int.bsc.es>
Date: Tue, 4 Feb 2025 15:26:31 +0100
Subject: [PATCH 07/14] ref_period and NA bug

---
 R/PeriodStandardization.R | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/R/PeriodStandardization.R b/R/PeriodStandardization.R
index b71270f..d9cedb2 100644
--- a/R/PeriodStandardization.R
+++ b/R/PeriodStandardization.R
@@ -87,7 +87,7 @@
 #'class(data) <- 's2dv_cube'
 #'SPEI <- CST_PeriodStandardization(data = data)
 #'@export
-CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', 
+CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', dates = NULL, 
                                       leadtime_dim = 'time', memb_dim = 'ensemble',
                                       ref_period = NULL,
                                       handle_infinity = FALSE, 
@@ -125,7 +125,10 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear',
 
   if (is.null(data_cor)) {
     data$data <- std
-    data$attrs$Variable$varName <- paste0(data$attrs$Variable$varName, ' standardized')
+    data_longname <- data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname
+    if (!is.null(data_longname)) {
+      data$attrs$Variable$metadata[[data$attrs$Variable$varName]]$longname <- paste(data_longname, 'standardized')
+    }
     if (return_params) {
       return(list(spei = data, params = params))
     } else {
@@ -133,7 +136,10 @@ CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear',
     }
   } else {
     data_cor$data <- std
-    data_cor$attrs$Variable$varName <- paste0(data_cor$attrs$Variable$varName, ' standardized')
+    data_cor_longname <- data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname
+    if (!is.null(data_cor_longname)) {
+      data_cor$attrs$Variable$metadata[[data_cor$attrs$Variable$varName]]$longname <- paste(data_cor_longname, 'standardized')
+    }
     data_cor$attrs$Datasets <- c(data_cor$attrs$Datasets, data$attrs$Datasets)
     data_cor$attrs$source_files <- c(data_cor$attrs$source_files, data$attrs$source_files)
     return(data_cor)
@@ -611,8 +617,8 @@ PeriodStandardization <- function(data, data_cor = NULL, dates = NULL,
   }
   if (handle_infinity) { 
     # could also use "param_error" ?; we are giving it the min/max value of the grid point
-    spei_mod[is.infinite(spei_mod) & spei_mod < 0] <- min(spei_mod[!is.infinite(spei_mod)])
-    spei_mod[is.infinite(spei_mod) & spei_mod > 0] <- max(spei_mod[!is.infinite(spei_mod)]) 
+    spei_mod[is.infinite(spei_mod) & spei_mod < 0] <- min(spei_mod[!is.infinite(spei_mod)],na.rm = T)
+    spei_mod[is.infinite(spei_mod) & spei_mod > 0] <- max(spei_mod[!is.infinite(spei_mod)],na.rm = T) 
   }
   if (return_params) {
     return(list(spei = spei_mod, params = params_result))
@@ -644,4 +650,4 @@ PeriodStandardization <- function(data, data_cor = NULL, dates = NULL,
   } else {
     return(NA)
   }
-}
\ No newline at end of file
+}
-- 
GitLab


From f4897b6b55571d197b2ceb32db5fdf95f63997d3 Mon Sep 17 00:00:00 2001
From: THEERTHA KARIYATHAN <tkariyat@bscearth421.int.bsc.es>
Date: Fri, 7 Feb 2025 12:29:27 +0100
Subject: [PATCH 08/14] na.rm in max/min()

---
 .Rbuildignore             | 2 ++
 .gitignore                | 1 +
 R/PeriodStandardization.R | 6 +++---
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index 2a2a753..da90668 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -12,3 +12,5 @@
 ^cran-comments\.md$
 ./vignettes/*.md
 ^inst/doc/paper-figure-PlotForecastPDF\.R$
+^.*\.Rproj$
+^\.Rproj\.user$
diff --git a/.gitignore b/.gitignore
index 23a5603..022a306 100644
--- a/.gitignore
+++ b/.gitignore
@@ -18,3 +18,4 @@ Rplots.pdf
 *.RData
 !data/*.RData
 .\.nfs*
+.Rproj.user
diff --git a/R/PeriodStandardization.R b/R/PeriodStandardization.R
index d9cedb2..dcef847 100644
--- a/R/PeriodStandardization.R
+++ b/R/PeriodStandardization.R
@@ -87,7 +87,7 @@
 #'class(data) <- 's2dv_cube'
 #'SPEI <- CST_PeriodStandardization(data = data)
 #'@export
-CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', dates = NULL, 
+CST_PeriodStandardization <- function(data, data_cor = NULL, time_dim = 'syear', 
                                       leadtime_dim = 'time', memb_dim = 'ensemble',
                                       ref_period = NULL,
                                       handle_infinity = FALSE, 
@@ -617,8 +617,8 @@ PeriodStandardization <- function(data, data_cor = NULL, dates = NULL,
   }
   if (handle_infinity) { 
     # could also use "param_error" ?; we are giving it the min/max value of the grid point
-    spei_mod[is.infinite(spei_mod) & spei_mod < 0] <- min(spei_mod[!is.infinite(spei_mod)],na.rm = T)
-    spei_mod[is.infinite(spei_mod) & spei_mod > 0] <- max(spei_mod[!is.infinite(spei_mod)],na.rm = T) 
+    spei_mod[is.infinite(spei_mod) & spei_mod < 0] <- min(spei_mod[!is.infinite(spei_mod)],na.rm = TRUE)
+    spei_mod[is.infinite(spei_mod) & spei_mod > 0] <- max(spei_mod[!is.infinite(spei_mod)],na.rm = TRUE) 
   }
   if (return_params) {
     return(list(spei = spei_mod, params = params_result))
-- 
GitLab


From df92e102e87b054fb22978f711bc7adcdd887851 Mon Sep 17 00:00:00 2001
From: tkariyat <theertha.kariyathan@bsc.es>
Date: Thu, 20 Mar 2025 12:01:53 +0100
Subject: [PATCH 09/14] Time aggregation functions not drop time dimension

---
 R/AccumulationExceedingThreshold.R            |  7 +--
 R/PeriodAccumulation.R                        |  8 ++--
 R/PeriodMax.R                                 | 10 ++--
 R/PeriodMean.R                                |  8 ++--
 R/PeriodMin.R                                 |  7 +--
 R/PeriodVariance.R                            |  7 +--
 R/TotalSpellTimeExceedingThreshold.R          |  7 +--
 R/TotalTimeExceedingThreshold.R               |  7 +--
 .../test-AccumulationExceedingThreshold.R     | 46 +++++++++----------
 tests/testthat/test-PeriodAccumulation.R      | 22 ++++-----
 tests/testthat/test-PeriodMax.R               | 10 ++--
 tests/testthat/test-PeriodMean.R              | 10 ++--
 tests/testthat/test-PeriodMin.R               | 10 ++--
 tests/testthat/test-PeriodVariance.R          | 10 ++--
 .../test-TotalSpellTimeExceedingThreshold.R   | 44 +++++++++---------
 .../test-TotalTimeExceedingThreshold.R        | 36 +++++++--------
 16 files changed, 129 insertions(+), 120 deletions(-)

diff --git a/R/AccumulationExceedingThreshold.R b/R/AccumulationExceedingThreshold.R
index b8ae9ae..054a8b7 100644
--- a/R/AccumulationExceedingThreshold.R
+++ b/R/AccumulationExceedingThreshold.R
@@ -113,7 +113,7 @@ CST_AccumulationExceedingThreshold <- function(data, threshold, op = '>', diff =
                                           na.rm = na.rm, ncores = ncores)
   data$data <- total
   data$dims <- dim(total)
-  data$coords[[time_dim]] <- NULL
+  data$coords[[time_dim]] <- 1 : length(data$dims[[time_dim]])
 
   if (!is.null(Dates)) {
     if (!is.null(start) && !is.null(end)) {
@@ -128,10 +128,10 @@ CST_AccumulationExceedingThreshold <- function(data, threshold, op = '>', diff =
       # Create time_bounds
       time_bounds <- NULL
       time_bounds$start <- ClimProjDiags::Subset(x = Dates, along = time_dim, 
-                                                 indices = 1, drop = 'selected')
+                                                 indices = 1, drop = FALSE)
       time_bounds$end <- ClimProjDiags::Subset(x = Dates, along = time_dim, 
                                                indices = dim(Dates)[time_dim], 
-                                               drop = 'selected')
+                                               drop = FALSE)
 
       # Add Dates in attrs
       data$attrs$Dates <- time_bounds$start
@@ -436,6 +436,7 @@ AccumulationExceedingThreshold <- function(data, threshold, op = '>', diff = FAL
                      ncores = ncores)$output1
     }
   }
+  dim(total) <- c(dim(total), setNames(1, time_dim))
   return(total)
 }
 
diff --git a/R/PeriodAccumulation.R b/R/PeriodAccumulation.R
index 8986e3f..8b0129f 100644
--- a/R/PeriodAccumulation.R
+++ b/R/PeriodAccumulation.R
@@ -129,12 +129,12 @@ CST_PeriodAccumulation <- function(data, start = NULL, end = NULL,
     data$attrs$Dates <- Dates 
   }
   if (is.null(rollwidth)) {
-    data$coords[[time_dim]] <- NULL
+    data$coords[[time_dim]] <- 1 : length(data$dims[[time_dim]])
     if (!is.null(dim(Dates))) {
       # Create time_bounds
       time_bounds <- NULL
-      time_bounds$start <- Subset(Dates, time_dim, 1, drop = 'selected')
-      time_bounds$end <- Subset(Dates, time_dim, dim(Dates)[time_dim], drop = 'selected')
+      time_bounds$start <- Subset(Dates, time_dim, 1, drop = FALSE)
+      time_bounds$end <- Subset(Dates, time_dim, dim(Dates)[time_dim], drop = FALSE)
 
       # Add Dates in attrs
       data$attrs$Dates <- time_bounds$start
@@ -321,7 +321,7 @@ PeriodAccumulation <- function(data, dates = NULL, start = NULL, end = NULL,
     pos <- match(dimnames, names(dim(total)))
     total <- aperm(total, pos)
   }
-
+  dim(total) <- c(dim(total), setNames(1, time_dim))
   return(total)
 }
 
diff --git a/R/PeriodMax.R b/R/PeriodMax.R
index 3ae23ec..f038aff 100644
--- a/R/PeriodMax.R
+++ b/R/PeriodMax.R
@@ -83,8 +83,8 @@ CST_PeriodMax <- function(data, start = NULL, end = NULL,
   
   data$data <- total
   data$dims <- dim(total)
-  data$coords[[time_dim]] <- NULL
-
+  data$coords[[time_dim]] <- 1 : length(data$dims[[time_dim]])
+  
   if (!is.null(Dates)) {
     if (!is.null(start) && !is.null(end)) {
       Dates <- SelectPeriodOnDates(dates = Dates, start = start, end = end,
@@ -98,10 +98,10 @@ CST_PeriodMax <- function(data, start = NULL, end = NULL,
       # Create time_bounds
       time_bounds <- NULL
       time_bounds$start <- ClimProjDiags::Subset(x = Dates, along = time_dim, 
-                                                 indices = 1, drop = 'selected')
+                                                 indices = 1, drop = FALSE)
       time_bounds$end <- ClimProjDiags::Subset(x = Dates, along = time_dim, 
                                                indices = dim(Dates)[time_dim], 
-                                               drop = 'selected')
+                                               drop = FALSE)
 
       # Add Dates in attrs
       data$attrs$Dates <- time_bounds$start
@@ -207,6 +207,8 @@ PeriodMax <- function(data, dates = NULL, start = NULL, end = NULL,
   }
   total <- Apply(list(data), target_dims = time_dim, fun = max,
                  na.rm = na.rm, ncores = ncores)$output1
+  
+  dim(total) <- c(dim(total), setNames(1, time_dim))
   return(total)
 }
 
diff --git a/R/PeriodMean.R b/R/PeriodMean.R
index f58bbeb..bebbedd 100644
--- a/R/PeriodMean.R
+++ b/R/PeriodMean.R
@@ -83,7 +83,7 @@ CST_PeriodMean <- function(data, start = NULL, end = NULL,
   
   data$data <- total
   data$dims <- dim(total)
-  data$coords[[time_dim]] <- NULL
+  data$coords[[time_dim]] <- 1 : length(data$dims[[time_dim]])
 
   if (!is.null(Dates)) {
     if (!is.null(start) && !is.null(end)) {
@@ -98,10 +98,10 @@ CST_PeriodMean <- function(data, start = NULL, end = NULL,
       # Create time_bounds
       time_bounds <- NULL
       time_bounds$start <- ClimProjDiags::Subset(x = Dates, along = time_dim, 
-                                                 indices = 1, drop = 'selected')
+                                                 indices = 1, drop = FALSE)
       time_bounds$end <- ClimProjDiags::Subset(x = Dates, along = time_dim, 
                                                indices = dim(Dates)[time_dim], 
-                                               drop = 'selected')
+                                               drop = FALSE)
 
       # Add Dates in attrs
       data$attrs$Dates <- time_bounds$start
@@ -206,6 +206,8 @@ PeriodMean <- function(data, dates = NULL, start = NULL, end = NULL,
   }
   total <- Apply(list(data), target_dims = time_dim, fun = mean,
                  na.rm = na.rm, ncores = ncores)$output1
+  
+  dim(total) <- c(dim(total), setNames(1, time_dim))
   return(total)
 }
 
diff --git a/R/PeriodMin.R b/R/PeriodMin.R
index 99ce801..91f1cd2 100644
--- a/R/PeriodMin.R
+++ b/R/PeriodMin.R
@@ -83,7 +83,7 @@ CST_PeriodMin <- function(data, start = NULL, end = NULL,
   
   data$data <- total
   data$dims <- dim(total)
-  data$coords[[time_dim]] <- NULL
+  data$coords[[time_dim]] <- 1 : length(data$dims[[time_dim]])
 
   if (!is.null(Dates)) {
     if (!is.null(start) && !is.null(end)) {
@@ -98,10 +98,10 @@ CST_PeriodMin <- function(data, start = NULL, end = NULL,
       # Create time_bounds
       time_bounds <- NULL
       time_bounds$start <- ClimProjDiags::Subset(x = Dates, along = time_dim, 
-                                                 indices = 1, drop = 'selected')
+                                                 indices = 1, drop = FALSE)
       time_bounds$end <- ClimProjDiags::Subset(x = Dates, along = time_dim, 
                                                indices = dim(Dates)[time_dim], 
-                                               drop = 'selected')
+                                               drop = FALSE)
 
       # Add Dates in attrs
       data$attrs$Dates <- time_bounds$start
@@ -207,6 +207,7 @@ PeriodMin <- function(data, dates = NULL, start = NULL, end = NULL,
   }
   total <- Apply(list(data), target_dims = time_dim, fun = min,
                  na.rm = na.rm, ncores = ncores)$output1
+  dim(total) <- c(dim(total), setNames(1, time_dim))
   return(total)
 }
 
diff --git a/R/PeriodVariance.R b/R/PeriodVariance.R
index 4e1e93e..5c52466 100644
--- a/R/PeriodVariance.R
+++ b/R/PeriodVariance.R
@@ -87,7 +87,7 @@ CST_PeriodVariance <- function(data, start = NULL, end = NULL,
   
   data$data <- total
   data$dims <- dim(total)
-  data$coords[[time_dim]] <- NULL
+  data$coords[[time_dim]] <- 1 : length(data$dims[[time_dim]])
 
   if (!is.null(Dates)) {
     if (!is.null(start) && !is.null(end)) {
@@ -102,10 +102,10 @@ CST_PeriodVariance <- function(data, start = NULL, end = NULL,
       # Create time_bounds
       time_bounds <- NULL
       time_bounds$start <- ClimProjDiags::Subset(x = Dates, along = time_dim, 
-                                                 indices = 1, drop = 'selected')
+                                                 indices = 1, drop = FALSE)
       time_bounds$end <- ClimProjDiags::Subset(x = Dates, along = time_dim, 
                                                indices = dim(Dates)[time_dim], 
-                                               drop = 'selected')
+                                               drop = FALSE)
 
       # Add Dates in attrs
       data$attrs$Dates <- time_bounds$start
@@ -216,6 +216,7 @@ PeriodVariance <- function(data, dates = NULL, start = NULL, end = NULL,
   total <- Apply(list(data), target_dims = time_dim, 
                  fun = .periodvariance,
                  na.rm = na.rm, ncores = ncores)$output1
+  dim(total) <- c(dim(total), setNames(1, time_dim))
   return(total)
 }
 
diff --git a/R/TotalSpellTimeExceedingThreshold.R b/R/TotalSpellTimeExceedingThreshold.R
index 1450703..2f420b8 100644
--- a/R/TotalSpellTimeExceedingThreshold.R
+++ b/R/TotalSpellTimeExceedingThreshold.R
@@ -115,7 +115,7 @@ CST_TotalSpellTimeExceedingThreshold <- function(data, threshold, spell, op = '>
                                             ncores = ncores)
   data$data <- total
   data$dims <- dim(total)
-  data$coords[[time_dim]] <- NULL
+  data$coords[[time_dim]] <- 1 : length(data$dims[[time_dim]])
 
   if (!is.null(Dates)) {
     if (!is.null(start) && !is.null(end)) {
@@ -130,10 +130,10 @@ CST_TotalSpellTimeExceedingThreshold <- function(data, threshold, spell, op = '>
       # Create time_bounds
       time_bounds <- NULL
       time_bounds$start <- ClimProjDiags::Subset(x = Dates, along = time_dim, 
-                                                 indices = 1, drop = 'selected')
+                                                 indices = 1, drop = FALSE)
       time_bounds$end <- ClimProjDiags::Subset(x = Dates, along = time_dim, 
                                                indices = dim(Dates)[time_dim], 
-                                               drop = 'selected')
+                                               drop = FALSE)
 
       # Add Dates in attrs
       data$attrs$Dates <- time_bounds$start
@@ -435,6 +435,7 @@ TotalSpellTimeExceedingThreshold <- function(data, threshold, spell, op = '>',
                      ncores = ncores)$output1
     }
   }
+  dim(total) <- c(dim(total), setNames(1, time_dim))
   return(total) 
 }  
 
diff --git a/R/TotalTimeExceedingThreshold.R b/R/TotalTimeExceedingThreshold.R
index 15b822c..70fc188 100644
--- a/R/TotalTimeExceedingThreshold.R
+++ b/R/TotalTimeExceedingThreshold.R
@@ -119,7 +119,7 @@ CST_TotalTimeExceedingThreshold <- function(data, threshold, op = '>',
                                        ncores = ncores)
   data$data <- total
   data$dims <- dim(total)
-  data$coords[[time_dim]] <- NULL
+  data$coords[[time_dim]] <- 1 : length(data$dims[[time_dim]])
 
   if (!is.null(Dates)) {
     if (!is.null(start) && !is.null(end)) {
@@ -134,10 +134,10 @@ CST_TotalTimeExceedingThreshold <- function(data, threshold, op = '>',
       # Create time_bounds
       time_bounds <- NULL
       time_bounds$start <- ClimProjDiags::Subset(x = Dates, along = time_dim, 
-                                                 indices = 1, drop = 'selected')
+                                                 indices = 1, drop = FALSE)
       time_bounds$end <- ClimProjDiags::Subset(x = Dates, along = time_dim, 
                                                indices = dim(Dates)[time_dim], 
-                                               drop = 'selected')
+                                               drop = FALSE)
 
       # Add Dates in attrs
       data$attrs$Dates <- time_bounds$start
@@ -431,6 +431,7 @@ TotalTimeExceedingThreshold <- function(data, threshold, op = '>',
                      ncores = ncores)$output1
     }
   }
+  dim(total) <- c(dim(total), setNames(1, time_dim))
   return(total)
 }
 
diff --git a/tests/testthat/test-AccumulationExceedingThreshold.R b/tests/testthat/test-AccumulationExceedingThreshold.R
index 2b55776..2e579b2 100644
--- a/tests/testthat/test-AccumulationExceedingThreshold.R
+++ b/tests/testthat/test-AccumulationExceedingThreshold.R
@@ -141,36 +141,36 @@ test_that("1. Input checks", {
 test_that("2. Output checks", {
   expect_equal(
     AccumulationExceedingThreshold(dat1, 10),
-    155
+    array(155, c(time = 1))
   )
   expect_equal(
     AccumulationExceedingThreshold(dat2_1, 10, time_dim = 'time'), 
-    array(c(375, 390), c(x = 2))
+    array(c(375, 390), c(x = 2, time = 1))
   )
   expect_equal(
     AccumulationExceedingThreshold(dat2_1, thres2_1, time_dim = 'time'), 
-    array(c(375, 390), c(x = 2))
+    array(c(375, 390), c(x = 2, time = 1))
   )
   expect_equal(
     AccumulationExceedingThreshold(dat2_1, thres2_1, time_dim = 'x'),
-    array(c(rep(0,5), seq(23, 79, 4)), c(time = 20))
+    array(c(rep(0, 5), seq(23, 79, 4)), c(time = 20, x = 1))
   )
   expect_equal(
     AccumulationExceedingThreshold(dat2_1, 10, time_dim = 'time'),
-    array(c(375, 390), c(x = 2))
+    array(c(375, 390), c(x = 2, time = 1))
   )
   # dimensions
   expect_equal(
     dim(AccumulationExceedingThreshold(dat2_3, thres2_3)),
-    c(sdate = 2, lat = 2)
+    c(sdate = 2, lat = 2, time = 1)
   )
   expect_equal(
     dim(AccumulationExceedingThreshold(dat2_3, thres2_4)),
-    c(sdate = 2, lat = 2)
+    c(sdate = 2, lat = 2, time = 1)
   )
   expect_equal(
     dim(AccumulationExceedingThreshold(dat2_4, thres2_4, time_dim = 'time')),
-    c(fyear = 3, sdate = 2, lat = 2)
+    c(fyear = 3, sdate = 2, lat = 2, time = 1)
   )
 
 })
@@ -180,27 +180,27 @@ test_that("3. Output checks", {
 
   expect_equal(
     dim(AccumulationExceedingThreshold(dat3_1, c(55,58), c('<', '>'))),
-    c(fyear = 3, sdate = 2, lat = 2)
+    c(fyear = 3, sdate = 2, lat = 2, time = 1)
   )
   expect_equal(
     AccumulationExceedingThreshold(dat3_1, c(55,58), c(">", "<")),
-    array(c(rep(0,11),113), dim = c(fyear = 3, sdate = 2, lat = 2))
+    array(c(rep(0, 11), 113), dim = c(fyear = 3, sdate = 2, lat = 2, time = 1))
   )
   expect_equal(
     AccumulationExceedingThreshold(dat3_1, c(55,58), c(">=", "<=")),
-    array(c(rep(0,10),55,171), dim = c(fyear = 3, sdate = 2, lat = 2))
+    array(c(rep(0, 10), 55, 171), dim = c(fyear = 3, sdate = 2, lat = 2, time = 1))
   )
   expect_equal(
     AccumulationExceedingThreshold(dat3_2, c(46, 35), op = c("<", ">"), time_dim = 'time'), 
-    array(c(76, 114), c(x = 2))
+    array(c(76, 114), c(x = 2, time = 1))
   )
   expect_equal(
     AccumulationExceedingThreshold(dat3_2, c(7,11), op = c('>=', '<='), time_dim = 'time'), 
-    array(c(27, 18), c(x = 2))
+    array(c(27, 18), c(x = 2, time = 1))
   )
   expect_equal(
     dim(AccumulationExceedingThreshold(dat2_3, list(thres2_4, thres2_4+1), op = c('>=', '<'))),
-    c(sdate = 2, lat = 2)
+    c(sdate = 2, lat = 2, time = 1)
   )
 
 })
@@ -211,7 +211,7 @@ test_that("4. Output checks", {
 
   expect_equal(
     dim(AccumulationExceedingThreshold(dat4, list(thres4_2, thres4_1), c('<=', '>'))),
-    c(fyear = 3, sdate = 2, lat = 2)
+    c(fyear = 3, sdate = 2, lat = 2, time = 1)
   )
   expect_equal(
     as.vector(AccumulationExceedingThreshold(dat4, list(thres4_1, thres4_2), c(">", "<="))[1:3]),
@@ -244,7 +244,7 @@ test_that("5. Seasonal forecasts", {
   res <- CST_AccumulationExceedingThreshold(exp, threshold = 280, time_dim = 'ftime')
 
   expect_equal(
-    round(res$data[, 2, 2, 2]),
+    round(res$data[, 2, 2, 2, 1]),
     c(0, 280, 281, 281)
   )
 
@@ -267,12 +267,12 @@ test_that("5. Seasonal forecasts", {
                                         start = list(1, 4), end = list(31, 10), na.rm = TRUE)
   
   expect_equal(
-    round(GDD[,1,1,1]),
+    round(GDD[, 1, 1, 1, 1]),
     c(549, 387, 125, 554, 245, 282)
   )
   expect_equal(
     dim(GDD),
-    c(member = 6, sdate = 3, lat = 4, lon = 4)
+    c(member = 6, sdate = 3, lat = 4, lon = 4, time = 1)
   )
   expect_error(
     AccumulationExceedingThreshold(exp - 17, threshold = 0, dates = Dates, start = list(1, 4), end = list(31, 10), time_dim = 'ftime'),
@@ -291,19 +291,19 @@ test_that("5. Seasonal forecasts", {
 
   expect_equal(
     AccumulationExceedingThreshold(input_1, threshold_1, diff = TRUE),
-    153
+    array(153, c(time = 1))
   )
   expect_equal(
     AccumulationExceedingThreshold(input_1, threshold_1),
-    204
+    array(204, c(time = 1))
   )
   expect_equal(
     AccumulationExceedingThreshold(input_2, threshold_2, op = '<'),
-    -105
+    array(-105, c(time = 1))
   )
   expect_equal(
     AccumulationExceedingThreshold(input_2, threshold_2, op = '<', diff = TRUE),
-    -55
+    array(-55, c(time = 1))
   )
 })
 
@@ -321,7 +321,7 @@ test_that("6. Subset Dates and check time_bounds", {
   # Check Dates
   expect_equal(
     dim(res$data)['sdate'], 
-    dim(res$attrs$Dates)
+    dim(res$attrs$Dates)['sdate']
   )
   # Check time_bounds
   expect_equal(
diff --git a/tests/testthat/test-PeriodAccumulation.R b/tests/testthat/test-PeriodAccumulation.R
index 9dcbcf9..3aa47ea 100644
--- a/tests/testthat/test-PeriodAccumulation.R
+++ b/tests/testthat/test-PeriodAccumulation.R
@@ -72,12 +72,12 @@ test_that("1. Initial checks", {
   )
   expect_equal(
     PeriodAccumulation(1:10), 
-    55
+    array(55, c(time = 1))
   )
   data <- array(1:24, c(sdate = 2, time = 3, lon = 4))
   expect_equal(
     PeriodAccumulation(data),
-    array(c(9, 12, 27, 30, 45, 48, 63, 66), c(sdate = 2, lon = 4))
+    array(c(9, 12, 27, 30, 45, 48, 63, 66), c(sdate = 2, lon = 4, time = 1))
   )
   # Test dates warning
   expect_warning(
@@ -104,7 +104,7 @@ test_that("2. Seasonal", {
   output$data <- array(c(sum(exp$data[1,1,21:82,1]), sum(exp$data[1,2,21:82,1]),
                          sum(exp$data[1,3,21:82,1]), sum(exp$data[1,1,21:82,2]),
                          sum(exp$data[1,2,21:82,2]), sum(exp$data[1,3,21:82,2])),
-                       c(memb = 1, sdate = 3, lon = 2))
+                       c(memb = 1, sdate = 3, lon = 2, ftime = 1))
 
   expect_equal(
     CST_PeriodAccumulation(exp, start = list(21, 4), end = list(21, 6), 
@@ -127,16 +127,16 @@ test_that("3. Subset Dates and check time_bounds", {
   )
   expect_equal(
     dim(res2$data), 
-    dim(exp$data)[-which(names(dim(exp$data)) == 'ftime')]
+    c(dim(exp$data)[-which(names(dim(exp$data)) == 'ftime')], ftime = 1)
   )
   # Check Dates
   expect_equal(
     dim(res$data)['sdate'], 
-    dim(res$attrs$Dates)
+    dim(res$attrs$Dates)['sdate']
   )
   expect_equal(
     dim(res2$data)['sdate'], 
-    dim(res2$attrs$Dates)
+    dim(res2$attrs$Dates)['sdate']
   )
   # Check time_bounds
   expect_equal(
@@ -196,29 +196,29 @@ test_that("4. Rolling", {
   # Output checks
   expect_equal(
     PeriodAccumulation(data = dat2, rollwidth = -2, dates = dates2, frequency = 'daily'),
-    array(c(4,6,8, 10, NA, NA), dim = c(sdate = 2, time = 3, member = 1))
+    array(c(4, 6, 8, 10, NA, NA), dim = c(sdate = 2, time = 3, member = 1, time = 1))
   )
   expect_equal(
     PeriodAccumulation(data = dat2, rollwidth = 3, dates = dates2, frequency = 'daily'),
-    array(c(rep(NA, 4), 9, 12), dim = c(sdate = 2, time = 3, member = 1))
+    array(c(rep(NA, 4), 9, 12), dim = c(sdate = 2, time = 3, member = 1, time = 1))
   )
   dat2_1 <- dat2
   dat2_1[1,1,1] <- NA
   expect_equal(
     PeriodAccumulation(data = dat2_1, rollwidth = 2, dates = dates2, na.rm = FALSE, 
                        frequency = 'daily'), 
-    array(c(rep(NA, 3), 6,8,10), dim = c(sdate = 2, time = 3, member = 1))
+    array(c(rep(NA, 3), 6, 8, 10), dim = c(sdate = 2, time = 3, member = 1, time = 1))
   )
   
   # Test rolling with start and end
   expect_equal(
     PeriodAccumulation(data = dat2, rollwidth = 1, dates = dates2, 
                        start = list(1, 4), end = list(2, 4), frequency = 'daily'),
-    array(c(1, 2, 3, 4), dim = c(sdate = 2, time = 2, member = 1))
+    array(c(1, 2, 3, 4), dim = c(sdate = 2, time = 2, member = 1, time = 1))
   )
   expect_equal(
     PeriodAccumulation(data = dat2, rollwidth = 2, dates = dates2, 
                        start = list(1, 4), end = list(2, 4), frequency = 'daily'),
-    array(c(NA, NA, 4, 6), dim = c(sdate = 2, time = 2, member = 1))
+    array(c(NA, NA, 4, 6), dim = c(sdate = 2, time = 2, member = 1, time = 1))
   )
 })
diff --git a/tests/testthat/test-PeriodMax.R b/tests/testthat/test-PeriodMax.R
index 1d7437a..ae29bb5 100644
--- a/tests/testthat/test-PeriodMax.R
+++ b/tests/testthat/test-PeriodMax.R
@@ -23,7 +23,7 @@ test_that("1. Sanity Checks", {
   suppressWarnings(
     expect_equal(
       PeriodMax(array(1, c(x = 1)), time_dim = 'x'), 
-      1
+      array(1, c(x = 1))
     )
   )
   expect_error(
@@ -33,7 +33,7 @@ test_that("1. Sanity Checks", {
   suppressWarnings(
     expect_equal(
       PeriodMax(array(1:10, c(time = 10))), 
-      10
+      array(10, c(time = 1))
     )
   )
   data <- array(1:24, c(sdate = 2, time = 3, lon = 4))
@@ -41,7 +41,7 @@ test_that("1. Sanity Checks", {
     expect_equal(
       PeriodMax(data),
       array(c(5, 6, 11, 12, 17, 18, 23, 24), 
-      c(sdate = 2, lon = 4))
+            c(sdate = 2, lon = 4, time = 1))
     )
   )
   # Test dates warning
@@ -81,7 +81,7 @@ test_that("2. Seasonal", {
   output$data <- array(c(max(exp$data[1,1,21:82,1]), max(exp$data[1,2,21:82,1]),
                          max(exp$data[1,3,21:82,1]), max(exp$data[1,1,21:82,2]),
                          max(exp$data[1,2,21:82,2]), max(exp$data[1,3,21:82,2])),
-                       c(memb = 1, sdate = 3, lon = 2))
+                       c(memb = 1, sdate = 3, lon = 2, time = 1))
   expect_equal(
     CST_PeriodMax(exp, start = list(21, 4), end = list(21, 6))$data,
     output$data
@@ -101,7 +101,7 @@ test_that("3. Subset Dates and check time_bounds", {
   # Check Dates
   expect_equal(
     dim(res$data)['sdate'], 
-    dim(res$attrs$Dates)
+    dim(res$attrs$Dates)['sdate']
   )
   # Check time_bounds
   expect_equal(
diff --git a/tests/testthat/test-PeriodMean.R b/tests/testthat/test-PeriodMean.R
index 9f8c4cf..6eab8ee 100644
--- a/tests/testthat/test-PeriodMean.R
+++ b/tests/testthat/test-PeriodMean.R
@@ -10,7 +10,7 @@ test_that("1. Sanity Checks", {
   suppressWarnings(
     expect_equal(
       PeriodMean(array(1, c(x = 1)), time_dim = 'x'), 
-      1
+      array(1, c(x = 1))
     )
   )
   expect_error(
@@ -33,7 +33,7 @@ test_that("1. Sanity Checks", {
   suppressWarnings(
     expect_equal(
       PeriodMean(array(1:10, c(time = 10))), 
-      5.5
+      array(5.5, c(time = 1))
     )
   )
   data <- array(1:24, c(sdate = 2, time = 3, lon = 4))
@@ -41,7 +41,7 @@ test_that("1. Sanity Checks", {
     expect_equal(
       PeriodMean(data),
       array(c(3, 4, 9, 10, 15, 16, 21, 22), 
-      c(sdate = 2, lon = 4))
+            c(sdate = 2, lon = 4, time = 1))
     )
   )
   # Test dates warning
@@ -81,7 +81,7 @@ test_that("2. Seasonal", {
   output$data <- array(c(mean(exp$data[1,1,21:82,1]), mean(exp$data[1,2,21:82,1]),
                          mean(exp$data[1,3,21:82,1]), mean(exp$data[1,1,21:82,2]),
                          mean(exp$data[1,2,21:82,2]), mean(exp$data[1,3,21:82,2])),
-                       c(memb = 1, sdate = 3, lon = 2))
+                       c(memb = 1, sdate = 3, lon = 2, time = 1))
   expect_equal(
     CST_PeriodMean(exp, start = list(21, 4), end = list(21, 6))$data,
     output$data
@@ -101,7 +101,7 @@ test_that("3. Subset Dates and check time_bounds", {
   # Check Dates
   expect_equal(
     dim(res$data)['sdate'], 
-    dim(res$attrs$Dates)
+    dim(res$attrs$Dates)['sdate']
   )
   # Check time_bounds
   expect_equal(
diff --git a/tests/testthat/test-PeriodMin.R b/tests/testthat/test-PeriodMin.R
index fb97fc2..51e671b 100644
--- a/tests/testthat/test-PeriodMin.R
+++ b/tests/testthat/test-PeriodMin.R
@@ -10,7 +10,7 @@ test_that("1. Sanity Checks", {
   suppressWarnings(
     expect_equal(
       PeriodMin(array(1, c(x = 1)), time_dim = 'x'), 
-      1
+      array(1, c(x = 1))
     )
   )
   expect_error(
@@ -32,13 +32,13 @@ test_that("1. Sanity Checks", {
   )
   expect_equal(
     PeriodMin(array(1:10, c(time = 10))), 
-    1
+    array(1, c(time = 1))
   )
   data <- array(1:24, c(sdate = 2, time = 3, lon = 4))
   expect_equal(
     PeriodMin(data),
     array(c(1, 2, 7, 8, 13, 14, 19, 20), 
-    c(sdate = 2, lon = 4))
+          c(sdate = 2, lon = 4, time = 1))
   )
   # Test dates warning
   expect_warning(
@@ -77,7 +77,7 @@ test_that("2. Seasonal", {
   output$data <- array(c(min(exp$data[1,1,21:82,1]), min(exp$data[1,2,21:82,1]),
                          min(exp$data[1,3,21:82,1]), min(exp$data[1,1,21:82,2]),
                          min(exp$data[1,2,21:82,2]), min(exp$data[1,3,21:82,2])),
-                       c(memb = 1, sdate = 3, lon = 2))
+                       c(memb = 1, sdate = 3, lon = 2, time = 1))
   expect_equal(
     CST_PeriodMin(exp, start = list(21, 4), end = list(21, 6))$data,
     output$data
@@ -97,7 +97,7 @@ test_that("3. Subset Dates and check time_bounds", {
   # Check Dates
   expect_equal(
     dim(res$data)['sdate'], 
-    dim(res$attrs$Dates)
+    dim(res$attrs$Dates)['sdate']
   )
   # Check time_bounds
   expect_equal(
diff --git a/tests/testthat/test-PeriodVariance.R b/tests/testthat/test-PeriodVariance.R
index e1de032..e5c7275 100644
--- a/tests/testthat/test-PeriodVariance.R
+++ b/tests/testthat/test-PeriodVariance.R
@@ -9,7 +9,7 @@ test_that("1. Sanity Checks", {
   )
   expect_equal(
     PeriodVariance(array(1:2, c(x = 2)), time_dim = 'x'), 
-    0.5
+    array(0.5, c(x = 1))
   )
   expect_error(
     PeriodVariance(data = NULL), 
@@ -30,14 +30,14 @@ test_that("1. Sanity Checks", {
   )
   expect_equal(
     PeriodVariance(array(1:10, c(time = 10))), 
-    9.166667,
+    array(9.166667, c(time = 1)),
     tolerance = 0.001
   )
   data <- array(1:24, c(sdate = 2, time = 3, lon = 4))
   expect_equal(
     PeriodVariance(data),
     array(rep(4, 8), 
-    c(sdate = 2, lon = 4))
+          c(sdate = 2, lon = 4, time = 1))
   )
   # Test dates warning
   expect_warning(
@@ -76,7 +76,7 @@ test_that("2. Seasonal", {
   output$data <- array(c(var(exp$data[1,1,21:82,1]), var(exp$data[1,2,21:82,1]),
                          var(exp$data[1,3,21:82,1]), var(exp$data[1,1,21:82,2]),
                          var(exp$data[1,2,21:82,2]), var(exp$data[1,3,21:82,2])),
-                       c(memb = 1, sdate = 3, lon = 2))
+                       c(memb = 1, sdate = 3, lon = 2, time = 1))
   expect_equal(
     CST_PeriodVariance(exp, start = list(21, 4), end = list(21, 6))$data,
     output$data
@@ -96,7 +96,7 @@ test_that("3. Subset Dates and check time_bounds", {
   # Check Dates
   expect_equal(
     dim(res$data)['sdate'], 
-    dim(res$attrs$Dates)
+    dim(res$attrs$Dates)['sdate']
   )
   # Check time_bounds
   expect_equal(
diff --git a/tests/testthat/test-TotalSpellTimeExceedingThreshold.R b/tests/testthat/test-TotalSpellTimeExceedingThreshold.R
index e65ec1e..d9a226e 100644
--- a/tests/testthat/test-TotalSpellTimeExceedingThreshold.R
+++ b/tests/testthat/test-TotalSpellTimeExceedingThreshold.R
@@ -156,36 +156,36 @@ test_that("1. Sanity checks", {
 test_that("2. Output checks", {
   expect_equal(
     TotalSpellTimeExceedingThreshold(dat1, thres1, spell = 2, time_dim = 'time'),  
-    array(c(0,rep(2,9)), c(lat = 10))
+    array(c(0, rep(2, 9)), c(lat = 10, time = 1))
   )    
   expect_equal(
     TotalSpellTimeExceedingThreshold(dat1_2, 10, spell = 2), 
-    array(c(15, 15), c(x = 2))
+    array(c(15, 15), c(x = 2, time = 1))
   )
   expect_equal(
     TotalSpellTimeExceedingThreshold(dat1_2,threshold1_2, spell = 2), 
-    array(c(15, 15), c(x = 2, member = 1))
+    array(c(15, 15), c(x = 2, member = 1, time = 1))
   )
   expect_equal(
     TotalSpellTimeExceedingThreshold(dat2_1, thres2_1, spell = 10), 
-    array(c(15, 15), c(x = 2))
+    array(c(15, 15), c(x = 2, time = 1))
   )
   expect_equal(
     TotalSpellTimeExceedingThreshold(dat2_1, thres2_1, spell = 2, time_dim = 'x'),
-    array(c(rep(0,5), rep(2,15)), c(time = 20))
+    array(c(rep(0, 5), rep(2, 15)), c(time = 20, x = 1))
   )
   # dimensions
   expect_equal(
     dim(TotalSpellTimeExceedingThreshold(dat2_3, thres2_3, spell = 3)),
-    c(sdate = 2, lat = 2)
+    c(sdate = 2, lat = 2, time = 1)
   )
   expect_equal(
     dim(TotalSpellTimeExceedingThreshold(dat2_3, thres2_4, spell = 3)),
-    c(sdate = 2, lat = 2)
+    c(sdate = 2, lat = 2, time = 1)
   )
   expect_equal(
     dim(TotalSpellTimeExceedingThreshold(dat2_4, thres2_4, spell = 3, time_dim = 'time')),
-    c(fyear = 3, sdate = 2, lat = 2)
+    c(fyear = 3, sdate = 2, lat = 2, time = 1)
   )
 })
 
@@ -194,28 +194,28 @@ test_that("2. Output checks", {
 test_that("3. Output checks", {
 
   expect_equal(
-    dim(TotalSpellTimeExceedingThreshold(dat3_1, c(55,58), spell = 3, c('<', '>'))),
-    c(fyear = 3, sdate = 2, lat = 2)
+    dim(TotalSpellTimeExceedingThreshold(dat3_1, c(55, 58), spell = 3, c('<', '>'))),
+    c(fyear = 3, sdate = 2, lat = 2, time = 1)
   )
   expect_equal(
-    TotalSpellTimeExceedingThreshold(dat3_1, c(30,60), spell = 3, c(">", "<")),
-    array(c(rep(0,6),rep(5, 5), 4), dim = c(fyear = 3, sdate = 2, lat = 2))
+    TotalSpellTimeExceedingThreshold(dat3_1, c(30, 60), spell = 3, c(">", "<")),
+    array(c(rep(0, 6),rep(5, 5), 4), dim = c(fyear = 3, sdate = 2, lat = 2, time = 1))
   )
   expect_equal(
-    TotalSpellTimeExceedingThreshold(dat3_1, c(55,58), spell = 3, c(">=", "<=")),
-    array(c(rep(0,11),3), dim = c(fyear = 3, sdate = 2, lat = 2))
+    TotalSpellTimeExceedingThreshold(dat3_1, c(55, 58), spell = 3, c(">=", "<=")),
+    array(c(rep(0, 11),3), dim = c(fyear = 3, sdate = 2, lat = 2, time = 1))
   )
   expect_equal(
     TotalSpellTimeExceedingThreshold(dat3_2, c(46, 35), spell = 3, op = c("<", ">"), time_dim = 'time'), 
-    array(c(0, 3), c(x = 2))
+    array(c(0, 3), c(x = 2, time = 1))
   )
   expect_equal(
     TotalSpellTimeExceedingThreshold(dat3_2, c(7,11), spell = 3, op = c('>=', '<='), time_dim = 'time'), 
-    array(c(3, 0), c(x = 2))
+    array(c(3, 0), c(x = 2, time = 1))
   )
   expect_equal(
     dim(TotalSpellTimeExceedingThreshold(dat2_3, list(thres2_4, thres2_4+1), spell = 3, op = c('>=', '<'))),
-    c(sdate = 2, lat = 2)
+    c(sdate = 2, lat = 2, time = 1)
   )
 
 })
@@ -226,7 +226,7 @@ test_that("4. Output checks", {
 
   expect_equal(
     dim(TotalSpellTimeExceedingThreshold(dat4, list(thres4_2, thres4_1), spell = 3, c('<=', '>'))),
-    c(fyear = 3, sdate = 2, lat = 2)
+    c(fyear = 3, sdate = 2, lat = 2, time = 1)
   )
   expect_equal(
     as.vector(TotalSpellTimeExceedingThreshold(dat4, list(thres4_1, thres4_2), spell = 3, c(">", "<="))[1:3]),
@@ -254,20 +254,20 @@ test_that("5. Seasonal Forecasts", {
   exp$data <- exp$data[1,1:3,1:3,,,]
   res <- CST_TotalSpellTimeExceedingThreshold(exp, threshold = 260, spell = 2, time_dim = 'ftime')
   expect_equal(
-    res$data[,,1,1],
+    res$data[, , 1, 1, 1],
     array(c(3,3,3,3,3,3,3,3,3), c(member = 3, sdate = 3))
   )
   # compare with percentile
   thresholdP <- Threshold(exp$data, threshold = 0.9)
   WSDI <- CST_TotalSpellTimeExceedingThreshold(exp, threshold = thresholdP, spell = 2, time_dim = 'ftime')
   expect_equal(
-    WSDI$data[3,3,3,],
+    WSDI$data[3, 3, 3, ,1],
     c(rep(0, 6), rep(2, 2), 0, 2, 0, 2, rep(0, 29), 2, rep(0, 11))
   )
   thresholdP1 <- thresholdP[1,,]
   WSDI1 <- CST_TotalSpellTimeExceedingThreshold(exp, threshold = thresholdP1, spell = 2, time_dim = 'ftime')
   expect_equal(
-    WSDI1$data[3,3,3,],
+    WSDI1$data[3, 3, 3, ,1],
     c(rep(0, 53)))
 })
 
@@ -285,7 +285,7 @@ test_that("6. Subset Dates and check time_bounds", {
   # Check Dates
   expect_equal(
     dim(res$data)['sdate'], 
-    dim(res$attrs$Dates)
+    dim(res$attrs$Dates)['sdate']
   )
   # Check time_bounds
   expect_equal(
diff --git a/tests/testthat/test-TotalTimeExceedingThreshold.R b/tests/testthat/test-TotalTimeExceedingThreshold.R
index cba27ae..53c8a84 100644
--- a/tests/testthat/test-TotalTimeExceedingThreshold.R
+++ b/tests/testthat/test-TotalTimeExceedingThreshold.R
@@ -149,36 +149,36 @@ test_that("1. Sanity checks", {
 test_that("2. Output checks", {
   expect_equal(
     TotalTimeExceedingThreshold(dat1, thres1, time_dim = 'time'),  
-    array(c(0,rep(2,9)), c(lat = 10))
+    array(c(0, rep(2, 9)), c(lat = 10, time = 1))
   )    
   expect_equal(
     TotalTimeExceedingThreshold(dat1_2, 10), 
-    array(c(15, 15), c(x = 2))
+    array(c(15, 15), c(x = 2, time = 1))
   )
   expect_equal(
     TotalTimeExceedingThreshold(dat1_2,threshold1_2), 
-    array(c(15, 15), c(x = 2, member = 1))
+    array(c(15, 15), c(x = 2, member = 1, time = 1))
   )
   expect_equal(
     TotalTimeExceedingThreshold(dat2_1, thres2_1), 
-    array(c(15, 15), c(x = 2))
+    array(c(15, 15), c(x = 2, time = 1))
   )
   expect_equal(
     TotalTimeExceedingThreshold(dat2_1, thres2_1, time_dim = 'x'),
-    array(c(rep(0,5), rep(2,15)), c(time = 20))
+    array(c(rep(0, 5), rep(2, 15)), c(time = 20, x = 1))
   )
   # dimensions
   expect_equal(
     dim(TotalTimeExceedingThreshold(dat2_3, thres2_3)),
-    c(sdate = 2, lat = 2)
+    c(sdate = 2, lat = 2, time = 1)
   )
   expect_equal(
     dim(TotalTimeExceedingThreshold(dat2_3, thres2_4)),
-    c(sdate = 2, lat = 2)
+    c(sdate = 2, lat = 2, time = 1)
   )
   expect_equal(
     dim(TotalTimeExceedingThreshold(dat2_4, thres2_4, time_dim = 'time')),
-    c(fyear = 3, sdate = 2, lat = 2)
+    c(fyear = 3, sdate = 2, lat = 2, time = 1)
   )
 })
 
@@ -187,27 +187,27 @@ test_that("2. Output checks", {
 test_that("3. Output checks", {
   expect_equal(
     dim(TotalTimeExceedingThreshold(dat3_1, c(55,58), c('<', '>'))),
-    c(fyear = 3, sdate = 2, lat = 2)
+    c(fyear = 3, sdate = 2, lat = 2, time = 1)
   )
   expect_equal(
     TotalTimeExceedingThreshold(dat3_1, c(30,60), c(">", "<")),
-    array(c(rep(0, 6), rep(5, 5), 4), dim = c(fyear = 3, sdate = 2, lat = 2))
+    array(c(rep(0, 6), rep(5, 5), 4), dim = c(fyear = 3, sdate = 2, lat = 2, time = 1))
   )
   expect_equal(
     TotalTimeExceedingThreshold(dat3_1, c(55, 58), c(">=", "<=")),
-    array(c(rep(0, 10), 1, 3), dim = c(fyear = 3, sdate = 2, lat = 2))
+    array(c(rep(0, 10), 1, 3), dim = c(fyear = 3, sdate = 2, lat = 2, time = 1))
   )
   expect_equal(
     TotalTimeExceedingThreshold(dat3_2, c(46, 35), op = c("<", ">"), time_dim = 'time'), 
-    array(c(2, 3), c(x = 2))
+    array(c(2, 3), c(x = 2, time = 1))
   )
   expect_equal(
     TotalTimeExceedingThreshold(dat3_2, c(7, 11), op = c('>=', '<='), time_dim = 'time'), 
-    array(c(3, 2), c(x = 2))
+    array(c(3, 2), c(x = 2, time = 1))
   )
   expect_equal(
     dim(TotalTimeExceedingThreshold(dat2_3, list(thres2_4, thres2_4+1), op = c('>=', '<'))),
-    c(sdate = 2, lat = 2)
+    c(sdate = 2, lat = 2, time = 1)
   )
 })
 
@@ -216,7 +216,7 @@ test_that("3. Output checks", {
 test_that("4. Output checks", {
   expect_equal(
     dim(TotalTimeExceedingThreshold(dat4, list(thres4_2, thres4_1), c('<=', '>'))),
-    c(fyear = 3, sdate = 2, lat = 2)
+    c(fyear = 3, sdate = 2, lat = 2, time = 1)
   )
   expect_equal(
     as.vector(TotalTimeExceedingThreshold(dat4, list(thres4_1, thres4_2), c(">", "<="))[1:3]),
@@ -245,7 +245,7 @@ test_that("5. Seasonal forecasts", {
   exp$data <- exp$data[1, 1:3, , , , ] - 247
   SU35_NoP <- CST_TotalTimeExceedingThreshold(exp, threshold = 35, time_dim = 'ftime')$data  
   expect_equal(
-    SU35_NoP[1, , 15, 3], 
+    SU35_NoP[1, , 15, 3, 1], 
     c(0, 1, 1, 1, 0, 0)
   )
   # convert to percentile
@@ -255,7 +255,7 @@ test_that("5. Seasonal forecasts", {
   data$data <- exp_percentile
   SU35_P <- CST_TotalTimeExceedingThreshold(data, threshold = obs_percentile, time_dim = 'ftime')$data
   expect_equal(
-    SU35_P[2, , 5, 5], 
+    SU35_P[2, , 5, 5, 1], 
     c(3, 3, 3, 3, 3, 3)
   )
 })
@@ -274,7 +274,7 @@ test_that("6. Subset Dates and check time_bounds", {
   # Check Dates
   expect_equal(
     dim(res$data)['sdate'], 
-    dim(res$attrs$Dates)
+    dim(res$attrs$Dates)['sdate']
   )
   # Check time_bounds
   expect_equal(
-- 
GitLab


From 02ab56525b693dbcdf8ba025d1617c700219c477 Mon Sep 17 00:00:00 2001
From: THEERTHA KARIYATHAN <tkariyat@bscearth421.int.bsc.es>
Date: Thu, 27 Mar 2025 12:27:47 +0100
Subject: [PATCH 10/14] description and news update

---
 DESCRIPTION |  5 +++--
 NEWS.md     | 18 ++++++++++++++++++
 2 files changed, 21 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 2fc850e..7fdadd0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,9 @@
 Package: CSIndicators
 Title: Climate Services' Indicators Based on Sub-Seasonal to Decadal Predictions
-Version: 1.1.1
+Version: 1.1.2
 Authors@R: c(
-  person("Victòria", "Agudetse", , "victoria.agudetse@bsc.es", role = c("cre")),
+  person("Theertha", "Kariyathan", ,"theertha.kariyathan@bsc.es", role = c("cre")),
+  person("Victòria", "Agudetse", , "victoria.agudetse@bsc.es", role = c("ctb")),
   person("Eva", "Rifà", , "eva.rifarovira@bsc.es", role = c("ctb")),
   person("Nuria", "Perez-Zanon", , "nuria.perez@bsc.es", role = c("aut"), comment = c(ORCID = "0000-0001-8568-3071")),
   person("Chou", "Chihchung", ,"chihchung.chou@bsc.es", role = "aut"),
diff --git a/NEWS.md b/NEWS.md
index 613ff3d..f83b34c 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,21 @@
+# CSIndicators 1.1.2 (Release date: 2025-03-27)
+
+### Fixes
+- CST_PeriodStandardization: Set na.rm = TRUE when replacing infinite values with maximum/minimum period values
+- CST_PeriodPET(): Add longname and other variable metadata 
+- Not drop singleton time dimensions in 
+ PeriodAccumulation
+ PeriodMean
+ PeriodMax
+ PeriodMin
+ PeriodVariance
+ AccumulationExceedingThreshold
+ TotalSpellTimeExceedingThreshold
+ TotalTimeExceedingThreshold
+
+### Other
+- add CONTRIBUTING.md
+
 # CSIndicators 1.1.1 (Release date: 2024-01-24)  
 
 ### Fixes
-- 
GitLab


From 7cc0a9600dcae1b186703e1d0442491707021758 Mon Sep 17 00:00:00 2001
From: THEERTHA KARIYATHAN <tkariyat@bscearth421.int.bsc.es>
Date: Thu, 27 Mar 2025 16:30:53 +0100
Subject: [PATCH 11/14] namespace, setNames

---
 .Rbuildignore                        | 1 +
 NAMESPACE                            | 1 +
 R/AccumulationExceedingThreshold.R   | 3 ++-
 R/PeriodAccumulation.R               | 1 +
 R/PeriodMax.R                        | 1 +
 R/PeriodMean.R                       | 1 +
 R/PeriodMin.R                        | 1 +
 R/PeriodVariance.R                   | 1 +
 R/TotalSpellTimeExceedingThreshold.R | 3 ++-
 R/TotalTimeExceedingThreshold.R      | 3 ++-
 10 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/.Rbuildignore b/.Rbuildignore
index da90668..89478ae 100644
--- a/.Rbuildignore
+++ b/.Rbuildignore
@@ -14,3 +14,4 @@
 ^inst/doc/paper-figure-PlotForecastPDF\.R$
 ^.*\.Rproj$
 ^\.Rproj\.user$
+^CONTRIBUTING.md
diff --git a/NAMESPACE b/NAMESPACE
index 15c3c9a..466e3c6 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -60,6 +60,7 @@ importFrom(stats,ecdf)
 importFrom(stats,qnorm)
 importFrom(stats,quantile)
 importFrom(stats,sd)
+importFrom(stats,setNames)
 importFrom(stats,window)
 importFrom(utils,read.delim)
 importFrom(zoo,rollapply)
diff --git a/R/AccumulationExceedingThreshold.R b/R/AccumulationExceedingThreshold.R
index 054a8b7..5235bac 100644
--- a/R/AccumulationExceedingThreshold.R
+++ b/R/AccumulationExceedingThreshold.R
@@ -203,6 +203,7 @@ CST_AccumulationExceedingThreshold <- function(data, threshold, op = '>', diff =
 #'GDD <- AccumulationExceedingThreshold(data, threshold = 0, start = list(1, 4),
 #'                                      end = list(31, 10))
 #'@import multiApply
+#'@importFrom stats setNames
 #'@export
 AccumulationExceedingThreshold <- function(data, threshold, op = '>', diff = FALSE,
                                            dates = NULL, start = NULL, end = NULL,
@@ -477,4 +478,4 @@ AccumulationExceedingThreshold <- function(data, threshold, op = '>', diff = FAL
   }
   
   return(res)
-}
\ No newline at end of file
+}
diff --git a/R/PeriodAccumulation.R b/R/PeriodAccumulation.R
index 8b0129f..424a1c8 100644
--- a/R/PeriodAccumulation.R
+++ b/R/PeriodAccumulation.R
@@ -222,6 +222,7 @@ CST_PeriodAccumulation <- function(data, start = NULL, end = NULL,
 #'
 #'@import multiApply
 #'@importFrom zoo rollapply
+#'@importFrom stats setNames
 #'@export
 PeriodAccumulation <- function(data, dates = NULL, start = NULL, end = NULL, 
                                time_dim = 'time', rollwidth = NULL, 
diff --git a/R/PeriodMax.R b/R/PeriodMax.R
index f038aff..b028d10 100644
--- a/R/PeriodMax.R
+++ b/R/PeriodMax.R
@@ -163,6 +163,7 @@ CST_PeriodMax <- function(data, start = NULL, end = NULL,
 #'res <- PeriodMax(data, dates = Dates, start = list(01, 12), end = list(01, 01))
 #'
 #'@import multiApply
+#'@importFrom stats setNames
 #'@export
 PeriodMax <- function(data, dates = NULL, start = NULL, end = NULL,
                       time_dim = 'time', na.rm = FALSE, ncores = NULL) {
diff --git a/R/PeriodMean.R b/R/PeriodMean.R
index bebbedd..16752e4 100644
--- a/R/PeriodMean.R
+++ b/R/PeriodMean.R
@@ -162,6 +162,7 @@ CST_PeriodMean <- function(data, start = NULL, end = NULL,
 #'SA <- PeriodMean(data, dates = Dates, start = list(01, 12), end = list(01, 01))
 #'
 #'@import multiApply
+#'@importFrom stats setNames
 #'@export
 PeriodMean <- function(data, dates = NULL, start = NULL, end = NULL,
                        time_dim = 'time', na.rm = FALSE, ncores = NULL) {
diff --git a/R/PeriodMin.R b/R/PeriodMin.R
index 91f1cd2..a9be2d5 100644
--- a/R/PeriodMin.R
+++ b/R/PeriodMin.R
@@ -163,6 +163,7 @@ CST_PeriodMin <- function(data, start = NULL, end = NULL,
 #'res <- PeriodMin(data, dates = Dates, start = list(01, 12), end = list(01, 01))
 #'
 #'@import multiApply
+#'@importFrom stats setNames
 #'@export
 PeriodMin <- function(data, dates = NULL, start = NULL, end = NULL,
                       time_dim = 'time', na.rm = FALSE, ncores = NULL) {
diff --git a/R/PeriodVariance.R b/R/PeriodVariance.R
index 5c52466..cc1883b 100644
--- a/R/PeriodVariance.R
+++ b/R/PeriodVariance.R
@@ -171,6 +171,7 @@ CST_PeriodVariance <- function(data, start = NULL, end = NULL,
 #'res <- PeriodVariance(data, dates = Dates, start = list(01, 12), end = list(01, 01))
 #'
 #'@import multiApply
+#'@importFrom stats setNames
 #'@export
 PeriodVariance <- function(data, dates = NULL, start = NULL, end = NULL,
                            time_dim = 'time', na.rm = FALSE, ncores = NULL) {
diff --git a/R/TotalSpellTimeExceedingThreshold.R b/R/TotalSpellTimeExceedingThreshold.R
index 2f420b8..72a51e0 100644
--- a/R/TotalSpellTimeExceedingThreshold.R
+++ b/R/TotalSpellTimeExceedingThreshold.R
@@ -219,6 +219,7 @@ CST_TotalSpellTimeExceedingThreshold <- function(data, threshold, spell, op = '>
 #'                                          end = list(21, 6))
 #' 
 #'@import multiApply
+#'@importFrom stats setNames
 #'@export
 TotalSpellTimeExceedingThreshold <- function(data, threshold, spell, op = '>',
                                              dates = NULL, start = NULL, end = NULL, 
@@ -485,4 +486,4 @@ TotalSpellTimeExceedingThreshold <- function(data, threshold, spell, op = '>',
                         return(days)
                         })))
   return(total)
-}
\ No newline at end of file
+}
diff --git a/R/TotalTimeExceedingThreshold.R b/R/TotalTimeExceedingThreshold.R
index 70fc188..31cbc58 100644
--- a/R/TotalTimeExceedingThreshold.R
+++ b/R/TotalTimeExceedingThreshold.R
@@ -221,6 +221,7 @@ CST_TotalTimeExceedingThreshold <- function(data, threshold, op = '>',
 #'                                   start = list(21, 4), end = list(21, 6))
 #'
 #'@import multiApply
+#'@importFrom stats setNames
 #'@export
 TotalTimeExceedingThreshold <- function(data, threshold, op = '>',
                                         dates = NULL, start = NULL, end = NULL,
@@ -468,4 +469,4 @@ TotalTimeExceedingThreshold <- function(data, threshold, op = '>',
     }
   }
   return(res)
-}
\ No newline at end of file
+}
-- 
GitLab


From 9a25e63497823faec536a858c29cd7970238118b Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Fri, 28 Mar 2025 09:31:29 +0100
Subject: [PATCH 12/14] Modify calls to Apply() to avoid using 'builtin' type
 functions, issue #54

---
 R/MergeRefToExp.R       | 9 ++++++---
 R/PeriodAccumulation.R  | 6 ++++--
 R/PeriodMax.R           | 3 +--
 R/PeriodMin.R           | 3 ++-
 R/SelectPeriodOnData.R  | 2 +-
 R/SelectPeriodOnDates.R | 2 +-
 6 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/R/MergeRefToExp.R b/R/MergeRefToExp.R
index 6d9fd6e..69f722b 100644
--- a/R/MergeRefToExp.R
+++ b/R/MergeRefToExp.R
@@ -184,8 +184,10 @@ CST_MergeRefToExp <- function(data1, data2, start1 = NULL, end1 = NULL,
       names(dim(dates2)) <- time_dim
     }
   }
-  res <- Apply(list(dates1, dates2), target_dims = time_dim,
-               'c', output_dims = time_dim, ncores = ncores)$output1
+  res <- Apply(list(dates1, dates2),
+               target_dims = time_dim,
+               fun = function(x, ...) {c(x, ...)},
+               output_dims = time_dim, ncores = ncores)$output1
 
   if (inherits(dates1, 'Date')) {
     data1$attrs$Dates <- as.Date(res, origin = '1970-01-01')
@@ -421,7 +423,8 @@ MergeRefToExp <- function(data1, data2, dates1 = NULL, dates2 = NULL,
     }
   }
 
-  data1 <- Apply(list(data1, data2), target_dims = time_dim, fun = 'c',
+  data1 <- Apply(list(data1, data2), target_dims = time_dim,
+                 fun = function(x, ...) {c(x, ...)},
                  output_dims = time_dim, ncores = ncores)$output1
 
   if (all(names(dim(data1)) %in% data1dims)) {
diff --git a/R/PeriodAccumulation.R b/R/PeriodAccumulation.R
index 8b0129f..a94d6f7 100644
--- a/R/PeriodAccumulation.R
+++ b/R/PeriodAccumulation.R
@@ -273,7 +273,7 @@ PeriodAccumulation <- function(data, dates = NULL, start = NULL, end = NULL,
 
   if (is.null(rollwidth)) {
     # period accumulation
-    total <- Apply(list(data), target_dims = time_dim, fun = sum,
+    total <- Apply(list(data), target_dims = time_dim, fun = function(...) {sum(...)},
                    na.rm = na.rm, ncores = ncores)$output1
   } else {
     # rolling accumulation
@@ -337,7 +337,9 @@ PeriodAccumulation <- function(data, dates = NULL, start = NULL, end = NULL,
     }
   }
 
-  data_accum <- rollapply(data = data_vector, width = rollwidth, FUN = sum, na.rm = na.rm)
+  data_accum <- rollapply(data = data_vector, width = rollwidth,
+                          FUN = function(...) {sum(...)},
+                          na.rm = na.rm)
   if (!forwardroll) {
     data_accum <- c(rep(NA, rollwidth-1), data_accum) 
   } else {
diff --git a/R/PeriodMax.R b/R/PeriodMax.R
index f038aff..ecb3376 100644
--- a/R/PeriodMax.R
+++ b/R/PeriodMax.R
@@ -205,11 +205,10 @@ PeriodMax <- function(data, dates = NULL, start = NULL, end = NULL,
       }
     }
   }
-  total <- Apply(list(data), target_dims = time_dim, fun = max,
+  total <- Apply(list(data), target_dims = time_dim, fun = function(...) {max(...)},
                  na.rm = na.rm, ncores = ncores)$output1
   
   dim(total) <- c(dim(total), setNames(1, time_dim))
   return(total)
 }
 
-
diff --git a/R/PeriodMin.R b/R/PeriodMin.R
index 91f1cd2..e4d0c64 100644
--- a/R/PeriodMin.R
+++ b/R/PeriodMin.R
@@ -205,7 +205,8 @@ PeriodMin <- function(data, dates = NULL, start = NULL, end = NULL,
       }
     }
   }
-  total <- Apply(list(data), target_dims = time_dim, fun = min,
+  total <- Apply(list(data), target_dims = time_dim,
+                 fun = function(...) {min(...)},
                  na.rm = na.rm, ncores = ncores)$output1
   dim(total) <- c(dim(total), setNames(1, time_dim))
   return(total)
diff --git a/R/SelectPeriodOnData.R b/R/SelectPeriodOnData.R
index 1cc2792..731abb5 100644
--- a/R/SelectPeriodOnData.R
+++ b/R/SelectPeriodOnData.R
@@ -121,7 +121,7 @@ SelectPeriodOnData <- function(data, dates, start, end,
                ncores = ncores)$output1
   # when 29Feb is included the length of the output changes:
   regular <- Apply(list(res), target_dims = time_dim,
-                   fun = sum, ncores = ncores)$output1
+                   fun = function(...) {sum(...)}, ncores = ncores)$output1
   dims <- dim(data)
   dims[names(dims) == time_dim] <- max(regular)
   if (any(regular != max(regular))) {
diff --git a/R/SelectPeriodOnDates.R b/R/SelectPeriodOnDates.R
index 550aad9..b95c509 100644
--- a/R/SelectPeriodOnDates.R
+++ b/R/SelectPeriodOnDates.R
@@ -53,7 +53,7 @@ SelectPeriodOnDates <- function(dates, start, end,
   }
   # when 29Feb is included the length of the output changes:
   regular <- Apply(list(res), target_dims = time_dim,
-                   fun = sum, ncores = ncores)$output1
+                   fun = function(...) {sum(...)}, ncores = ncores)$output1
   dims <- dim(dates)
   dims[names(dims) == time_dim] <- max(regular)
   if (any(regular != max(regular))) {
-- 
GitLab


From 840fe0f479f0440d71173ee6e87cdf74a2fd95fd Mon Sep 17 00:00:00 2001
From: vagudets <victoria.agudetse@bsc.es>
Date: Fri, 28 Mar 2025 09:58:06 +0100
Subject: [PATCH 13/14] Update NEWS.md

---
 NEWS.md | 1 +
 1 file changed, 1 insertion(+)

diff --git a/NEWS.md b/NEWS.md
index f83b34c..025519f 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,6 +1,7 @@
 # CSIndicators 1.1.2 (Release date: 2025-03-27)
 
 ### Fixes
+- Avoid using 'builtin' type functions in call to multiApply::Apply()
 - CST_PeriodStandardization: Set na.rm = TRUE when replacing infinite values with maximum/minimum period values
 - CST_PeriodPET(): Add longname and other variable metadata 
 - Not drop singleton time dimensions in 
-- 
GitLab


From 7f3fdeb97f4e6a08bdef298752707b50b6664676 Mon Sep 17 00:00:00 2001
From: THEERTHA KARIYATHAN <tkariyat@bscearth421.int.bsc.es>
Date: Tue, 1 Apr 2025 09:43:13 +0200
Subject: [PATCH 14/14] update citation

---
 inst/CITATION | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/inst/CITATION b/inst/CITATION
index af27d37..5e2c82a 100644
--- a/inst/CITATION
+++ b/inst/CITATION
@@ -17,7 +17,7 @@ bibentry(
   author = c(person("Núria", "Pérez-Zanón", email = "nuria.perez@bsc.es"), person("", "et al.")),
   title = "CSIndicators: Get tailored climate indicators for applications in your sector",
   doi = "10.1016/j.cliser.2023.100393",
-  url = "https://www.sciencedirect.com/science/article/pii/S2405880723000547",
+  url = URLencode("https://doi.org/10.1016/j.cliser.2023.100393"),
   journal = "Climate Services",
   publisher = "Elsevier",
   year = "2023"
-- 
GitLab