.Rbuildignore

 .*\.git$
 .*\.gitignore$
+.*\.gitlab$
 .*\.tar.gz$
 .*\.pdf$
 ./.nc$
 .*^(?!data)\.RData$
 .*\.gitlab-ci.yml$
+.lintr
 ^tests$
 #^inst/doc$
-^inst/doc/UseCase2_PrecipitationDownscaling_RainFARM_RF100\.R$
-^inst/doc/UseCase1_WindEvent_March2018\.R$
-^inst/doc/UseCase2_PrecipitationDownscaling_RainFARM_RF4\.R$
-^inst/doc/UseCase3_data_preparation_SCHEME_model\.R$
-^inst/doc/launch_UseCase2_PrecipitationDownscaling_RF4\.sh$
+^inst/doc/usecase/UseCase2_PrecipitationDownscaling_RainFARM_RF100\.R$
+^inst/doc/usecase/UseCase1_WindEvent_March2018\.R$
+^inst/doc/usecase/UseCase2_PrecipitationDownscaling_RainFARM_RF4\.R$
+^inst/doc/usecase/UseCase3_data_preparation_SCHEME_model\.R$
+^inst/doc/usecase/launch_UseCase2_PrecipitationDownscaling_RF4\.sh$

.gitlab-ci.yml

@@ -9,3 +9,10 @@ build:
     - R CMD build --resave-data .
     - R CMD check --as-cran --no-manual --run-donttest CSTools_*.tar.gz
     - R -e 'covr::package_coverage()'
+
+lint-check:
+  stage: build
+  script:
+    - module load R/4.1.2-foss-2015a-bare
+    - echo "Run lintr on the package..."
+    - Rscript -e 'lintr::lint_package(path = ".")'

.lintr

+linters: linters_with_tags( # lintr_3.1.1
+    tags = c("package_development", "readability", "best_practices"),
+    line_length_linter = line_length_linter(100L),
+    T_and_F_symbol_linter = NULL,
+    quotes_linter = NULL,
+    commented_code_linter = NULL,
+    implicit_integer_linter = NULL,
+    vector_logic_linter = NULL,
+    extraction_operator_linter = NULL,
+    function_left_parentheses_linter = NULL,
+    semicolon_linter = NULL,
+    indentation_linter = NULL,
+    unnecessary_nested_if_linter = NULL, 
+    if_not_else_linter = NULL,
+    object_length_linter = NULL,
+    infix_spaces_linter(exclude_operators = "~")
+  )
+exclusions: list(
+    "inst",
+    "R/AnalogsPred_train.R",
+    "R/BEI_PDFBest.R",
+    "R/BEI_Weights.R",
+    "R/CST_AdamontAnalog.R",
+    "R/CST_AdamontQQCorr.R",
+    "R/Analogs.R",
+    "R/CST_AnalogsPredictors.R",
+    "R/CST_BEI_Weighting.R",
+    "R/CST_CategoricalEnsCombination.R",
+    "R/CST_DynBiasCorrection.R",
+    "R/CST_EnsClustering.R",
+    "R/PlotCombinedMap.R",
+    "R/PlotForecastPDF.R",
+    "R/PlotMostLikelyQuantileMap.R",
+    "R/PlotPDFsOLE.R",
+    "R/PlotTriangles4Categories.R",
+    "R/PlotWeeklyClim.R",
+    "tests/testthat/",
+    "tests/testthat.R"
+  )

DESCRIPTION

 Package: CSTools
 Title: Assessing Skill of Climate Forecasts on Seasonal-to-Decadal Timescales
-Version: 5.0.1
+Version: 5.2.0
 Authors@R: c(
     person("Nuria", "Perez-Zanon", , "nuria.perez@bsc.es", role = "aut", comment = c(ORCID = "0000-0001-8568-3071")),
     person("Louis-Philippe", "Caron", , "louis-philippe.caron@bsc.es", role = "aut", comment = c(ORCID = "0000-0001-5221-0147")),
@@ -62,6 +62,7 @@ Depends:
     easyVerification
 Imports:
     s2dv,
+    startR,
     rainfarmr,
     multiApply (>= 2.1.1),
     ClimProjDiags,
@@ -78,17 +79,17 @@ Imports:
     utils,
     verification,
     lubridate,
-    scales
+    scales,
+    easyNCDF
 Suggests:
     zeallot,
     testthat,
     knitr,
     markdown,
-    rmarkdown,
-    startR
+    rmarkdown
 VignetteBuilder: knitr
 License: GPL-3
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 Config/testthat/edition: 3

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)
@@ -69,6 +70,7 @@ export(s2dv_cube)
 export(training_analogs)
 import(RColorBrewer)
 import(abind)
+import(easyNCDF)
 import(ggplot2)
 import(lubridate)
 import(multiApply)

NEWS.md

+# CSTools 5.2.0 (Release date: 25-01-2024) 
+
+### Development
+- New function CST_ChangeDimNames
+- CST_SplitDim: added dimension names and split also Dates
+- CST_SaveExp: save time bounds and global attributes; improved code
+
+### Other
+- Updated README
+- Added citation file
+
+# CSTools 5.1.1 (Release date: 19-10-2023) 
+
+### Fixes
+- Added startR namespace in all CST_Start calls of the vignettes and sample data.
+
+# CSTools 5.1.0 (Release date: 17-10-2023) 
+
+### Fixes
+- Calibration() show warnings in atomic function when multiple cores are used. 
+- PlotForecastPDF fix background color in different machines.
+- Correct CST_Subset indices for metadata.
+- CST_Analogs: Add sdate_dim parameter and improve initial checks.
+- Remove CST_Anomaly repeated checks in order to accept no member dimensions in obs.  
+- CST_SaveExp developments: improve warning, save metadata correctly. 
+- Improve print method in order that time_bounds are correctly displayed.
+
+### Development
+- PlotWeeklyClim to allow years outside the reference period.
+- PlotWeeklyClim to allow setting y limits.
+- New function CST_Start().
+- PlotCombinedMap() has upper triangle_end; the color bars can have different breaks.
+- New print method.
+- CST_MultiEOF development treat spatial NAs.
+- Correct PlotCombinedMap error.
+- Substitute mentions of CST_Load by CST_Start.
+- Modify necessary vignettes to the use of CST_Start.
+
 # CSTools 5.0.1 (Release date: 06-06-2023)  
 - Resubmit to CRAN because it was archived due to dependency issue  
   
-**Fixes**  
+### Fixes
 - Standardize the coordinates of 's2dv_cube' by setting the coordinates to vectors with NULL dimensions  
 - Include a check for SaveExp output filenames that only contain date information  
 - In SaveExp the dates parameter is allowed to have additional time dimensions of length 1  
 - Removed dot from the internal function named mergedatasets() used in CST_CategoricalEnsCombination  
   
-**New Features**  
+### Development
 - New parameter 'startdates' in CST_SaveExp used to manually decide the name of the output files  
   
-**Other**  
+### Other 
 - Switch to testthat version 3  
 
 # CSTools 5.0.0 (Release date: 05-04-2023)  
-**Fixes**  
+
+### Fixes 
 - Correct vignettes: Analogs, MultiModelSkill and MultivarRMSE  
 - Add 'ncores' to s2dv function calls in CST_Anomaly  
 - Reduce computing time of examples and tests and improve documentation  
 
-**New features**   
+### Development
 - Add dat_dim parameter in CST_BiasCorrection and CST_Calibration   
 - New plotting function for case studies temporal visualisation: PlotWeeklyClim  
 - Deprecate indices in dim_anom parameter of CST_Anomaly  
@@ -31,26 +70,28 @@
 - New color set in PlotForecastPDF Vitigeoss colors  
 - New function CST_InsertDim  
   
-**Other**  
+### Other 
 - Added contribution from ArticXchange project due to PlotWeeklyClim  
 - Update NEWS.md with the correct format  
 - Change Licence  
 
 # CSTools 4.1.1 (Release date: 10-11-2022)  
-**Fixes**    
+
+### Fixes   
 - CST_Analogs corrected input of ClimProjDiags::Subset()  
 - PlotCombinedMap corrected use of 'cex_bar_titles' parameter  
 - CST_Anomaly added 'memb_dim', 'dat_dim' and 'ftime_dim' and improved use for 'dim_anom' parameters  
   
-# CSTools 4.1.0 (Release date: 25-10-2022)  
-**New features**    
+# CSTools 4.1.0 (Release date: 25-10-2022)
+
+### Development   
 - Dependency on package 's2dverification' is changed to 's2dv'  
 - CST_BiasCorrection new parameters 'memb_dim', 'sdate_dim', 'ncores'  
 - CST_Calibration is able to calibrate forecast with new parameter 'exp_cor'  
 - CST_QuantileMapping uses cross-validation and provides option to remove NAs; new parameters 'memb_dim', 'sdate_dim', 'window_dim' and 'na.rm'; 'sample_dim' and 'sample_length' are removed  
 - s2dv_cube() new parameter 'time_dim'  
 
-**Fixes**    
+### Fixes
 - as.s2dv_cube() detects latitude and longitude structure in startR_array object  
 - Data correction: 'lonlat_data' is renamed to 'lonlat_temp'; 'lonlat_prec' is corrected by one-day shift  
 - Typo and parameter correction in vignette 'MostLikelyTercile_vignette'  
@@ -58,20 +99,22 @@
 - PlotMostLikelyQuantileMap() works with s2dv::PlotLayout  
   
 # CSTools 4.0.1 (Release date: 05-10-2021)  
-**New features**    
+
+### Development  
 - Dynamical Bias Correction method: `CST_ProxiesAttractors` and `CST_DynBiasCorrection` (optionally `Predictability`)  
 - CST_BiasCorrection and BiasCorrection allows to calibrate a forecast given the calibration in the hindcast by using parameter 'exp_cor'  
 - Use cases  
 - CST_SaveExp includes parameter extra_string  
 - PlotCombinedMap includes parameter cex_bar_titles  
 
-**Fixes**   
+### Fixes
 - Calibration retains correlation absolute value   
 - Calibration fixed when cal.methodi == rpc-based, apply_to == sign, eval.method == 'leave-one-out' and the correlation is not significant  
 - PlotMostLikelyQuantileMap reoder latitudes of an array provided in 'dots' parameter  
 
 # CSTools 4.0.0 (Release date: 23-02-2021)  
-**New features**  
+
+### Development
 - ADAMONT downscaling method: requires CST_AdamontAnalogs and CST_AdamontQQCor functions  
 - Analogs method using Predictors: requires training_analogs and  CST_AnalogsPredictors  
 - PlotPDFsOLE includes parameters to modify legend style  
@@ -88,7 +131,7 @@
 - Analogs vignette  
 - Data Storage and retrieval vignette  
 
-**Fixes**    
+### Fixes
 - PlotForecastPDF correctly displays terciles labels   
 - CST_SaveExp correctly save time units  
 - CST_SplitDims returns ordered output following ascending order provided in indices when it is numeric  
@@ -100,7 +143,8 @@
 - Decrease package size compresing vignettes figures and removing areave_data sample  
   
 # CSTools 3.1.0 (Release date: 02-07-2020)  
-**New features**    
+
+### Development   
 - EnsClustering vignette  
 - EnsClustering has a new parameter 'time_dim'  
 - CST_BiasCorrection has na.rm paramter  
@@ -111,7 +155,7 @@
 - CST_RFTemp/RF_Temp functions available for downscaling temperature  
 - Weather Regimes vignette  
 
-**Fixes**   
+### Fixes
 - CST_Anomaly handles exp, obs or both  
 - PlotForecastPDF vignette displays figures correctly  
 - Calibration function is exposed to users  
@@ -123,17 +167,19 @@
 - CST_SaveExp uses multiApply and save time dimension correctly  
 
 # CSTools 3.0.0 (Release date: 10-02-2020)  
-**New features**    
+
+### Development  
 - CST_MergeDims and MergeDims  
 - Version working with R 3.4.2  
 - PlotForecastPDF handles independent terciles, extremes and observations for each panel  
 
-**Fixes**   
+### Fixes
 - CST_Calibration handles missing values  
 - BEI functions handle missing values  
 
-# CSTools 2.0.0 (Release date: 25-11-2019)  
-**New features**   
+# CSTools 2.0.0 (Release date: 25-11-2019)
+
+### Development
 - CST_Analogs Analogs downscaling method,   
 - CST_MultiEOFS for multiple variables,   
 - Ensemble Clustering,  
@@ -151,13 +197,14 @@
 - Adding reference to S2S4E H2020 project into the DESCRIPTION file  
 - Adding NEWS.md file  
   
-**Fixes**   
+### Fixes  
 - Minor fix in CST_BiasCorrection when checking parameter 'obs'  
 - Minor fix in data lonlat_prec to be of class 's2dv_cube'  
 - Minor fix in RainFARM vignette  
   
 ### CSTools 1.0.1 (Release date: 19-06-2019)  
-**Fixes and new features**    
+
+### Fixes and development   
 - Correcting test of PlotForecastPDF for compatibility with ggplot2 release  
 - New function PlotCombinedMap  
 - Adding reference to MEDSCOPE ERA4CS Project into the DESCRIPTION file  

R/CST_Analogs.R

@@ -24,7 +24,7 @@
 #'This function has not constrains of specific regions, variables to downscale,
 #'or data to be used (seasonal forecast data, climate projections data, 
 #'reanalyses data). The regrid into a finner scale is done interpolating with 
-#'CST_Load. Then, this interpolation is corrected selecting the analogs in the 
+#'CST_Start. Then, this interpolation is corrected selecting the analogs in the 
 #'large and local scale in based of the observations. The function is an 
 #'adapted version of the method of Yiou et al 2013. For an advanced search of 
 #'Analogs (multiple Analogs, different criterias, further information from the
@@ -54,6 +54,8 @@
 #'  analog of parameter 'expVar'.
 #'@param obsVar An 's2dv_cube' containing the field of the same variable as the 
 #'  passed in parameter 'expVar' for the same region.
+#'@param sdate_dim A character string indicating the name of the start date 
+#'  dimension. By default, it is set to 'sdate'.
 #'@param region A vector of length four indicating the minimum longitude, the 
 #'  maximum longitude, the minimum latitude and the maximum latitude.
 #'@param criteria A character string indicating the criteria to be used for the
@@ -77,7 +79,8 @@
 #'  and dates are taken from element \code{$attrs$Dates} from expL.
 #'@param time_obsL A character string indicating the date of the observations 
 #'  in the date format (i.e. "yyyy-mm-dd"). By default it is NULL and dates are 
-#'  taken from element \code{$attrs$Dates} from obsL.
+#'  taken from element \code{$attrs$Dates} from obsL. It must have time 
+#'  dimensions.
 #'@param region A vector of length four indicating the minimum longitude, 
 #'  the maximum longitude, the minimum latitude and the maximum latitude.
 #'@param nAnalogs Number of Analogs to be selected to apply the criterias 
@@ -101,8 +104,7 @@
 #'  best analog, for instance for downscaling. 
 #'@param ncores The number of cores to use in parallel computation
 #'
-#'@seealso \code{\link{CST_Load}}, \code{\link[s2dv]{Load}} and 
-#'\code{\link[s2dv]{CDORemap}}
+#'@seealso \code{\link{CST_Start}}, \code{\link[startR]{Start}}
 #'
 #'@return An 's2dv_cube' object containing an array with the dowscaled values of 
 #'the best analogs in element 'data'. If 'AnalogsInfo' is TRUE, 'data' is a list 
@@ -117,6 +119,7 @@
 #'                        format = "%d-%m-%y")
 #'dim(time_obsL) <- c(time = 10)
 #'time_expL <- time_obsL[1]
+#'dim(time_expL) <- c(time = 1)
 #'lon <-  seq(-1, 5, 1.5)
 #'lat <- seq(30, 35, 1.5)
 #'coords <- list(lon = seq(-1, 5, 1.5), lat = seq(30, 35, 1.5))
@@ -131,9 +134,11 @@
 #' 
 #'@import multiApply
 #'@import abind
+#'@import s2dv
 #'@importFrom ClimProjDiags SelBox Subset
 #'@export
-CST_Analogs <- function(expL, obsL, expVar = NULL, obsVar = NULL, region = NULL,
+CST_Analogs <- function(expL, obsL, expVar = NULL, obsVar = NULL, 
+                        sdate_dim = 'sdate', region = NULL,
                         criteria = 'Large_dist', excludeTime = NULL,
                         time_expL = NULL, time_obsL = NULL,
                         nAnalogs = NULL, AnalogsInfo = FALSE,
@@ -141,16 +146,13 @@ CST_Analogs <- function(expL, obsL, expVar = NULL, obsVar = NULL, region = NULL,
 
   # Check 's2dv_cube'
   if (!inherits(expL, "s2dv_cube") || !inherits(obsL, "s2dv_cube")) {
-    stop("Parameter 'expL' and 'obsL' must be of the class 's2dv_cube', ",
-         "as output by CSTools::CST_Load.")
+    stop("Parameter 'expL' and 'obsL' must be of the class 's2dv_cube'.")
   }
   if (!is.null(expVar) && !inherits(expVar, "s2dv_cube")) {
-    stop("Parameter 'expVar' must be of the class 's2dv_cube', ",
-         "as output by CSTools::CST_Load.")
+    stop("Parameter 'expVar' must be of the class 's2dv_cube'.")
   }        
   if (!is.null(obsVar) && !inherits(obsVar, "s2dv_cube")) {
-    stop("Parameter 'obsVar' must be of the class 's2dv_cube', ",
-         "as output by CSTools::CST_Load.")
+    stop("Parameter 'obsVar' must be of the class 's2dv_cube'.")
   }
 
   # Check 'obsL' object structure
@@ -215,7 +217,8 @@ CST_Analogs <- function(expL, obsL, expVar = NULL, obsVar = NULL, region = NULL,
                  lonL = as.vector(obsL$coords[[lon_name]]),
                  latL = as.vector(obsL$coords[[lat_name]]), 
                  expVar = expVar$data,
-                 obsVar = obsVar$data, criteria = criteria, 
+                 obsVar = obsVar$data, sdate_dim = sdate_dim,
+                 criteria = criteria, 
                  excludeTime = excludeTime, region = region,
                  lonVar = as.vector(lonVar), latVar = as.vector(latVar),
                  nAnalogs = nAnalogs, AnalogsInfo = AnalogsInfo,
@@ -228,6 +231,7 @@ CST_Analogs <- function(expL, obsL, expVar = NULL, obsVar = NULL, region = NULL,
   }
 
   expL$data <- res
+  expL$dims <- dim(res)
 
   if (!is.null(obsL$coords[[lon_name]]) | !is.null(obsL$coords[[lat_name]])) {
     if (is.null(region)) {
@@ -285,7 +289,7 @@ CST_Analogs <- function(expL, obsL, expVar = NULL, obsVar = NULL, region = NULL,
 #'ones. This function has not constrains of specific regions, variables to 
 #'downscale, or data to be used (seasonal forecast data, climate projections 
 #'data, reanalyses data). The regrid into a finner scale is done interpolating 
-#'with CST_Load. Then, this interpolation is corrected selecting the analogs in
+#'with CST_Start. Then, this interpolation is corrected selecting the analogs in
 #'the large and local scale in based of the observations. The function is an 
 #'adapted version of the method of Yiou et al 2013.       
 #'
@@ -308,10 +312,12 @@ CST_Analogs <- function(expL, obsL, expVar = NULL, obsVar = NULL, region = NULL,
 #'  the same latitudinal and longitudinal dimensions as parameter 'expL' and a 
 #'  single temporal dimension with the maximum number of available observations.
 #'@param time_obsL A character string indicating the date of the observations 
-#'  in the format "dd-mm-yyyy". Reference time to search for analogs. 
+#'  in the format "dd-mm-yyyy". Reference time to search for analogs. It must 
+#'  have time dimensions.
 #'@param time_expL An array of N named dimensions (coinciding with time 
 #'  dimensions in expL) of character string(s) indicating the date(s) of the 
-#'  experiment in the format "dd-mm-yyyy". Time(s) to find the analogs.
+#'  experiment in the format "dd-mm-yyyy". Time(s) to find the analogs. If it 
+#'  is not an scalar it must have named dimensions.
 #'@param lonL A vector containing the longitude of parameter 'expL'.
 #'@param latL A vector containing the latitude of parameter 'expL'.
 #'@param excludeTime An array of N named dimensions (coinciding with time 
@@ -326,6 +332,8 @@ CST_Analogs <- function(expL, obsL, expVar = NULL, obsVar = NULL, region = NULL,
 #'  function will be the analog of parameter 'expVar'.
 #'@param obsVar An array of N named dimensions containing the field of the 
 #'  same variable as the passed in parameter 'expVar' for the same region.
+#'@param sdate_dim A character string indicating the name of the start date 
+#'  dimension. By default, it is set to 'sdate'.
 #'@param AnalogsInfo A logical value. If it is TRUE it returns a list
 #'  with two elements: 1) the downscaled field and
 #'  2) the AnalogsInfo which contains: a) the number of the best 
@@ -372,6 +380,7 @@ CST_Analogs <- function(expL, obsL, expVar = NULL, obsVar = NULL, region = NULL,
 #'obsSLP <- c(rnorm(1:180), expSLP * 1.2)
 #'dim(obsSLP) <- c(time = 10, lat = 4, lon = 5)
 #'time_obsSLP <- paste(rep("01", 10), rep("01", 10), 1994 : 2003, sep = "-")
+#'dim(time_obsSLP) <- c(time = 10)
 #'downscale_field <- Analogs(expL = expSLP, obsL = obsSLP, 
 #'                           time_obsL = time_obsSLP,time_expL = "01-01-1994")
 #'
@@ -417,11 +426,12 @@ CST_Analogs <- function(expL, obsL, expVar = NULL, obsVar = NULL, region = NULL,
 #'                          AnalogsInfo = TRUE)
 #'@import multiApply
 #'@import abind
+#'@import s2dv
 #'@importFrom ClimProjDiags SelBox Subset
 #'@export
 Analogs <- function(expL, obsL, time_obsL, time_expL = NULL, 
-                    lonL = NULL, latL = NULL, expVar = NULL,
-                    obsVar = NULL, criteria = "Large_dist", 
+                    lonL = NULL, latL = NULL, expVar = NULL, obsVar = NULL, 
+                    sdate_dim = 'sdate', criteria = "Large_dist", 
                     excludeTime = NULL, lonVar = NULL, latVar = NULL, 
                     region = NULL, nAnalogs = NULL, 
                     AnalogsInfo = FALSE, ncores = NULL) {
@@ -536,12 +546,61 @@ Analogs <- function(expL, obsL, time_obsL, time_expL = NULL,
   }
   if (!inherits(time_obsL, "character")) {
     warning('imposing time_obsL to be a character')
+    dims_time_obsL <- dim(time_obsL)
     time_obsL <- format(as.Date(time_obsL), '%d-%m-%Y')
+    dim(time_obsL) <- dims_time_obsL
   }
   if (!inherits(time_expL, "character")) {
     warning('imposing time_expL to be a character')
+    dims_time_expL <- dim(time_expL)
     time_expL <- format(as.Date(time_expL), '%d-%m-%Y')
+    dim(time_expL) <- dims_time_expL
   }
+  # time_obsL, time_expL (2)
+  if (is.null(names(dim(time_obsL)))) {
+    stop("Parameter 'time_obsL' must have named dimensions.")
+  }
+  if (!is.character(sdate_dim)) {
+    stop("Parameter 'sdate_dim' must be a character string.")
+  }
+  if (!sdate_dim %in% names(dim(time_obsL))) {
+    if (length(dim(time_obsL)) == 1) {
+      dim(time_obsL) <- c(dim(time_obsL), sdate = 1)
+    } else {
+      stop("Parameters 'time_obsL' must have 'sdate_dim' dimension name. ",
+           "If it has multiple time dimensions.")
+    }
+  }
+  if (length(time_expL) != 1) {
+    if (is.null(names(dim(time_expL)))) {
+      stop("Parameter 'time_expL' must have named dimensions.")
+    }
+  } else {
+    dim(time_expL) <- 1
+  }
+  if (!sdate_dim %in% names(dim(time_expL))) {
+    if (length(dim(time_expL)) == 1) {
+      dim(time_expL) <- c(dim(time_expL), sdate = 1)
+    } else {
+      stop("Parameters 'time_expL' must have 'sdate_dim' dimension name. ",
+           "If it has multiple time dimensions.")
+    }
+  }
+  if (length(dim(time_obsL)) == 2) {
+    if (which(sdate_dim %in% names(dim(time_obsL))) == 1) {
+      time_obsL <- Reorder(time_obsL, c(2,1))
+    }
+  } else {
+    warning("Parameter 'time_obsL' should have forecast time and start date dimension in this order.")
+  }
+  if (length(dim(time_expL)) == 2) {
+    if (which(sdate_dim %in% names(dim(time_expL))) == 1) {
+      time_expL <- Reorder(time_expL, c(2,1))
+    }
+  } else {
+    warning("Parameter 'time_expL' should have forecast time and start date dimension in this order.")
+  }
+
   # excludeTime
   if (!is.null(excludeTime)) {
     if (!inherits(excludeTime, "character")) {
@@ -549,23 +608,7 @@ Analogs <- function(expL, obsL, time_obsL, time_expL = NULL,
       excludeTime <- format(as.Date(excludeTime),'%d-%m-%Y')
     }
   }
-  # time_obsL
-  if (is.null(time_obsL)) {
-    stop("Parameter 'time_obsL' cannot be NULL")
-  }
-  if (any(names(dim(obsL)) %in% 'ftime')) {
-    if (any(names(dim(obsL)) %in% 'time')) {
-      stop("Multiple temporal dimensions ('ftime' and 'time') found",
-           "in parameter 'obsL'.")
-    } else {
-      time_pos_obsL <-  which(names(dim(obsL)) == 'ftime')
-      names(dim(obsL))[time_pos_obsL] <- 'time'
-      if (any(names(dim(expL)) %in% 'ftime')) {
-        time_pos_expL <-  which(names(dim(expL)) == 'ftime')
-        names(dim(expL))[time_pos_expL] <- 'time'
-      }
-    }
-  }
+  # obsVar, expVar
   if (!is.null(obsVar)) {
     if (any(names(dim(obsVar)) %in% 'ftime')) {
       if (any(names(dim(obsVar)) %in% 'time')) {
@@ -581,6 +624,20 @@ Analogs <- function(expL, obsL, time_obsL, time_expL = NULL,
       }
     }
   }
+  # obsL
+  if (any(names(dim(obsL)) %in% 'ftime')) {
+    if (any(names(dim(obsL)) %in% 'time')) {
+      stop("Multiple temporal dimensions ('ftime' and 'time') found",
+           "in parameter 'obsL'.")
+    } else {
+      time_pos_obsL <-  which(names(dim(obsL)) == 'ftime')
+      names(dim(obsL))[time_pos_obsL] <- 'time'
+      if (any(names(dim(expL)) %in% 'ftime')) {
+        time_pos_expL <-  which(names(dim(expL)) == 'ftime')
+        names(dim(expL))[time_pos_expL] <- 'time'
+      }
+    }
+  }
   if ((any(names(dim(obsL)) %in% 'sdate')) &&
       (any(names(dim(obsL)) %in% 'time'))) {
     dims_obsL <- dim(obsL)
@@ -604,7 +661,7 @@ Analogs <- function(expL, obsL, time_obsL, time_expL = NULL,
       if (any(names(dim(obsL)) %in% 'time')) {
         dims_obsL <- dim(obsL)
         pos_time <- which(names(dim(obsL)) == 'time')
-        if(length(time_obsL) != dim(obsL)[pos_time]) {
+        if (length(time_obsL) != dim(obsL)[pos_time]) {
           stop("'time_obsL' and 'obsL' must have same length in the temporal
                 dimension.")
         }
@@ -618,6 +675,7 @@ Analogs <- function(expL, obsL, time_obsL, time_expL = NULL,
       }
     }
   }
+  # obsVar
   if (!is.null(obsVar)) {
     if (any(names(dim(obsVar)) %in% 'sdate')) {
       if (any(names(dim(obsVar)) %in% 'time')) {

R/CST_Anomaly.R

@@ -9,10 +9,10 @@
 #'computation is carried out independently for experimental and observational 
 #'data products.
 #'
-#'@param exp An object of class \code{s2dv_cube} as returned by \code{CST_Load} 
+#'@param exp An object of class \code{s2dv_cube} as returned by \code{CST_Start} 
 #'  function, containing the seasonal forecast experiment data in the element 
 #'  named \code{$data}.
-#'@param obs An object of class \code{s2dv_cube} as returned by \code{CST_Load} 
+#'@param obs An object of class \code{s2dv_cube} as returned by \code{CST_Start} 
 #'  function, containing the observed data in the element named \code{$data}.
 #'@param dim_anom A character string indicating the name of the dimension 
 #'  along which the climatology will be computed. The default value is 'sdate'.
@@ -57,7 +57,7 @@
 #'anom <- CST_Anomaly(exp = exp, obs = obs, cross = FALSE, memb = TRUE)
 #'
 #'@seealso \code{\link[s2dv]{Ano_CrossValid}}, \code{\link[s2dv]{Clim}} and 
-#'\code{\link{CST_Load}}
+#'\code{\link{CST_Start}}
 #'
 #'@import multiApply
 #'@importFrom s2dv InsertDim Clim Ano_CrossValid Reorder
@@ -69,8 +69,7 @@ CST_Anomaly <- function(exp = NULL, obs = NULL, dim_anom = 'sdate',
   # Check 's2dv_cube'
   if (!inherits(exp, 's2dv_cube') & !is.null(exp) || 
       !inherits(obs, 's2dv_cube') & !is.null(obs)) {
-    stop("Parameter 'exp' and 'obs' must be of the class 's2dv_cube', ",
-         "as output by CSTools::CST_Load.")
+    stop("Parameter 'exp' and 'obs' must be of the class 's2dv_cube'.")
   }
   # exp and obs
   if (is.null(exp$data) & is.null(obs$data)) {
@@ -91,13 +90,10 @@ CST_Anomaly <- function(exp = NULL, obs = NULL, dim_anom = 'sdate',
       any(is.null(names(dim(obs$data))))| any(nchar(names(dim(obs$data))) == 0)) {
     stop("Parameter 'exp' and 'obs' must have dimension names in element 'data'.")
   }
-  if (!all(names(dim(exp$data)) %in% names(dim(obs$data))) |
-      !all(names(dim(obs$data)) %in% names(dim(exp$data)))) {
-    stop("Parameter 'exp' and 'obs' must have same dimension names in element 'data'.")
-  }
   dim_exp <- dim(exp$data)
   dim_obs <- dim(obs$data)
-  dimnames_data <- names(dim_exp)
+  dimnames_exp <- names(dim_exp)
+  dimnames_obs <- names(dim_obs)
   # dim_anom
   if (!is.character(dim_anom)) {
     stop("Parameter 'dim_anom' must be a character string.")
@@ -129,19 +125,12 @@ CST_Anomaly <- function(exp = NULL, obs = NULL, dim_anom = 'sdate',
     if (!is.character(memb_dim) | length(memb_dim) > 1) {
       stop("Parameter 'memb_dim' must be a character string.")
     }
-    if (!memb_dim %in% names(dim_exp) | !memb_dim %in% names(dim_obs)) {
-      stop("Parameter 'memb_dim' is not found in 'exp' or in 'obs' dimension.")
-    }
   }
   # dat_dim
   if (!is.null(dat_dim)) {
     if (!is.character(dat_dim)) {
       stop("Parameter 'dat_dim' must be a character vector.")
     }
-    if (!all(dat_dim %in% names(dim_exp)) | !all(dat_dim %in% names(dim_obs))) {
-      stop("Parameter 'dat_dim' is not found in 'exp' or 'obs' dimension in element 'data'. ",
-           "Set it as NULL if there is no dataset dimension.")
-    }
   }
   # filter_span
   if (!is.null(filter_span)) {
@@ -161,7 +150,7 @@ CST_Anomaly <- function(exp = NULL, obs = NULL, dim_anom = 'sdate',
     if (!is.character(ftime_dim)) {
       stop("Parameter 'ftime_dim' must be a character string.")
     }
-    if (!ftime_dim %in% names(dim_exp) | !memb_dim %in% names(dim_obs)) {
+    if (!ftime_dim %in% names(dim_exp) | !ftime_dim %in% names(dim_obs)) {
       stop("Parameter 'ftime_dim' is not found in 'exp' or in 'obs' dimension in element 'data'.")
     }
   }
@@ -206,15 +195,17 @@ CST_Anomaly <- function(exp = NULL, obs = NULL, dim_anom = 'sdate',
     ano <- NULL
 
     # Permuting back dimensions to original order
-    clim_exp <- Reorder(clim_exp, dimnames_data)
-    clim_obs <- Reorder(clim_obs, dimnames_data)
+    clim_exp <- Reorder(clim_exp, dimnames_exp)
+    clim_obs <- Reorder(clim_obs, dimnames_obs)
 
     ano$exp <- exp$data - clim_exp
     ano$obs <- obs$data - clim_obs 
   }
 
   exp$data <- ano$exp
+  exp$dims <- dim(ano$exp)
   obs$data <- ano$obs
+  obs$dims <- dim(ano$obs)
   
   #  Outputs
   # ~~~~~~~~~

R/CST_BiasCorrection.R

@@ -5,14 +5,14 @@
 #'described in Torralba et al. (2017). The adjusted forecasts have an equivalent 
 #'standard deviation and mean to that of the reference dataset.
 #'
-#'@param exp An object of class \code{s2dv_cube} as returned by \code{CST_Load} 
+#'@param exp An object of class \code{s2dv_cube} as returned by \code{CST_Start} 
 #'  function, containing the seasonal forecast experiment data in the element 
 #'  named \code{$data} with at least time and member dimensions.
-#'@param obs An object of class \code{s2dv_cube} as returned by \code{CST_Load} 
+#'@param obs An object of class \code{s2dv_cube} as returned by \code{CST_Start} 
 #'  function, containing the observed data in the element named \code{$data} 
 #'  with at least time dimension.
 #'@param exp_cor An object of class \code{s2dv_cube} as returned by 
-#'  \code{CST_Load} function, containing the seasonal forecast experiment to be 
+#'  \code{CST_Start} function, containing the seasonal forecast experiment to be 
 #'  corrected with at least time dimension. If it is NULL, the 'exp' forecast 
 #'  will be corrected. If there is only one corrected dataset, it should not  
 #'  have dataset dimension. If there is a corresponding corrected dataset for  
@@ -44,9 +44,9 @@
 #'
 #'@examples
 #'mod1 <- 1 : (1 * 3 * 4 * 5 * 6 * 7)
-#'dim(mod1) <- c(dataset = 1, member = 3, sdate = 4, ftime = 5, lat = 6, lon = 7)
+#'dim(mod1) <- c(dataset = 1, member = 3, sdate = 4, time = 5, lat = 6, lon = 7)
 #'obs1 <- 1 : (1 * 1 * 4 * 5 * 6 * 7)
-#'dim(obs1) <- c(dataset = 1, member = 1, sdate = 4, ftime = 5, lat = 6, lon = 7)
+#'dim(obs1) <- c(dataset = 1, member = 1, sdate = 4, time = 5, lat = 6, lon = 7)
 #'lon <- seq(0, 30, 5)
 #'lat <- seq(0, 25, 5)
 #'coords <- list(lat = lat, lon = lon)
@@ -134,9 +134,9 @@ CST_BiasCorrection <- function(exp, obs, exp_cor = NULL, na.rm = FALSE,
 #'
 #'@examples
 #'mod1 <- 1 : (1 * 3 * 4 * 5 * 6 * 7)
-#'dim(mod1) <- c(dataset = 1, member = 3, sdate = 4, ftime = 5, lat = 6, lon = 7)
+#'dim(mod1) <- c(dataset = 1, member = 3, sdate = 4, time = 5, lat = 6, lon = 7)
 #'obs1 <- 1 : (1 * 1 * 4 * 5 * 6 * 7)
-#'dim(obs1) <- c(dataset = 1, member = 1, sdate = 4, ftime = 5, lat = 6, lon = 7)
+#'dim(obs1) <- c(dataset = 1, member = 1, sdate = 4, time = 5, lat = 6, lon = 7)
 #'a <- BiasCorrection(exp = mod1, obs = obs1)
 #'@import multiApply
 #'@export

R/CST_Calibration.R

@@ -18,16 +18,16 @@
 #'(2014). It is equivalent to function \code{Calibration} but for objects 
 #'of class \code{s2dv_cube}.
 #'
-#'@param exp An object of class \code{s2dv_cube} as returned by \code{CST_Load} 
+#'@param exp An object of class \code{s2dv_cube} as returned by \code{CST_Start} 
 #'  function with at least 'sdate' and 'member' dimensions, containing the  
 #'  seasonal hindcast experiment data in the element named \code{data}. The 
 #'  hindcast is used to calibrate the forecast in case the forecast is provided; 
 #'  if not, the same hindcast will be calibrated instead.
-#'@param obs An object of class \code{s2dv_cube} as returned by \code{CST_Load} 
+#'@param obs An object of class \code{s2dv_cube} as returned by \code{CST_Start} 
 #'  function with at least 'sdate' dimension, containing the observed data in 
 #'  the element named \code{$data}.
 #'@param exp_cor An optional object of class \code{s2dv_cube} as returned by 
-#'  \code{CST_Load} function with at least 'sdate' and 'member' dimensions, 
+#'  \code{CST_Start} function with at least 'sdate' and 'member' dimensions, 
 #'  containing the seasonal forecast experiment data in the element named 
 #'  \code{data}. If the forecast is provided, it will be calibrated using the 
 #'  hindcast and observations; if not, the hindcast will be calibrated instead. 
@@ -106,7 +106,7 @@
 #'Quarterly Journal of the Royal Meteorological Society, 141(688), 807-818.  
 #'\doi{10.1002/qj.2397}
 #' 
-#'@seealso \code{\link{CST_Load}}
+#'@seealso \code{\link{CST_Start}}
 #' 
 #'@examples
 #'# Example 1:
@@ -287,7 +287,7 @@ CST_Calibration <- function(exp, obs, exp_cor = NULL, cal.method = "mse_min",
 #'Quarterly Journal of the Royal Meteorological Society, 141(688), 807-818.  
 #'\doi{10.1002/qj.2397}
 #' 
-#'@seealso \code{\link{CST_Load}}
+#'@seealso \code{\link{CST_Start}}
 #' 
 #'@examples
 #'mod1 <- 1 : (1 * 3 * 4 * 5 * 6 * 7)

R/CST_ChangeDimNames.R

+#'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(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 (!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'.")
+  }
+  if (!all(original_names %in% names(data$dims))) {
+    stop("Some of the dimensions in 'original_names' could not be found in ",
+         "'data'.")
+  }
+  for (index in 1:length(original_names)) {
+    original_name <- original_names[index]
+    new_name <- new_names[index]
+    # Step 1: Change dims
+    names(data$dims)[which(names(data$dims) == original_name)] <- new_name
+    # Step 2: Change coords
+    names(data$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
+    }
+  }
+  # 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)
+}
+

R/CST_MergeDims.R

@@ -15,8 +15,6 @@
 #'  \code{merge_dims} will be used.
 #'@param na.rm A logical indicating if the NA values should be removed or not.
 #'
-#'@import abind
-#'@importFrom ClimProjDiags Subset
 #'@examples
 #'data <- 1 : c(2 * 3 * 4 * 5 * 6 * 7)
 #'dim(data) <- c(time = 7, lat = 2, lon = 3, monthly = 4, member = 6,
@@ -33,11 +31,35 @@ CST_MergeDims <- function(data, merge_dims = c('ftime', 'monthly'),
                           rename_dim = NULL, na.rm = FALSE) {
   # Check 's2dv_cube'
   if (!inherits(data, 's2dv_cube')) {
-    stop("Parameter 'data' must be of the class 's2dv_cube', ",
-         "as output by CSTools::CST_Load.")
+    stop("Parameter 'data' must be of the class 's2dv_cube'.")
   }
+  if (is.null(rename_dim)) {
+    rename_dim <- merge_dims[1]
+  }
+  # data
   data$data <- MergeDims(data$data, merge_dims = merge_dims,
                          rename_dim = rename_dim, na.rm = na.rm)
+  # dims
+  data$dims <- dim(data$data)
+
+  # rename_dim               
+  if (length(rename_dim) > 1) {
+    rename_dim <- as.character(rename_dim[1])
+  }
+  # coords
+  data$coords[merge_dims] <- NULL
+  data$coords[[rename_dim]] <- 1:dim(data$data)[rename_dim]
+  attr(data$coords[[rename_dim]], 'indices') <- TRUE
+
+  # attrs
+  if (all(merge_dims %in% names(dim(data$attrs$Dates)))) {
+    data$attrs$Dates <- MergeDims(data$attrs$Dates, merge_dims = merge_dims,
+                                  rename_dim = rename_dim, na.rm = na.rm)
+  } else if (any(merge_dims %in% names(dim(data$attrs$Dates)))) {
+    warning("The dimensions of 'Dates' array will be different from ",
+            "the temporal dimensions in 'data'. Parameter 'merge_dims' ",
+            "only includes one temporal dimension of 'Dates'.")
+  }
   return(data)
 }
 #'Function to Split Dimension
@@ -56,12 +78,12 @@ CST_MergeDims <- function(data, merge_dims = c('ftime', 'monthly'),
 #'  \code{merge_dims} will be used.
 #'@param na.rm A logical indicating if the NA values should be removed or not.
 #'
-#'@import abind
-#'@importFrom ClimProjDiags Subset
 #'@examples
 #'data <- 1 : 20
 #'dim(data) <- c(time = 10, lat = 2)
 #'new_data <- MergeDims(data, merge_dims = c('time', 'lat'))
+#'@import abind
+#'@importFrom ClimProjDiags Subset
 #'@export
 MergeDims <- function(data, merge_dims = c('time', 'monthly'), 
                       rename_dim = NULL, na.rm = FALSE) {

R/CST_QuantileMapping.R

@@ -58,13 +58,11 @@ CST_QuantileMapping <- function(exp, obs, exp_cor = NULL, sdate_dim = 'sdate',
                                 ncores = NULL, ...) {
   # Check 's2dv_cube'
   if (!inherits(exp, 's2dv_cube') || !inherits(obs, 's2dv_cube')) {
-    stop("Parameter 'exp' and 'obs' must be of the class 's2dv_cube', ",
-         "as output by CSTools::CST_Load.")
+    stop("Parameter 'exp' and 'obs' must be of the class 's2dv_cube'.")
   }
   if (!is.null(exp_cor)) {
     if (!inherits(exp_cor, 's2dv_cube')) {
-      stop("Parameter 'exp_cor' must be of the class 's2dv_cube', ",
-           "as output by CSTools::CST_Load.")
+      stop("Parameter 'exp_cor' must be of the class 's2dv_cube'.")
     }
   }
 

R/CST_RFTemp.R

@@ -144,7 +144,7 @@ CST_RFTemp <- function(data, oro, xlim = NULL, ylim = NULL, lapse = 6.5,
 #'The output grid can be irregularly spaced in lon and/or lat.
 #'@references Method described in ERA4CS MEDSCOPE milestone M3.2: 
 #'High-quality climate prediction data available to WP4 here:
-#'\ url{https://www.medscope-project.eu/the-project/deliverables-reports/}
+#'\url{https://www.medscope-project.eu/the-project/deliverables-reports/}
 #'and in H2020 ECOPOTENTIAL Deliverable No. 8.1:
 #'High resolution (1-10 km) climate, land use and ocean change scenarios here: 
 #'\url{https://ec.europa.eu/research/participants/documents/downloadPublic?documentIds=080166e5b6cd2324&appId=PPGMS}.

R/CST_SaveExp.R

@@ -4,64 +4,88 @@
 #'
 #'@description This function allows to divide and save a object of class 
 #''s2dv_cube' into a NetCDF file, allowing to reload the saved data using 
-#'\code{Start} function from StartR package. If the original 's2dv_cube' object 
-#'has been created from \code{CST_Load()}, then it can be reloaded with 
-#'\code{Load()}.
+#'\code{CST_Start} or \code{CST_Load} functions. It also allows to save any 
+#''s2dv_cube' object that follows the NetCDF attributes conventions.
 #'
 #'@param data An object of class \code{s2dv_cube}.
 #'@param destination A character string containing the directory name in which 
 #'  to save the data. NetCDF file for each starting date are saved into the 
-#'  folder tree: \cr
-#'  destination/Dataset/variable/. By default the function 
-#'  creates and saves the data into the working directory.
+#'  folder tree: 'destination/Dataset/variable/'. By default the function 
+#'  saves the data into the working directory.
 #'@param sdate_dim A character string indicating the name of the start date 
 #'  dimension. By default, it is set to 'sdate'. It can be NULL if there is no
 #'  start date dimension.
 #'@param ftime_dim A character string indicating the name of the forecast time  
-#'  dimension. By default, it is set to 'time'. It can be NULL if there is no 
-#'  forecast time dimension.
+#'  dimension. If 'Dates' are used, it can't be NULL. If there is no forecast 
+#'  time dimension, 'Dates' will be set to NULL and will not be used. By 
+#'  default, it is set to 'time'. 
 #'@param dat_dim A character string indicating the name of dataset dimension. 
-#'  By default, it is set to 'dataset'. It can be NULL if there is no dataset  
-#'  dimension.
+#'  It can be NULL if there is no dataset dimension. By default, it is set to 
+#'  'dataset'. 
 #'@param var_dim A character string indicating the name of variable dimension. 
-#'  By default, it is set to 'var'. It can be NULL if there is no variable  
-#'  dimension.
-#'@param memb_dim A character string indicating the name of the member dimension.
-#'  By default, it is set to 'member'. It can be NULL if there is no member 
-#'  dimension. 
+#'  It can be NULL if there is no variable dimension. By default, it is set to 
+#'  'var'. 
+#'@param memb_dim A character string indicating the name of the member 
+#'  dimension. It can be NULL if there is no member dimension. By default, it is
+#'   set to 'member'. 
 #'@param startdates A vector of dates that will be used for the filenames 
-#'  when saving the data in multiple files. It must be a vector of the same 
-#'  length as the start date dimension of data. It must be a vector of class 
-#'  \code{Dates}, \code{'POSIXct'} or character with lenghts between 1 and 10. 
-#'  If it is NULL, the coordinate corresponding the the start date dimension or 
-#'  the first Date of each time step will be used as the name of the files.
-#'  It is NULL by default.
+#'  when saving the data in multiple files (single_file = FALSE). It must be a 
+#'  vector of the same length as the start date dimension of data. It must be a 
+#'  vector of class \code{Dates}, \code{'POSIXct'} or character with lenghts 
+#'  between 1 and 10. If it is NULL, the coordinate corresponding the the start 
+#'  date dimension or the first Date of each time step will be used as the name 
+#'  of the files. It is NULL by default.
 #'@param single_file A logical value indicating if all object is saved in a 
 #'  single file (TRUE) or in multiple files (FALSE). When it is FALSE, 
-#'  the array is separated for Datasets, variable and start date. It is FALSE  
-#'  by default.
-#'@param extra_string A character string to be include as part of the file name, 
-#'  for instance, to identify member or realization. It would be added to the 
-#'  file name between underscore characters.
+#'  the array is separated for datasets, variable and start date. When there are 
+#'  no specified time dimensions, the data will be saved in a single file by 
+#'  default. The output file name when 'single_file' is TRUE is a character 
+#'  string containing: '<var>_<first_sdate>_<last_sdate>.nc'; when it is FALSE, 
+#'  it is '<var>_<sdate>.nc'. It is FALSE by default. 
+#'@param drop_dims (optional) A vector of character strings indicating the 
+#'  dimension names of length 1 that need to be dropped in order that they don't 
+#'  appear in the netCDF file. Only is allowed to drop dimensions that are not 
+#'  used in the computation. The dimensions used in the computation are the ones 
+#'  specified in: sdate_dim, ftime_dim, dat_dim, var_dim and memb_dim. It is 
+#'  NULL by default.
+#'@param extra_string (Optional) A character string to be included as part of 
+#'  the file name, for instance, to identify member or realization. When 
+#'  single_file is TRUE, the 'extra_string' will substitute all the default 
+#'  file name; when single_file is FALSE, the 'extra_string' will be added 
+#'  in the file name as: '<var>_<extra_string>_<sdate>.nc'. It is NULL by 
+#'  default.
+#'@param units_hours_since (Optional) A logical value only available for the 
+#'  case: 'Dates' have forecast time and start date dimension, 'single_file' is 
+#'  TRUE and 'time_bounds' are not used. When it is TRUE, it saves the forecast 
+#'  time with units of 'hours since'; if it is FALSE, the time units will be a 
+#'  number of time steps with its corresponding frequency (e.g. n days, n months 
+#'  or n hours). It is FALSE by default. 
+#'@param global_attrs (Optional) A list with elements containing the global 
+#'  attributes to be saved in the NetCDF.
 #'
 #'@return Multiple or single NetCDF files containing the data array.\cr
-#'\item{\code{single_file = TRUE}}{
+#'\item{\code{single_file is TRUE}}{
 #'  All data is saved in a single file located in the specified destination  
-#'  path with the following name: 
-#'  <variable_name>_<extra_string>_<first_sdate>_<last_sdate>.nc. Multiple 
-#'  variables are saved separately in the same file. The forecast time units 
-#'  is extracted from the frequency of the time steps (hours, days, months). 
-#'  The first value of forecast time is 1. If no frequency is found, the units 
-#'  will be 'hours since' each start date and the time steps are assumed to be 
-#'  equally spaced.
+#'  path with the following name (by default): 
+#'  '<variable_name>_<first_sdate>_<last_sdate>.nc'. Multiple variables
+#'  are saved separately in the same file. The forecast time units 
+#'  are calculated from each start date (if sdate_dim is not NULL) or from 
+#'  the time step. If 'units_hours_since' is TRUE, the forecast time units 
+#'  will be 'hours since <each start date>'. If 'units_hours_since' is FALSE, 
+#'  the forecast time units are extracted from the frequency of the time steps 
+#'  (hours, days, months); if no frequency is found, the units will be ’hours 
+#'  since’. When the time units are 'hours since' the time ateps are assumed to 
+#'  be equally spaced.
 #'}
-#'\item{\code{single_file = FALSE}}{
+#'\item{\code{single_file is FALSE}}{
 #'  The data array is subset and stored into multiple files. Each file 
 #'  contains the data subset for each start date, variable and dataset. Files 
-#'  with different variables and Datasets are stored in separated directories 
-#'  within the following directory tree: destination/Dataset/variable/. 
-#'  The name of each file will be: 
-#'  <variable_name>_<extra_string>_<sdate>.nc.
+#'  with different variables and datasets are stored in separated directories 
+#'  within the following directory tree: 'destination/Dataset/variable/'. 
+#'  The name of each file will be by default: '<variable_name>_<sdate>.nc'. 
+#'  The forecast time units are calculated from each start date (if sdate_dim 
+#'  is not NULL) or from the time step. The forecast time units will be 'hours 
+#'  since <each start date>'.
 #'}
 #' 
 #'@seealso \code{\link[startR]{Start}}, \code{\link{as.s2dv_cube}} and 
@@ -69,26 +93,21 @@
 #'
 #'@examples
 #'\dontrun{
-#'data <- lonlat_temp$exp
-#'destination <- "./"
-#'CST_SaveExp(data = data, destination = destination, ftime_dim = 'ftime', 
-#'            var_dim = NULL, ftime_dim = 'ftime', var_dim = NULL)
+#'data <- lonlat_temp_st$exp
+#'CST_SaveExp(data = data, ftime_dim = 'ftime', var_dim = 'var', 
+#'            dat_dim = 'dataset', sdate_dim = 'sdate')
 #'}
 #'
-#'@import ncdf4
-#'@importFrom s2dv Reorder
-#'@importFrom ClimProjDiags Subset
-#'@import multiApply
 #'@export
-CST_SaveExp <- function(data, destination = "./", sdate_dim = 'sdate',  
-                        ftime_dim = 'time', dat_dim = 'dataset',
-                        var_dim = 'var', memb_dim = 'member', 
-                        startdates = NULL, single_file = FALSE, 
-                        extra_string = NULL) {
+CST_SaveExp <- function(data, destination = "./", startdates = NULL, 
+                        sdate_dim = 'sdate', ftime_dim = 'time', 
+                        memb_dim = 'member', dat_dim = 'dataset', 
+                        var_dim = 'var', drop_dims = NULL, 
+                        single_file = FALSE, extra_string = NULL, 
+                        global_attrs = NULL, units_hours_since = FALSE) {
   # Check 's2dv_cube'
   if (!inherits(data, 's2dv_cube')) {
-    stop("Parameter 'data' must be of the class 's2dv_cube', ",
-         "as output by CSTools::CST_Load.")
+    stop("Parameter 'data' must be of the class 's2dv_cube'.")
   }
   # Check object structure
   if (!all(c('data', 'attrs') %in% names(data))) {
@@ -98,22 +117,11 @@ CST_SaveExp <- function(data, destination = "./", sdate_dim = 'sdate',
   if (!inherits(data$attrs, 'list')) {
     stop("Level 'attrs' must be a list with at least 'Dates' element.")
   }
-  if (!all(c('coords') %in% names(data))) {
-    warning("Element 'coords' not found. No coordinates will be used.")
-  }
   # metadata
-  if (is.null(data$attrs$Variable$metadata)) {
-    warning("No metadata found in element Variable from attrs.")
-  } else {
+  if (!is.null(data$attrs$Variable$metadata)) {
     if (!inherits(data$attrs$Variable$metadata, 'list')) {
       stop("Element metadata from Variable element in attrs must be a list.")
     }
-    if (!any(names(data$attrs$Variable$metadata) %in% names(data$coords))) {
-      warning("Metadata is not found for any coordinate.")
-    } else if (!any(names(data$attrs$Variable$metadata) %in% 
-                    data$attrs$Variable$varName)) {
-      warning("Metadata is not found for any variable.")
-    }
   }
   # Dates
   if (is.null(data$attrs$Dates)) {
@@ -127,49 +135,31 @@ CST_SaveExp <- function(data, destination = "./", sdate_dim = 'sdate',
     if (!is.character(sdate_dim)) {
       stop("Parameter 'sdate_dim' must be a character string.")
     }
-    if (length(sdate_dim) > 1) {
-      warning("Parameter 'sdate_dim' has length greater than 1 and ",
-              "only the first element will be used.")
-      sdate_dim <- sdate_dim[1]
-    }
-  } else if (length(dim(data$attrs$Dates)) == 1) {
-    sdate_dim <- 'sdate'
-    dim(data$data) <- c(sdate = 1, dim(data$data))
-    data$dims <- dim(data$data)
-    dim(data$attrs$Dates) <- c(sdate = 1, dim(data$attrs$Dates))
-    data$coords[[sdate_dim]] <- data$attrs$Dates[1]
   }
   # startdates
   if (is.null(startdates)) {
-    startdates <- data$coords[[sdate_dim]]
-  } else {
-    if (!is.character(startdates)) {
-      warning(paste0("Parameter 'startdates' is not a character string, ",
-                     "it will not be used."))
+    if (is.character(data$coords[[sdate_dim]])) {
       startdates <- data$coords[[sdate_dim]]
     }
-    if (!is.null(sdate_dim)) {
-      if (dim(data$data)[sdate_dim] != length(startdates)) {
-        warning(paste0("Parameter 'startdates' doesn't have the same length ",
-                       "as dimension '", sdate_dim,"', it will not be used."))
-        startdates <- data$coords[[sdate_dim]]
-      }
-    }
   }
 
   SaveExp(data = data$data,
           destination = destination, 
-          Dates = data$attrs$Dates, 
           coords = data$coords,
+          Dates = data$attrs$Dates, 
+          time_bounds = data$attrs$time_bounds,
+          startdates = startdates,
           varname = data$attrs$Variable$varName,
           metadata = data$attrs$Variable$metadata,
           Datasets = data$attrs$Datasets, 
-          startdates = startdates,
-          dat_dim = dat_dim, sdate_dim = sdate_dim, 
-          ftime_dim = ftime_dim, var_dim = var_dim, 
-          memb_dim = memb_dim,
+          sdate_dim = sdate_dim, ftime_dim = ftime_dim, 
+          memb_dim = memb_dim, 
+          dat_dim = dat_dim, var_dim = var_dim, 
+          drop_dims = drop_dims, 
+          single_file = single_file,
           extra_string = extra_string, 
-          single_file = single_file)
+          global_attrs = global_attrs,
+          units_hours_since = units_hours_since)
 }
 #'Save a multidimensional array with metadata to data in NetCDF format
 #'@description This function allows to save a data array with metadata into a 
@@ -182,13 +172,26 @@ CST_SaveExp <- function(data, destination = "./", sdate_dim = 'sdate',
 #'@param data A multi-dimensional array with named dimensions.
 #'@param destination A character string indicating the path where to store the 
 #'  NetCDF files.
-#'@param Dates A named array of dates with the corresponding sdate and forecast 
-#'  time dimension.
 #'@param coords A named list with elements of the coordinates corresponding to 
 #'  the dimensions of the data parameter. The names and length of each element 
 #'  must correspond to the names of the dimensions. If any coordinate is not 
 #'  provided, it is set as an index vector with the values from 1 to the length 
 #'  of the corresponding dimension.
+#'@param Dates A named array of dates with the corresponding sdate and forecast 
+#'  time dimension. If there is no sdate_dim, you can set it to NULL. 
+#'  It must have ftime_dim dimension.
+#'@param time_bounds (Optional) A list of two arrays of dates containing 
+#'  the lower (first array) and the upper (second array) time bounds 
+#'  corresponding to Dates. Each array must have the same dimensions as Dates.
+#'  If 'Dates' parameter is NULL, 'time_bounds' are not used. It is NULL by 
+#'  default.
+#'@param startdates A vector of dates that will be used for the filenames 
+#'  when saving the data in multiple files (single_file = FALSE). It must be a 
+#'  vector of the same length as the start date dimension of data. It must be a 
+#'  vector of class \code{Dates}, \code{'POSIXct'} or character with lenghts 
+#'  between 1 and 10. If it is NULL, the coordinate corresponding the the start 
+#'  date dimension or the first Date of each time step will be used as the name 
+#'  of the files. It is NULL by default.
 #'@param varname A character string indicating the name of the variable to be 
 #'  saved.
 #'@param metadata A named list where each element is a variable containing the
@@ -196,12 +199,6 @@ CST_SaveExp <- function(data, destination = "./", sdate_dim = 'sdate',
 #'  lists for each variable.
 #'@param Datasets A vector of character string indicating the names of the 
 #'  datasets.
-#'@param startdates A vector of dates that will be used for the filenames 
-#'  when saving the data in multiple files. It must be a vector of the same 
-#'  length as the start date dimension of data. It must be a vector of class 
-#'  \code{Dates}, \code{'POSIXct'} or character with lenghts between 1 and 10. 
-#'  If it is NULL, the first Date of each time step will be used as the name of 
-#'  the files. It is NULL by default.
 #'@param sdate_dim A character string indicating the name of the start date 
 #'  dimension. By default, it is set to 'sdate'. It can be NULL if there is no
 #'  start date dimension.
@@ -214,64 +211,89 @@ CST_SaveExp <- function(data, destination = "./", sdate_dim = 'sdate',
 #'@param var_dim A character string indicating the name of variable dimension. 
 #'  By default, it is set to 'var'. It can be NULL if there is no variable  
 #'  dimension.
-#'@param memb_dim A character string indicating the name of the member dimension.
-#'  By default, it is set to 'member'. It can be NULL if there is no member 
-#'  dimension.  
+#'@param memb_dim A character string indicating the name of the member 
+#'  dimension. By default, it is set to 'member'. It can be NULL if there is no 
+#'  member dimension.  
+#'@param drop_dims (optional) A vector of character strings indicating the 
+#'  dimension names of length 1 that need to be dropped in order that they don't 
+#'  appear in the netCDF file. Only is allowed to drop dimensions that are not 
+#'  used in the computation. The dimensions used in the computation are the ones 
+#'  specified in: sdate_dim, ftime_dim, dat_dim, var_dim and memb_dim. It is 
+#'  NULL by default.
 #'@param single_file A logical value indicating if all object is saved in a 
-#'  unique file (TRUE) or in separated directories (FALSE). When it is FALSE, 
-#'  the array is separated for Datasets, variable and start date. It is FALSE  
-#'  by default.
-#'@param extra_string A character string to be include as part of the file name, 
-#'  for instance, to identify member or realization. It would be added to the 
-#'  file name between underscore characters.
+#'  single file (TRUE) or in multiple files (FALSE). When it is FALSE, 
+#'  the array is separated for datasets, variable and start date. When there are 
+#'  no specified time dimensions, the data will be saved in a single file by 
+#'  default. The output file name when 'single_file' is TRUE is a character 
+#'  string containing: '<var>_<first_sdate>_<last_sdate>.nc'; when it is FALSE, 
+#'  it is '<var>_<sdate>.nc'. It is FALSE by default. 
+#'@param extra_string (Optional) A character string to be included as part of 
+#'  the file name, for instance, to identify member or realization. When 
+#'  single_file is TRUE, the 'extra_string' will substitute all the default 
+#'  file name; when single_file is FALSE, the 'extra_string' will be added 
+#'  in the file name as: '<var>_<extra_string>_<sdate>.nc'. It is NULL by 
+#'  default.
+#'@param global_attrs (Optional) A list with elements containing the global 
+#'  attributes to be saved in the NetCDF.
+#'@param units_hours_since (Optional) A logical value only available for the 
+#'  case: Dates have forecast time and start date dimension, single_file is 
+#'  TRUE and 'time_bounds' is NULL. When it is TRUE, it saves the forecast time 
+#'  with units of 'hours since'; if it is FALSE, the time units will be a number 
+#'  of time steps with its corresponding frequency (e.g. n days, n months or n 
+#'  hours). It is FALSE by default. 
 #'
 #'@return Multiple or single NetCDF files containing the data array.\cr
-#'\item{\code{single_file = TRUE}}{
+#'\item{\code{single_file is TRUE}}{
 #'  All data is saved in a single file located in the specified destination  
-#'  path with the following name: 
-#'  <variable_name>_<extra_string>_<first_sdate>_<last_sdate>.nc. Multiple 
-#'  variables are saved separately in the same file. The forecast time units 
-#'  is extracted from the frequency of the time steps (hours, days, months). 
-#'  The first value of forecast time is 1. If no frequency is found, the units 
-#'  will be 'hours since' each start date and the time steps are assumed to be 
-#'  equally spaced.
+#'  path with the following name (by default): 
+#'  '<variable_name>_<first_sdate>_<last_sdate>.nc'. Multiple variables
+#'  are saved separately in the same file. The forecast time units 
+#'  are calculated from each start date (if sdate_dim is not NULL) or from 
+#'  the time step. If 'units_hours_since' is TRUE, the forecast time units 
+#'  will be 'hours since <each start date>'. If 'units_hours_since' is FALSE, 
+#'  the forecast time units are extracted from the frequency of the time steps 
+#'  (hours, days, months); if no frequency is found, the units will be ’hours 
+#'  since’. When the time units are 'hours since' the time ateps are assumed to 
+#'  be equally spaced.
 #'}
-#'\item{\code{single_file = FALSE}}{
+#'\item{\code{single_file is FALSE}}{
 #'  The data array is subset and stored into multiple files. Each file 
 #'  contains the data subset for each start date, variable and dataset. Files 
-#'  with different variables and Datasets are stored in separated directories 
-#'  within the following directory tree: destination/Dataset/variable/. 
-#'  The name of each file will be: 
-#'  <variable_name>_<extra_string>_<sdate>.nc.
+#'  with different variables and datasets are stored in separated directories 
+#'  within the following directory tree: 'destination/Dataset/variable/'. 
+#'  The name of each file will be by default: '<variable_name>_<sdate>.nc'. 
+#'  The forecast time units are calculated from each start date (if sdate_dim 
+#'  is not NULL) or from the time step. The forecast time units will be 'hours 
+#'  since <each start date>'.
 #'}
 #' 
 #'@examples
 #'\dontrun{
-#'data <- lonlat_temp$exp$data
-#'lon <- lonlat_temp$exp$coords$lon
-#'lat <- lonlat_temp$exp$coords$lat
+#'data <- lonlat_temp_st$exp$data
+#'lon <- lonlat_temp_st$exp$coords$lon
+#'lat <- lonlat_temp_st$exp$coords$lat
 #'coords <- list(lon = lon, lat = lat)
-#'Datasets <- lonlat_temp$exp$attrs$Datasets
+#'Datasets <- lonlat_temp_st$exp$attrs$Datasets
 #'varname <- 'tas'
-#'Dates <- lonlat_temp$exp$attrs$Dates
-#'destination = './'
-#'metadata <- lonlat_temp$exp$attrs$Variable$metadata
-#'SaveExp(data = data, destination = destination, coords = coords, 
-#'        Datasets = Datasets, varname = varname, Dates = Dates, 
-#'        metadata = metadata, single_file = TRUE, ftime_dim = 'ftime', 
-#'        var_dim = NULL)
+#'Dates <- lonlat_temp_st$exp$attrs$Dates
+#'metadata <- lonlat_temp_st$exp$attrs$Variable$metadata
+#'SaveExp(data = data, coords = coords, Datasets = Datasets, varname = varname, 
+#'        Dates = Dates, metadata = metadata, single_file = TRUE, 
+#'        ftime_dim = 'ftime', var_dim = 'var', dat_dim = 'dataset')
 #'}
 #' 
-#'@import ncdf4
+#'@import easyNCDF
 #'@importFrom s2dv Reorder
 #'@import multiApply
 #'@importFrom ClimProjDiags Subset
 #'@export
-SaveExp <- function(data, destination = "./", Dates = NULL, coords = NULL, 
+SaveExp <- function(data, destination = "./", coords = NULL, 
+                    Dates = NULL, time_bounds = NULL, startdates = NULL, 
                     varname = NULL, metadata = NULL, Datasets = NULL, 
-                    startdates = NULL, dat_dim = 'dataset', sdate_dim = 'sdate', 
-                    ftime_dim = 'time', var_dim = 'var', memb_dim = 'member',
-                    single_file = FALSE, extra_string = NULL) {
+                    sdate_dim = 'sdate', ftime_dim = 'time', 
+                    memb_dim = 'member', dat_dim = 'dataset', var_dim = 'var', 
+                    drop_dims = NULL, single_file = FALSE, extra_string = NULL,
+                    global_attrs = NULL, units_hours_since = FALSE) {
   ## Initial checks
   # data
   if (is.null(data)) {
@@ -281,45 +303,47 @@ SaveExp <- function(data, destination = "./", Dates = NULL, coords = NULL,
   if (is.null(dimnames)) {
     stop("Parameter 'data' must be an array with named dimensions.")
   }
+  if (!is.null(attributes(data)$dimensions)) {
+    attributes(data)$dimensions <- NULL
+  }
   # destination
   if (!is.character(destination) | length(destination) > 1) {
     stop("Parameter 'destination' must be a character string of one element ",
          "indicating the name of the file (including the folder if needed) ",
          "where the data will be saved.")
   }
-  # Dates
-  if (!is.null(Dates)) {
-    if (!inherits(Dates, "POSIXct") & !inherits(Dates, "Date")) {
-      stop("Parameter 'Dates' must be of 'POSIXct' or 'Dates' class.")
-    }
-    if (is.null(dim(Dates))) {
-      stop("Parameter 'Dates' must have dimension names.")
+  # drop_dims
+  if (!is.null(drop_dims)) {
+    if (!is.character(drop_dims) | any(!drop_dims %in% names(dim(data)))) {
+      warning("Parameter 'drop_dims' must be character string containing ", 
+              "the data dimension names to be dropped. It will not be used.")
+    } else if (!all(dim(data)[drop_dims] %in% 1)) {
+      warning("Parameter 'drop_dims' can only contain dimension names ", 
+              "that are of length 1. It will not be used.")
+    } else if (any(drop_dims %in% c(ftime_dim, sdate_dim, dat_dim, memb_dim, var_dim))) {
+      warning("Parameter 'drop_dims' contains dimensions used in the computation. ",
+              "It will not be used.")
+      drop_dims <- NULL
+    } else {
+      data <- Subset(x = data, along = drop_dims, 
+                     indices = lapply(1:length(drop_dims), function(x) 1), 
+                     drop = 'selected')
+      dimnames <- names(dim(data))
     }
   }
   # coords
   if (!is.null(coords)) {
-    if (!all(names(coords) %in% dimnames)) {
-      coords <- coords[-which(!names(coords) %in% dimnames)]
-    }
-    for (i_coord in dimnames) {
-      if (i_coord %in% names(coords)) {
-        if (length(coords[[i_coord]]) != dim(data)[i_coord]) {
-          warning(paste0("Coordinate '", i_coord, "' has different lenght as ",
-                         "its dimension and it will not be used."))
-          coords[[i_coord]] <- 1:dim(data)[i_coord]
-        }
-      } else {
-        warning(paste0("Coordinate '", i_coord, "' is not provided ",
-                       "and it will be set as index in element coords."))
-        coords[[i_coord]] <- 1:dim(data)[i_coord]
-      }
+    if (!inherits(coords, 'list')) {
+      stop("Parameter 'coords' must be a named list of coordinates.")
+    }
+    if (is.null(names(coords))) {
+      stop("Parameter 'coords' must have names corresponding to coordinates.")
     }
   } else {
     coords <- sapply(dimnames, function(x) 1:dim(data)[x])
   }
   # varname
   if (is.null(varname)) {
-    warning("Parameter 'varname' is NULL. It will be assigned to 'X'.")
     varname <- 'X'
   } else if (length(varname) > 1) {
     multiple_vars <- TRUE
@@ -330,11 +354,6 @@ SaveExp <- function(data, destination = "./", Dates = NULL, coords = NULL,
     stop("Parameter 'varname' must be a character string with the ",
          "variable names.")
   }
-  # metadata
-  if (is.null(metadata)) {
-    warning("Parameter 'metadata' is not provided so the metadata saved ",
-            "will be incomplete.")
-  }
   # single_file
   if (!inherits(single_file, 'logical')) {
     warning("Parameter 'single_file' must be a logical value. It will be ", 
@@ -347,27 +366,22 @@ SaveExp <- function(data, destination = "./", Dates = NULL, coords = NULL,
       stop("Parameter 'extra_string' must be a character string.")
     }
   }
+  # global_attrs
+  if (!is.null(global_attrs)) {
+    if (!inherits(global_attrs, 'list')) {
+      stop("Parameter 'global_attrs' must be a list.")
+    }
+  }
 
   ## Dimensions checks
   # Spatial coordinates
   if (!any(dimnames %in% .KnownLonNames()) | 
       !any(dimnames %in% .KnownLatNames())) {
-    warning("Spatial coordinates not found.")
     lon_dim <- NULL
     lat_dim <- NULL
   } else {
     lon_dim <- dimnames[which(dimnames %in% .KnownLonNames())]
     lat_dim <- dimnames[which(dimnames %in% .KnownLatNames())]
-    if (length(lon_dim) > 1) {
-      warning("Found more than one longitudinal dimension. Only the first one ", 
-              "will be used.")
-      lon_dim <- lon_dim[1]
-    }
-    if (length(lat_dim) > 1) {
-      warning("Found more than one latitudinal dimension. Only the first one ", 
-              "will be used.")
-      lat_dim <- lat_dim[1]
-    }
   }
   # ftime_dim
   if (!is.null(ftime_dim)) {
@@ -375,12 +389,8 @@ SaveExp <- function(data, destination = "./", Dates = NULL, coords = NULL,
       stop("Parameter 'ftime_dim' must be a character string.")
     }
     if (!all(ftime_dim %in% dimnames)) {
-      stop("Parameter 'ftime_dim' is not found in 'data' dimension.")
-    }
-    if (length(ftime_dim) > 1) {
-      warning("Parameter 'ftime_dim' has length greater than 1 and ",
-              "only the first element will be used.")
-      ftime_dim <- ftime_dim[1]
+      stop("Parameter 'ftime_dim' is not found in 'data' dimension. Set it ", 
+           "as NULL if there is no forecast time dimension.")
     }
   }
   # sdate_dim
@@ -388,11 +398,6 @@ SaveExp <- function(data, destination = "./", Dates = NULL, coords = NULL,
     if (!is.character(sdate_dim)) {
       stop("Parameter 'sdate_dim' must be a character string.")
     }
-    if (length(sdate_dim) > 1) {
-      warning("Parameter 'sdate_dim' has length greater than 1 and ",
-              "only the first element will be used.")
-      sdate_dim <- sdate_dim[1]
-    }
     if (!all(sdate_dim %in% dimnames)) {
       stop("Parameter 'sdate_dim' is not found in 'data' dimension.")
     }
@@ -416,11 +421,6 @@ SaveExp <- function(data, destination = "./", Dates = NULL, coords = NULL,
       stop("Parameter 'dat_dim' is not found in 'data' dimension. Set it ", 
            "as NULL if there is no Datasets dimension.")
     }
-    if (length(dat_dim) > 1) {
-      warning("Parameter 'dat_dim' has length greater than 1 and ",
-              "only the first element will be used.")
-      dat_dim <- dat_dim[1]
-    }
     n_datasets <- dim(data)[dat_dim]
   } else {
     n_datasets <- 1
@@ -434,11 +434,6 @@ SaveExp <- function(data, destination = "./", Dates = NULL, coords = NULL,
       stop("Parameter 'var_dim' is not found in 'data' dimension. Set it ", 
            "as NULL if there is no variable dimension.")
     }
-    if (length(var_dim) > 1) {
-      warning("Parameter 'var_dim' has length greater than 1 and ",
-              "only the first element will be used.")
-      var_dim <- var_dim[1]
-    }
     n_vars <- dim(data)[var_dim]
   } else {
     n_vars <- 1
@@ -453,30 +448,121 @@ SaveExp <- function(data, destination = "./", Dates = NULL, coords = NULL,
       single_file <- TRUE
     }
   }
-  # Dates dimension check
+  # Dates (1): initial checks
   if (!is.null(Dates)) {
-    if (all(names(dim(Dates)) == c(ftime_dim, sdate_dim)) | 
-        all(names(dim(Dates)) == c(sdate_dim, ftime_dim))) {
-      if (is.null(startdates)) {
-        startdates <- Subset(Dates, along = ftime_dim, 1, drop = 'selected')
-      } else if ((!inherits(startdates, "POSIXct") & !inherits(startdates, "Date")) && 
-                 (!is.character(startdates) | (any(nchar(startdates) > 10) | any(nchar(startdates) < 1)))) {
-        warning("Parameter 'startdates' should be a character string containing ", 
-                "the start dates in the format 'yyyy-mm-dd', 'yyyymmdd', 'yyyymm', ", 
-                "'POSIXct' or 'Dates' class. Files will be named with Dates instead.")
-        startdates <- Subset(Dates, along = ftime_dim, 1, drop = 'selected')
-        if (!is.null(format(startdates, "%Y%m%d"))) {
-          startdates <- format(startdates, "%Y%m%d")
-        }
+    if (!any(inherits(Dates, "POSIXct"), inherits(Dates, "Date"))) {
+      stop("Parameter 'Dates' must be of 'POSIXct' or 'Dates' class.")
+    }
+    if (is.null(dim(Dates))) {
+      stop("Parameter 'Dates' must have dimension names.")
+    }
+    if (all(is.null(ftime_dim), is.null(sdate_dim))) {
+      warning("Parameters 'ftime_dim' and 'sdate_dim' can't both be NULL ",
+              "if 'Dates' are used. 'Dates' will not be used.")
+      Dates <- NULL
+    }
+    # sdate_dim in Dates
+    if (!is.null(sdate_dim)) {
+      if (!sdate_dim %in% names(dim(Dates))) {
+        warning("Parameter 'sdate_dim' is not found in 'Dates' dimension. ",
+                "Dates will not be used.")
+        Dates <- NULL
+      }
+    }
+    # ftime_dim in Dates
+    if (!is.null(ftime_dim)) {
+      if (!ftime_dim %in% names(dim(Dates))) {
+        warning("Parameter 'ftime_dim' is not found in 'Dates' dimension. ",
+                "Dates will not be used.")
+        Dates <- NULL
       }
-    } else if (all(dim(Dates)[!names(dim(Dates)) %in% c(ftime_dim, sdate_dim)] == 1)) {
-      dim(Dates) <- dim(Dates)[names(dim(Dates)) %in% c(ftime_dim, sdate_dim)]
+    }
+  }
+  # time_bounds 
+  if (!is.null(time_bounds)) {
+    if (!inherits(time_bounds, 'list')) {
+      stop("Parameter 'time_bounds' must be a list with two dates arrays.")
+    }
+    time_bounds_dims <- lapply(time_bounds, function(x) dim(x))
+    if (!identical(time_bounds_dims[[1]], time_bounds_dims[[2]])) {
+      stop("Parameter 'time_bounds' must have 2 arrays with same dimensions.")
+    }
+    if (is.null(Dates)) {
+      time_bounds <- NULL
     } else {
-      stop("Parameter 'Dates' must have start date dimension and ", 
-           "forecast time dimension.")
+      name_tb <- sort(names(time_bounds_dims[[1]]))
+      name_dt <- sort(names(dim(Dates)))
+      if (!identical(dim(Dates)[name_dt], time_bounds_dims[[1]][name_tb])) {
+        stop(paste0("Parameter 'Dates' and 'time_bounds' must have same length ",
+                    "of all dimensions."))
+      }
+    }
+  }
+  # Dates (2): Check dimensions
+  if (!is.null(Dates)) {
+    if (any(dim(Dates)[!names(dim(Dates)) %in% c(ftime_dim, sdate_dim)] != 1)) {
+      stop("Parameter 'Dates' can have only 'sdate_dim' and 'ftime_dim' ",
+           "dimensions of length greater than 1.")
+    }
+    # drop dimensions of length 1 different from sdate_dim and ftime_dim
+    dim(Dates) <- dim(Dates)[names(dim(Dates)) %in% c(ftime_dim, sdate_dim)]
+
+    # add ftime if needed
+    if (is.null(ftime_dim)) {
+      warning("A 'time' dimension of length 1 will be added to 'Dates'.") 
+      dim(Dates) <- c(time = 1, dim(Dates))
+      dim(data) <- c(time = 1, dim(data))
+      dimnames <- names(dim(data))
+      ftime_dim <- 'time'
+      if (!is.null(time_bounds)) {
+        time_bounds <- lapply(time_bounds, function(x) {
+          dim(x) <- c(time = 1, dim(x))
+          return(x)
+        })
+      }
+      units_hours_since <- TRUE
+    }
+    # add sdate if needed
+    if (is.null(sdate_dim)) {
+      if (!single_file) {
+        dim(Dates) <- c(dim(Dates), sdate = 1)
+        dim(data) <- c(dim(data), sdate = 1)
+        dimnames <- names(dim(data))
+        sdate_dim <- 'sdate'
+        if (!is.null(time_bounds)) {
+          time_bounds <- lapply(time_bounds, function(x) {
+            dim(x) <- c(dim(x), sdate = 1)
+            return(x)
+          })
+        }
+        if (!is.null(startdates)) {
+          if (length(startdates) != 1) {
+            warning("Parameter 'startdates' must be of length 1 if 'sdate_dim' is NULL.",
+                    "They won't be used.")
+            startdates <- NULL
+          }
+        }
+      }
+      units_hours_since <- TRUE
     }
   }
   # startdates
+  if (!is.null(Dates)) {
+    # check startdates
+    if (is.null(startdates)) {
+      startdates <- Subset(Dates, along = ftime_dim, 1, drop = 'selected')
+    } else if (any(nchar(startdates) > 10, nchar(startdates) < 1)) {
+      warning("Parameter 'startdates' should be a character string containing ", 
+              "the start dates in the format 'yyyy-mm-dd', 'yyyymmdd', 'yyyymm', ", 
+              "'POSIXct' or 'Dates' class. Files will be named with Dates instead.")
+      startdates <- Subset(Dates, along = ftime_dim, 1, drop = 'selected')
+    }
+  } else if (!single_file) {
+    warning("Dates must be provided if 'data' must be saved in separated files. ",
+            "All data will be saved in a single file.")
+    single_file <- TRUE
+  }
+  # startdates
   if (is.null(startdates)) {
     if (is.null(sdate_dim)) {
       startdates <- 'XXX'
@@ -484,20 +570,21 @@ SaveExp <- function(data, destination = "./", Dates = NULL, coords = NULL,
       startdates <- rep('XXX', dim(data)[sdate_dim])
     }
   } else {
-    if (is.null(sdate_dim)) {
-      if (length(startdates) != 1) {
-        warning("Parameter 'startdates' has length more than 1. Only first ", 
-                "value will be used.")
-        startdates <- startdates[[1]]
+    if (any(inherits(startdates, "POSIXct"), inherits(startdates, "Date"))) {
+      startdates <- format(startdates, "%Y%m%d")
+    }
+    if (!is.null(sdate_dim)) {
+      if (dim(data)[sdate_dim] != length(startdates)) {
+        warning(paste0("Parameter 'startdates' doesn't have the same length ",
+                       "as dimension '", sdate_dim,"', it will not be used."))
+        startdates <- Subset(Dates, along = ftime_dim, 1, drop = 'selected')
+        startdates <- format(startdates, "%Y%m%d")
       }
     }
   }
+
   # Datasets
   if (is.null(Datasets)) {
-    if (!single_file) {
-      warning("Parameter 'Datasets' is NULL. Files will be saved with a ", 
-              "directory name of 'XXX'.")
-    }
     Datasets <- rep('XXX', n_datasets )
   }
   if (inherits(Datasets, 'list')) {
@@ -513,128 +600,74 @@ SaveExp <- function(data, destination = "./", Dates = NULL, coords = NULL,
     Datasets <- Datasets[1:n_datasets]
   }
 
+  ## NetCDF dimensions definition
+  excluded_dims <- var_dim
+  if (!is.null(Dates)) {
+    excluded_dims <- c(excluded_dims, sdate_dim, ftime_dim)
+  }
+  if (!single_file) {
+    excluded_dims <- c(excluded_dims, dat_dim)
+  }
+
   ## Unknown dimensions check
-  alldims <- c(dat_dim, var_dim, sdate_dim, lon_dim, lat_dim, memb_dim, ftime_dim)
+  alldims <- c(dat_dim, var_dim, sdate_dim, lon_dim, lat_dim, ftime_dim, memb_dim)
   if (!all(dimnames %in% alldims)) {
     unknown_dims <- dimnames[which(!dimnames %in% alldims)]
-    # warning("Detected unknown dimension: ", paste(unknown_dims, collapse = ', '))
     memb_dim <- c(memb_dim, unknown_dims)
-    alldims <- c(dat_dim, var_dim, sdate_dim, lon_dim, lat_dim, memb_dim, ftime_dim)
-  }
-  # Reorder
-  if (any(dimnames != alldims)) {
-    data <- Reorder(data, alldims)
-    dimnames <- names(dim(data))
-    if (!is.null(attr(data, 'dimensions'))) {
-      attr(data, 'dimensions') <- dimnames
-    }
   }
 
-  ## NetCDF dimensions definition
-  defined_dims <- NULL
-  extra_info_dim <- NULL
-  if (is.null(Dates)) {
-    filedims <- dimnames[which(!dimnames %in% c(dat_dim, var_dim))]
-  } else {
-    filedims <- dimnames[which(!dimnames %in% c(dat_dim, var_dim, sdate_dim, ftime_dim))]
-  }
+  filedims <- c(dat_dim, var_dim, sdate_dim, lon_dim, lat_dim, ftime_dim, memb_dim)
+  filedims <- filedims[which(!filedims %in% excluded_dims)]
+
+  # Delete unneded coords
+  coords[c(names(coords)[!names(coords) %in% filedims])] <- NULL
+  out_coords <- NULL
   for (i_coord in filedims) {
-    dim_info <- list()
     # vals
     if (i_coord %in% names(coords)) {
-      if (is.numeric(coords[[i_coord]])) {
-        dim_info[['vals']] <- as.vector(coords[[i_coord]])
+      if (length(coords[[i_coord]]) != dim(data)[i_coord]) {
+        warning(paste0("Coordinate '", i_coord, "' has different lenght as ",
+                       "its dimension and it will not be used."))
+        out_coords[[i_coord]] <- 1:dim(data)[i_coord]
+      } else if (is.numeric(coords[[i_coord]])) {
+        out_coords[[i_coord]] <- as.vector(coords[[i_coord]])
       } else {
-        dim_info[['vals']] <- 1:dim(data)[i_coord]
+        out_coords[[i_coord]] <- 1:dim(data)[i_coord]
       }
     } else {
-      dim_info[['vals']] <- 1:dim(data)[i_coord]
-    }
-    # name
-    dim_info[['name']] <- i_coord
-    # len
-    dim_info[['len']] <- as.numeric(dim(data)[i_coord])
-    # unlim
-    dim_info[['unlim']] <- FALSE
-    # create_dimvar
-    dim_info[['create_dimvar']] <- TRUE
+      out_coords[[i_coord]] <- 1:dim(data)[i_coord]
+    }
+    dim(out_coords[[i_coord]]) <- dim(data)[i_coord]
+    
     ## metadata
     if (i_coord %in% names(metadata)) {
       if ('variables' %in% names(attributes(metadata[[i_coord]]))) {
         # from Start: 'lon' or 'lat'
-        attrs <- attributes(metadata[[i_coord]])[['variables']][[i_coord]]
-        i_coord_info <- attrs[!sapply(attrs, inherits, 'list')]
+        attrs <- attributes(metadata[[i_coord]])[['variables']]
+        attrs[[i_coord]]$dim <- NULL
+        attr(out_coords[[i_coord]], 'variables') <- attrs
       } else if (inherits(metadata[[i_coord]], 'list')) {
         # from Start and Load: main var
-        i_coord_info <- metadata[[i_coord]]
+        attr(out_coords[[i_coord]], 'variables') <- list(metadata[[i_coord]])
+        names(attributes(out_coords[[i_coord]])$variables) <- i_coord
       } else if (!is.null(attributes(metadata[[i_coord]]))) {
         # from Load
-        i_coord_info <- attributes(metadata[[i_coord]])
-      } else {
-        stop("Metadata is not correct.")
+        attrs <- attributes(metadata[[i_coord]])
+        # We remove because some attributes can't be saved
+        attrs <- NULL 
+        attr(out_coords[[i_coord]], 'variables') <- list(attrs)
+        names(attributes(out_coords[[i_coord]])$variables) <- i_coord
       }
-      # len
-      if ('size' %in% names(i_coord_info)) {
-        if (i_coord_info[['size']] != dim(data)[i_coord]) {
-          dim_info[['original_len']] <- i_coord_info[['size']]
-          i_coord_info[['size']] <- NULL
-        }
-      }
-      # units
-      if (!('units' %in% names(i_coord_info))) {
-        dim_info[['units']] <- ''
-      } else {
-        dim_info[['units']] <- i_coord_info[['units']]
-        i_coord_info[['units']] <- NULL
-      }
-      # calendar
-      if (!('calendar' %in% names(i_coord_info))) {
-        dim_info[['calendar']] <- NA
-      } else {
-        dim_info[['calendar']] <- i_coord_info[['calendar']]
-        i_coord_info[['calendar']] <- NULL
-      }
-      # longname
-      if ('long_name' %in% names(i_coord_info)) {
-        dim_info[['longname']] <- i_coord_info[['long_name']]
-        i_coord_info[['long_name']] <- NULL
-      } else if ('longname' %in% names(i_coord_info)) {
-        dim_info[['longname']] <- i_coord_info[['longname']]
-        i_coord_info[['longname']] <- NULL
-      } else {
-        if (i_coord %in% .KnownLonNames()) {
-          dim_info[['longname']] <- 'longitude'
-        } else if (i_coord %in% .KnownLatNames()) {
-          dim_info[['longname']] <- 'latitude'
-        }
-      }
-      # extra information
-      if (!is.null(names(i_coord_info))) {
-        extra_info_dim[[i_coord]] <- i_coord_info
-      }
-    } else {
-      # units
-      dim_info[['units']] <- "adim"
-      # longname
-      dim_info[['longname']] <- i_coord
-      # calendar
-      dim_info[['calendar']] <- NA
-    }
-    new_dim <- list(ncdim_def(name = dim_info[['name']], units = dim_info[['units']], 
-                              vals = dim_info[['vals']], unlim = dim_info[['unlim']], 
-                              create_dimvar = dim_info[['create_dimvar']], 
-                              calendar = dim_info[['calendar']], 
-                              longname = dim_info[['longname']]))
-    names(new_dim) <- i_coord
-    defined_dims <- c(defined_dims, new_dim)
+    }
   }
 
-  defined_vars <- list()
   if (!single_file) {
     for (i in 1:n_datasets) {
       path <- file.path(destination, Datasets[i], varname)
       for (j in 1:n_vars) {
-        dir.create(path[j], recursive = TRUE)
+        if (!dir.exists(path[j])) {
+          dir.create(path[j], recursive = TRUE)
+        }
         startdates <- gsub("-", "", startdates)
         dim(startdates) <- c(length(startdates))
         names(dim(startdates)) <- sdate_dim
@@ -647,293 +680,240 @@ SaveExp <- function(data, destination = "./", Dates = NULL, coords = NULL,
         } else {
           data_subset <- Subset(data, c(dat_dim, var_dim), list(i, j), drop = 'selected')
         }
+        target <- names(dim(data_subset))[which(!names(dim(data_subset)) %in% c(sdate_dim, ftime_dim))]
+        target_dims_data <- c(target, ftime_dim)
         if (is.null(Dates)) {
           input_data <- list(data_subset, startdates)
-          target_dims <- list(c(lon_dim, lat_dim, memb_dim, ftime_dim), NULL)
+          target_dims <- list(target_dims_data, NULL)
+        } else if (!is.null(time_bounds)) {
+          input_data <- list(data_subset, startdates, Dates, 
+                             time_bounds[[1]], time_bounds[[2]])
+          target_dims = list(target_dims_data, NULL, 
+                             ftime_dim, ftime_dim, ftime_dim)
         } else {
           input_data <- list(data_subset, startdates, Dates)
-          target_dims = list(c(lon_dim, lat_dim, memb_dim, ftime_dim), NULL, ftime_dim)
+          target_dims = list(target_dims_data, NULL, ftime_dim)
         }
         Apply(data = input_data,
               target_dims = target_dims,
-              fun = .saveExp, 
+              fun = .saveexp, 
               destination = path[j],
-              defined_dims = defined_dims, 
+              coords = out_coords, 
               ftime_dim = ftime_dim, 
               varname = varname[j], 
               metadata_var = metadata[[varname[j]]], 
-              extra_info_dim = extra_info_dim, 
-              extra_string = extra_string)
+              extra_string = extra_string,
+              global_attrs = global_attrs)
       }
     }
   } else {
-    # Datasets definition
-    # From here
-    if (!is.null(dat_dim)) {
-      new_dim <- list(ncdim_def(name = dat_dim, units = "adim",
-                                vals = 1 : dim(data)[dat_dim],
-                                longname = 'Datasets', create_dimvar = TRUE))
-      names(new_dim) <- dat_dim
-      defined_dims <- c(new_dim, defined_dims)
-      extra_info_dim[[dat_dim]] <- list(Datasets = paste(Datasets, collapse = ', '))
-    }
-    first_sdate <- last_sdate <- NULL
+    # time_bnds
+    if (!is.null(time_bounds)) {
+      time_bnds <- c(time_bounds[[1]], time_bounds[[2]])
+    }
+    # Dates
+    remove_metadata_dim <- TRUE
     if (!is.null(Dates)) {
-      # sdate definition
-      sdates <- Subset(Dates, along = ftime_dim, 1, drop = 'selected')
-      differ <- as.numeric((sdates - sdates[1])/3600)
-      new_dim <- list(ncdim_def(name = sdate_dim, units = paste('hours since', sdates[1]),
-                                vals = differ,
-                                longname = sdate_dim, create_dimvar = TRUE))
-      names(new_dim) <- sdate_dim
-      defined_dims <- c(defined_dims, new_dim)
-      first_sdate <- sdates[1]
-      last_sdate <- sdates[length(sdates)]
-      # ftime definition
-      Dates <- Reorder(Dates, c(ftime_dim, sdate_dim))
-      differ_ftime <- apply(Dates, 2, function(x){as.numeric((x - x[1])/3600)})
-      dim(differ_ftime) <- dim(Dates)
-      differ_ftime_subset <- Subset(differ_ftime, along = sdate_dim, 1, drop = 'selected')
-      if (all(apply(differ_ftime, 1, function(x){length(unique(x)) == 1}))) {
-        if (all(diff(differ_ftime_subset/24) == 1)) {
+      if (is.null(sdate_dim)) {
+        sdates <- Dates[1]
+        # ftime definition
+        leadtimes <- as.numeric(difftime(Dates, sdates, units = "hours"))
+      } else {
+        # sdate definition
+        sdates <- Subset(Dates, along = ftime_dim, 1, drop = 'selected')
+        differ <- as.numeric(difftime(sdates, sdates[1], units = "hours"))
+        dim(differ) <- dim(data)[sdate_dim]
+        differ <- list(differ)
+        names(differ) <- sdate_dim
+        out_coords <- c(differ, out_coords)
+        attrs <- list(units = paste('hours since', sdates[1]),
+                      calendar = 'proleptic_gregorian', longname = sdate_dim)
+        attr(out_coords[[sdate_dim]], 'variables')[[sdate_dim]] <- attrs
+        # ftime definition
+        Dates <- Reorder(Dates, c(ftime_dim, sdate_dim)) 
+        differ_ftime <- array(dim = dim(Dates))
+        for (i in 1:length(sdates)) {
+          differ_ftime[, i] <- as.numeric(difftime(Dates[, i], Dates[1, i], 
+                                          units = "hours"))
+        }
+        dim(differ_ftime) <- dim(Dates)
+        leadtimes <- Subset(differ_ftime, along = sdate_dim, 1, drop = 'selected')
+        if (!all(apply(differ_ftime, 1, function(x){length(unique(x)) == 1}))) {
+          warning("Time steps are not equal for all start dates. Only ", 
+                  "forecast time values for the first start date will be saved ", 
+                  "correctly.")
+        }
+      }
+      if (all(!units_hours_since, is.null(time_bounds))) {
+        if (all(diff(leadtimes/24) == 1)) {
           # daily values
-          dim_time <- list(ncdim_def(name = ftime_dim, units = 'days',
-                                     vals = round(differ_ftime_subset/24) + 1, 
-                                     calendar = 'proleptic_gregorian',
-                                     longname = ftime_dim, unlim = TRUE))
-          names(dim_time) <- ftime_dim
-          defined_dims <- c(defined_dims, dim_time)     
-        } else if (all(diff(differ_ftime_subset/24) %in% c(28, 29, 30, 31))) {
+          units <- 'days'
+          leadtimes_vals <- round(leadtimes/24) + 1
+        } else if (all(diff(leadtimes/24) %in% c(28, 29, 30, 31))) {
           # monthly values
-          dim_time <- list(ncdim_def(name = ftime_dim, units = 'months',
-                                     vals = round(differ_ftime_subset/730) + 1, 
-                                     calendar = 'proleptic_gregorian',
-                                     longname = ftime_dim, unlim = TRUE))
-          names(dim_time) <- ftime_dim
-          defined_dims <- c(defined_dims, dim_time)   
+          units <- 'months'
+          leadtimes_vals <- round(leadtimes/(30.437*24)) + 1   
         } else {
           # other frequency
-          dim_time <- list(ncdim_def(name = ftime_dim, units = 'hours',
-                                     vals = differ_ftime_subset + 1, 
-                                     calendar = 'proleptic_gregorian',
-                                     longname = ftime_dim, unlim = TRUE))
-          names(dim_time) <- ftime_dim
-          defined_dims <- c(defined_dims, dim_time)  
+          units <- 'hours'
+          leadtimes_vals <- leadtimes + 1
         }
       } else {
-        warning("Time steps are not equal for all start dates. Only ", 
-                "forecast time values for the first start date will be saved ", 
-                "correctly.")
-        dim_time <- list(ncdim_def(name = ftime_dim, 
-                                   units = paste('hours since', 
-                                           paste(sdates, collapse = ', ')),
-                                   vals = differ_ftime_subset, 
-                                   calendar = 'proleptic_gregorian',
-                                   longname = ftime_dim, unlim = TRUE))
-        names(dim_time) <- ftime_dim
-        defined_dims <- c(defined_dims, dim_time)
+        units <- paste('hours since', paste(sdates, collapse = ', '))
+        leadtimes_vals <- leadtimes
       }
-    }
 
+      # Add time_bnds
+      if (!is.null(time_bounds)) {
+        if (is.null(sdate_dim)) {
+          sdates <- Dates[1]
+          time_bnds <- c(time_bounds[[1]], time_bounds[[2]])
+          leadtimes_bnds <- as.numeric(difftime(time_bnds, sdates, units = "hours"))
+          dim(leadtimes_bnds) <- c(dim(Dates), bnds = 2)
+        } else {
+          # assuming they have sdate and ftime
+          time_bnds <- lapply(time_bounds, function(x) {
+            x <- Reorder(x, c(ftime_dim, sdate_dim))
+            return(x)
+          })
+          time_bnds <- c(time_bounds[[1]], time_bounds[[2]])
+          dim(time_bnds) <- c(dim(Dates), bnds = 2)
+          differ_bnds <- array(dim = c(dim(time_bnds)))
+          for (i in 1:length(sdates)) {
+            differ_bnds[, i, ] <- as.numeric(difftime(time_bnds[, i, ], Dates[1, i], 
+                                            units = "hours"))
+          }
+          # NOTE (TODO): Add a warning when they are not equally spaced?
+          leadtimes_bnds <- Subset(differ_bnds, along = sdate_dim, 1, drop = 'selected')
+        }
+        # Add time_bnds
+        leadtimes_bnds <- Reorder(leadtimes_bnds, c('bnds', ftime_dim))
+        leadtimes_bnds <- list(leadtimes_bnds)
+        names(leadtimes_bnds) <- 'time_bnds'
+        out_coords <- c(leadtimes_bnds, out_coords)
+        attrs <- list(units = paste('hours since', paste(sdates, collapse = ', ')),
+                      calendar = 'proleptic_gregorian',
+                      long_name = 'time bounds', unlim = FALSE)
+        attr(out_coords[['time_bnds']], 'variables')$time_bnds <- attrs
+      }
+      # Add ftime var
+      dim(leadtimes_vals) <- dim(data)[ftime_dim]
+      leadtimes_vals <- list(leadtimes_vals)
+      names(leadtimes_vals) <- ftime_dim
+      out_coords <- c(leadtimes_vals, out_coords)
+      attrs <- list(units = units, calendar = 'proleptic_gregorian',
+                    longname = ftime_dim, 
+                    dim = list(list(name = ftime_dim, unlim = TRUE)))
+      if (!is.null(time_bounds)) {
+        attrs$bounds = 'time_bnds'
+      }
+      attr(out_coords[[ftime_dim]], 'variables')[[ftime_dim]] <- attrs
+      for (j in 1:n_vars) {
+        remove_metadata_dim <- FALSE
+        metadata[[varname[j]]]$dim <- list(list(name = ftime_dim, unlim = TRUE))
+      }
+      # Reorder ftime_dim to last
+      if (length(dim(data)) != which(names(dim(data)) == ftime_dim)) {
+        order <- c(names(dim(data))[which(!names(dim(data)) %in% c(ftime_dim))], ftime_dim)
+        data <- Reorder(data, order)
+      }
+    }
     # var definition
-    defined_vars <- list()
     extra_info_var <- NULL
     for (j in 1:n_vars) {
-      var_info <- list()
-      i_var_info <- metadata[[varname[j]]][!sapply(metadata[[varname[j]]], inherits, 'list')]
-      ## Define metadata
-      # name
-      var_info[['name']] <- varname[j]
-      # units
-      if ('units' %in% names(i_var_info)) {
-        var_info[['units']] <- i_var_info[['units']]
-        i_var_info[['units']] <- NULL
+      varname_j <- varname[j]
+      metadata_j <- metadata[[varname_j]]
+      if (is.null(var_dim)) {
+        out_coords[[varname_j]] <- data
       } else {
-        var_info[['units']] <- ''
+        out_coords[[varname_j]] <- Subset(data, var_dim, j, drop = 'selected')
       }
-      # dim
-      var_info[['dim']] <- defined_dims
-      # missval
-      if ('missval' %in% names(i_var_info)) {
-        var_info[['missval']] <- i_var_info[['missval']]
-        i_var_info[['missval']] <- NULL
-      } else {
-        var_info[['missval']] <- NULL
+      if (!is.null(metadata_j)) {
+        if (remove_metadata_dim) metadata_j$dim <- NULL
+        attr(out_coords[[varname_j]], 'variables') <- list(metadata_j)
+        names(attributes(out_coords[[varname_j]])$variables) <- varname_j
       }
-      # longname
-      if (any(c('longname', 'long_name') %in% names(i_var_info))) {
-        longname <- names(i_var_info)[which(names(i_var_info) %in% c('longname', 'long_name'))]
-        var_info[['longname']] <- i_var_info[[longname]]
-        i_var_info[[longname]] <- NULL
-      } else {
-        var_info[['longname']] <- varname[j]
+      # Add global attributes
+      if (!is.null(global_attrs)) {
+        attributes(out_coords[[varname_j]])$global_attrs <- global_attrs
       }
-      # prec
-      if ('prec' %in% names(i_var_info)) {
-        var_info[['prec']] <- i_var_info[['prec']]
-        i_var_info[['prec']] <- NULL
-      } else {
-        prec <- typeof(data)
-        if (prec == 'character') {
-          var_info[['prec']] <- 'char'
-        }
-        if (any(prec %in% c('short', 'float', 'double', 'integer', 'char', 'byte'))) {
-          var_info[['prec']] <- prec
-        } else {
-          var_info[['prec']] <- 'double'
-        }
-      }
-      # extra information
-      if (!is.null(names(i_var_info))) {
-        extra_info_var[[varname[j]]] <- i_var_info
-      }
-      new_var <- list(ncvar_def(name = var_info[['name']],
-                                units = var_info[['units']],
-                                dim = var_info[['dim']], 
-                                missval = var_info[['missval']],
-                                longname = var_info[['longname']], 
-                                prec = var_info[['prec']]))
-
-      names(new_var) <- varname[j]
-      defined_vars <- c(defined_vars, new_var)
     }
     if (is.null(extra_string)) {
+      first_sdate <- startdates[1]
+      last_sdate <- startdates[length(startdates)]
       gsub("-", "", first_sdate)
       file_name <- paste0(paste(c(varname, 
                                   gsub("-", "", first_sdate), 
                                   gsub("-", "", last_sdate)), 
                                   collapse = '_'), ".nc")
     } else {
-      file_name <- paste0(paste(c(varname, extra_string, 
-                                  gsub("-", "", first_sdate), 
-                                  gsub("-", "", last_sdate)), 
-                                  collapse = '_'), ".nc")
-    }
-    full_filename <- file.path(destination, file_name)
-    file_nc <- nc_create(full_filename, defined_vars)
-    if (is.null(var_dim)) {
-      ncvar_put(file_nc, varname, vals = data)
-    } else {
-      for (j in 1:n_vars) {
-        ncvar_put(file_nc, defined_vars[[j]]$name, 
-                  vals = Subset(data, var_dim, j, drop = 'selected'))
-      }
-    }
-    # Additional dimension attributes
-    for (dim in names(defined_dims)) {
-      if (dim %in% names(extra_info_dim)) {
-        for (info_dim in names(extra_info_dim[[dim]])) {
-          ncatt_put(file_nc, dim, info_dim, as.character(extra_info_dim[[dim]][[info_dim]]))
-        }
-      }
-    }
-    # Additional dimension attributes
-    for (var in names(defined_vars)) {
-      if (var %in% names(extra_info_var)) {
-        for (info_var in names(extra_info_var[[var]])) {
-          ncatt_put(file_nc, var, info_var, as.character(extra_info_var[[var]][[info_var]]))
-        }
+      nc <- substr(extra_string, nchar(extra_string)-2, nchar(extra_string))
+      if (nc == ".nc") {
+        file_name <- extra_string
+      } else {
+        file_name <- paste0(extra_string, ".nc")
       }
     }
-    nc_close(file_nc)
+    full_filename <- file.path(destination, file_name)
+    ArrayToNc(out_coords, full_filename)
   }
 }
 
-.saveExp <- function(data, startdates = NULL, dates = NULL, destination = "./", 
-                     defined_dims, ftime_dim = 'time',  varname = 'var', 
-                     metadata_var = NULL, extra_info_dim = NULL, 
-                     extra_string = NULL) {
-  # ftime_dim
+.saveexp <- function(data, coords, destination = "./",
+                     startdates = NULL, dates = NULL, 
+                     time_bnds1 = NULL, time_bnds2 = NULL, 
+                     ftime_dim = 'time', varname = 'var', 
+                     metadata_var = NULL, extra_string = NULL,
+                     global_attrs = NULL) {
+  remove_metadata_dim <- TRUE
   if (!is.null(dates)) {
-    differ <- as.numeric((dates - dates[1])/3600)
-    dim_time <- list(ncdim_def(name = ftime_dim, units = paste('hours since', dates[1]),
-                               vals = differ, calendar = 'proleptic_gregorian',
-                               longname = ftime_dim, unlim = TRUE))
-    names(dim_time) <- ftime_dim
-    defined_dims <- c(defined_dims, dim_time)
+    if (!any(is.null(time_bnds1), is.null(time_bnds2))) {
+      time_bnds <- c(time_bnds1, time_bnds2)
+      time_bnds <- as.numeric(difftime(time_bnds, dates[1], units = "hours"))
+      dim(time_bnds) <- c(dim(data)[ftime_dim], bnds = 2)
+      time_bnds <- Reorder(time_bnds, c('bnds', ftime_dim))
+      time_bnds <- list(time_bnds)
+      names(time_bnds) <- 'time_bnds'
+      coords <- c(time_bnds, coords)
+      attrs <- list(units = paste('hours since', dates[1]),
+                    calendar = 'proleptic_gregorian',
+                    longname = 'time bounds')
+      attr(coords[['time_bnds']], 'variables')$time_bnds <- attrs
+    }
+    # Add ftime_dim
+    differ <- as.numeric(difftime(dates, dates[1], units = "hours"))
+    dim(differ) <- dim(data)[ftime_dim]
+    differ <- list(differ)
+    names(differ) <- ftime_dim
+    coords <- c(differ, coords)
+    attrs <- list(units = paste('hours since', dates[1]),
+                  calendar = 'proleptic_gregorian',
+                  longname = ftime_dim,
+                  dim = list(list(name = ftime_dim, unlim = TRUE)))
+    if (!is.null(time_bnds1)) {
+      attrs$bounds = 'time_bnds'
+    }
+    attr(coords[[ftime_dim]], 'variables')[[ftime_dim]] <- attrs
+    metadata_var$dim <- list(list(name = ftime_dim, unlim = TRUE))
+    remove_metadata_dim <- FALSE
+  }
+  # Add data
+  coords[[varname]] <- data
+  if (!is.null(metadata_var)) {
+    if (remove_metadata_dim) metadata_var$dim <- NULL
+    attr(coords[[varname]], 'variables') <- list(metadata_var)
+    names(attributes(coords[[varname]])$variables) <- varname
+  }
+  # Add global attributes
+  if (!is.null(global_attrs)) {
+    attributes(coords[[varname]])$global_attrs <- global_attrs
   }
 
-  ## Define var metadata
-  var_info <- NULL
-  extra_info_var <- NULL
-  i_var_info <- metadata_var[!sapply(metadata_var, inherits, 'list')]
-
-  # name
-  var_info[['name']] <- varname
-  # units
-  if ('units' %in% names(i_var_info)) {
-    var_info[['units']] <- i_var_info[['units']]
-    i_var_info[['units']] <- NULL
-  } else {
-    var_info[['units']] <- ''
-  }
-  # dim
-  var_info[['dim']] <- defined_dims
-  # missval
-  if ('missval' %in% names(i_var_info)) {
-    var_info[['missval']] <- i_var_info[['missval']]
-    i_var_info[['missval']] <- NULL
-  } else {
-    var_info[['missval']] <- NULL
-  }
-  # longname
-  if (any(c('longname', 'long_name') %in% names(i_var_info))) {
-    longname <- names(i_var_info)[which(names(i_var_info) %in% c('longname', 'long_name'))]
-    var_info[['longname']] <- i_var_info[[longname]]
-    i_var_info[[longname]] <- NULL
-  } else {
-    var_info[['longname']] <- varname
-  }
-  # prec
-  if ('prec' %in% names(i_var_info)) {
-    var_info[['prec']] <- i_var_info[['prec']]
-    i_var_info[['prec']] <- NULL
-  } else {
-    prec <- typeof(data)
-    if (prec == 'character') {
-      var_info[['prec']] <- 'char'
-    }
-    if (any(prec %in% c('short', 'float', 'double', 'integer', 'char', 'byte'))) {
-      var_info[['prec']] <- prec
-    } else {
-      var_info[['prec']] <- 'double'
-    }
-  }
-  # extra information
-  if (!is.null(names(i_var_info))) {
-    extra_info_var <- i_var_info
-  }
-
-  datanc <- ncvar_def(name = var_info[['name']],
-                      units = var_info[['units']],
-                      dim = var_info[['dim']], 
-                      missval = var_info[['missval']],
-                      longname = var_info[['longname']], 
-                      prec = var_info[['prec']])
-
   if (is.null(extra_string)) {
     file_name <- paste0(varname, "_", startdates, ".nc")
   } else {
     file_name <- paste0(varname, "_", extra_string, "_", startdates, ".nc")
   }
   full_filename <- file.path(destination, file_name)
-  file_nc <- nc_create(full_filename, datanc)
-  ncvar_put(file_nc, datanc, data)
-
+  ArrayToNc(coords, full_filename)
+}
\ No newline at end of file
-  # Additional attributes
-  for (dim in names(defined_dims)) {
-    if (dim %in% names(extra_info_dim)) {
-      for (info_dim in names(extra_info_dim[[dim]])) {
-        ncatt_put(file_nc, dim, info_dim, as.character(extra_info_dim[[dim]][[info_dim]]))
-      }
-    }
-  }
-  # Additional dimension attributes
-  if (!is.null(extra_info_var)) {
-    for (info_var in names(extra_info_var)) {
-      ncatt_put(file_nc, varname, info_var, as.character(extra_info_var[[info_var]]))
-    }
-  }
-
-  nc_close(file_nc)
-}

R/CST_SplitDim.R

@@ -10,7 +10,7 @@
 #'
 #'@param data A 's2dv_cube' object
 #'@param split_dim A character string indicating the name of the dimension to 
-#'  split.
+#'  split. It is set as 'time' by default.
 #'@param indices A vector of numeric indices or dates. If left at NULL, the 
 #'  dates provided in the s2dv_cube object (element Dates) will be used.
 #'@param freq A character string indicating the frequency: by 'day', 'month' and 
@@ -21,6 +21,12 @@
 #'  dimension.
 #'@param insert_ftime An integer indicating the number of time steps to add at 
 #'  the begining of the time series.
+#'@param ftime_dim A character string indicating the name of the forecast time
+#'  dimension. It is set as 'time' by default. 
+#'@param sdate_dim A character string indicating the name of the start date 
+#'  dimension. It is set as 'sdate' by default. 
+#'@param return_indices A logical value that if it is TRUE, the indices 
+#'  used in splitting the dimension will be returned. It is FALSE by default.
 #'
 #'@details Parameter 'insert_ftime' has been included for the case of using 
 #'daily data, requiring split the temporal dimensions by months (or similar) and 
@@ -51,63 +57,97 @@
 #'new_data <- CST_SplitDim(data, indices = time, freq = 'year')
 #'@import abind
 #'@importFrom ClimProjDiags Subset
+#'@importFrom s2dv Reorder
 #'@export
 CST_SplitDim <- function(data, split_dim = 'time', indices = NULL,
                          freq = 'monthly', new_dim_name = NULL, 
-                         insert_ftime = NULL) {
+                         insert_ftime = NULL, ftime_dim = 'time',
+                         sdate_dim = 'sdate', return_indices = FALSE) {
   # Check 's2dv_cube'
   if (!inherits(data, 's2dv_cube')) {
-    stop("Parameter 'data' must be of the class 's2dv_cube', ",
-         "as output by CSTools::CST_Load.")
+    stop("Parameter 'data' must be of the class 's2dv_cube'.")
   }
   if (!is.null(insert_ftime)) {
     if (!is.numeric(insert_ftime)) {
       stop("Parameter 'insert_ftime' should be an integer.")
+    }
+    if (length(insert_ftime) > 1) {
+      warning("Parameter 'insert_ftime' must be of length 1, and only the",
+              " first element will be used.")
+      insert_ftime <- insert_ftime[1]
+    }
+    # Check Dates
+    if (is.null(dim(data$attrs$Dates))) {
+      warning("Parameter 'Dates' must have dimensions, 'insert_ftime' won't ",
+              "be used.")
+      insert_ftime <- NULL
+    }
+  }
+  if (!is.null(insert_ftime)) {
+    # adding NAs at the begining of the data in ftime dim
+    ftimedim <- which(names(dim(data$data)) == ftime_dim)
+    dims <- dim(data$data)
+    dims[ftimedim] <- insert_ftime
+    empty_array <- array(NA, dims)
+    data$data <- abind(empty_array, data$data, along = ftimedim)
+    names(dim(data$data)) <- names(dims)
+    # Reorder dates
+    data$attrs$Dates <- Reorder(data$attrs$Dates, c(ftime_dim, sdate_dim))
+    dates <- data$attrs$Dates
+    dates_subset <- Subset(dates, sdate_dim, 1)
+    # adding dates to Dates for the new NAs introduced
+    if ((dates_subset[2] - dates_subset[1]) == 1) {
+      timefreq <- 'days'
     } else {
-      if (length(insert_ftime) > 1) {
-        warning("Parameter 'insert_ftime' must be of length 1, and only the",
-                " first element will be used.")
-        insert_ftime <- insert_ftime[1]
-      }
-      # adding NAs at the begining of the data in ftime dim
-      ftimedim <- which(names(dim(data$data)) == 'ftime')
-      dims <- dim(data$data)
-      dims[ftimedim] <- insert_ftime
-      empty_array <- array(NA, dims)
-      data$data <- abind(empty_array, data$data, along = ftimedim)
-      names(dim(data$data)) <- names(dims)
-      # adding dates to Dates for the new NAs introduced
-      if ((data$attrs$Dates[2] - data$attrs$Dates[1]) == 1) {
-        timefreq <- 'days'
-      } else {
-        timefreq <- 'months'
-        warning("Time frequency of forecast time is considered monthly.")
-      }
-      start <- data$attrs$Dates
-      dim(start) <- c(ftime = length(start)/dims['sdate'], sdate = dims['sdate'])
-      # new <- array(NA, prod(dim(data$data)[c('ftime', 'sdate')]))
-      # Pending fix transform to UTC when concatenaiting
-      data$attrs$Dates <- do.call(c, lapply(1:dim(start)[2], function(x) {
-                                  seq(start[1,x] - as.difftime(insert_ftime, 
-                                  units = timefreq),
-                                  start[dim(start)[1],x], by = timefreq, tz = "UTC")}))
+      timefreq <- 'months'
+      warning("Time frequency of forecast time is considered monthly.")
     }
+    
+    dim(dates) <- c(length(dates)/dims[sdate_dim], dims[sdate_dim])
+    names(dim(dates)) <- c(ftime_dim, sdate_dim)
+    # new <- array(NA, prod(dim(data$data)[c('ftime', 'sdate')]))
+    # Pending fix transform to UTC when concatenaiting
+    data$attrs$Dates <- do.call(c, lapply(1:dim(dates)[2], function(x) {
+                                seq(dates[1,x] - as.difftime(insert_ftime, 
+                                units = timefreq),
+                                dates[dim(dates)[1],x], by = timefreq, tz = "UTC")}))
   }
   if (is.null(indices)) {
-    if (any(split_dim %in% c('ftime', 'time', 'sdate'))) {
+    if (any(split_dim %in% c(ftime_dim, sdate_dim))) {
       indices <- data$attrs$Dates
-      if (any(names(dim(data$data)) %in% 'sdate')) {
+      if (any(names(dim(data$data)) %in% sdate_dim)) {
         if (!any(names(dim(data$data)) %in% split_dim)) {
           stop("Parameter 'split_dims' must be one of the dimension ",
                "names in parameter 'data'.")
         }
-        indices <- indices[1 : dim(data$data)[which(names(dim(data$data)) == split_dim)]]     
+        indices <- indices[1:dim(data$data)[which(names(dim(data$data)) == split_dim)]]     
       }
     }
   }
-  data$data <- SplitDim(data$data, split_dim = split_dim, indices = indices,
-                        freq = freq, new_dim_name = new_dim_name)
-  return(data)
+  # Call the function
+  res <- SplitDim(data = data$data, split_dim = split_dim, 
+                  indices = indices, freq = freq, 
+                  new_dim_name = new_dim_name, 
+                  dates = data$attrs$Dates, 
+                  return_indices = return_indices)
+  if (inherits(res, 'list')) {
+    data$data <- res$data
+    # Split dim on Dates
+    if (!is.null(res$dates)) {
+      data$attrs$Dates <- res$dates
+    }
+  } else {
+    data$data <- res
+  }
+  data$dims <- dim(data$data)
+
+  # Coordinates
+  # TO DO: Subset splitted coordinate and add the new dimension coordinate.
+  if (return_indices) {
+    return(list(data = data, indices = res$indices))
+  } else {
+    return(data)
+  }
 }
 #'Function to Split Dimension
 #'
@@ -129,6 +169,11 @@ CST_SplitDim <- function(data, split_dim = 'time', indices = NULL,
 #'  the length in which to subset the dimension.
 #'@param new_dim_name A character string indicating the name of the new 
 #'  dimension.
+#'@param dates An optional parameter containing an array of dates of class 
+#'  'POSIXct' with the corresponding time dimensions of 'data'. It is NULL 
+#'  by default.
+#'@param return_indices A logical value that if it is TRUE, the indices 
+#'  used in splitting the dimension will be returned. It is FALSE by default.
 #'@examples
 #'data <- 1 : 20
 #'dim(data) <- c(time = 10, lat = 2)
@@ -145,7 +190,8 @@ CST_SplitDim <- function(data, split_dim = 'time', indices = NULL,
 #'@importFrom ClimProjDiags Subset
 #'@export
 SplitDim <- function(data, split_dim = 'time', indices, freq = 'monthly',
-                     new_dim_name = NULL) {
+                     new_dim_name = NULL, dates = NULL, 
+                     return_indices = FALSE) {
   # check data
   if (is.null(data)) {
     stop("Parameter 'data' cannot be NULL.")
@@ -167,7 +213,7 @@ SplitDim <- function(data, split_dim = 'time', indices, freq = 'monthly',
             "one and only the first element will be used.")
   }
   if (!any(names(dims) %in% split_dim)) {
-    stop("Parameter 'split_dims' must be one of the dimension ",
+    stop("Parameter 'split_dim' must be one of the dimension ",
          "names in parameter 'data'.")
   }
   pos_split <- which(names(dims) == split_dim)
@@ -210,8 +256,8 @@ SplitDim <- function(data, split_dim = 'time', indices, freq = 'monthly',
       })
       if ('try-error' %in% class(indices) | 
         sum(is.na(indices)) == length(indices)) {
-        stop("Dates provided in parameter 'indices' must be of class",
-             " 'POSIXct' or convertable to 'POSIXct'.")
+        stop("Dates provided in parameter 'indices' must be of class ",
+             "'POSIXct' or convertable to 'POSIXct'.")
         }
     }
   }
@@ -230,7 +276,7 @@ SplitDim <- function(data, split_dim = 'time', indices, freq = 'monthly',
     } else if (freq == 'year') {
       indices <- as.numeric(strftime(indices, format = "%Y"))
       repited <- unique(indices)
-    } else if (freq == 'monthly' ) {
+    } else if (freq == 'monthly') {
       indices <- as.numeric(strftime(indices, format = "%m%Y"))
       repited <- unique(indices)
     } else {
@@ -255,15 +301,41 @@ SplitDim <- function(data, split_dim = 'time', indices, freq = 'monthly',
   data <- lapply(repited, function(x) {rebuild(x, data, along = split_dim,
                                        indices = indices, max_times)})
   data <- abind(data, along = length(dims) + 1)
-  if (is.character(freq)) {
-    names(dim(data)) <- c(names(dims), freq)
-  } else {
-    names(dim(data)) <- c(names(dims), 'index')
+
+  # Add new dim name
+  if (is.null(new_dim_name)) {
+    if (is.character(freq)) {
+      new_dim_name <- freq
+    } else {
+      new_dim_name <- 'index'
+    }   
   }
-  if (!is.null(new_dim_name)) {
-    names(dim(data)) <- c(names(dims), new_dim_name)
+  names(dim(data)) <- c(names(dims), new_dim_name)
+
+  # Split also Dates
+  dates_exist <- FALSE
+  if (!is.null(dates)) {
+    if (any(split_dim %in% names(dim(dates)))) {
+      datesdims <- dim(dates)
+      dates <- lapply(repited, function(x) {rebuild(x, dates, along = split_dim,
+                      indices = indices, max_times)})
+      dates <- abind(dates, along = length(datesdims) + 1)
+      dates <- as.POSIXct(dates, origin = '1970-01-01', tz = "UTC")
+      names(dim(dates)) <- c(names(datesdims), new_dim_name)
+    }
+    dates_exist <- TRUE
+  }
+
+  # Return objects
+  if (all(dates_exist, return_indices)) {
+    return(list(data = data, dates = dates, indices = indices))
+  } else if (all(dates_exist, !return_indices)) {
+    return(list(data = data, dates = dates))
+  } else if (all(!dates_exist, return_indices)) {
+    return(list(data = data, indices = indices))
+  } else {
+    return(data)
   }
-  return(data)
 }
 
 rebuild <- function(x, data, along, indices, max_times) {

R/CST_Start.R

@@ -9,7 +9,10 @@
 #'`s2dv_cube` object.
 #'
 #'It receives any number of parameters (`...`) that are automatically forwarded 
-#'to the `startR::Start` function. See details in `?startR::Start`.
+#'to the `startR::Start` function. See details in `?startR::Start`. The 
+#'auxiliary functions used to define dimensions need to be called within the 
+#'startR namespace (e.g. startR::indices(), startR::values(), startR::Sort(), 
+#'startR::CircularSort(), startR::CDORemapper(), ...).
 #' 
 #'@param ... Parameters that are automatically forwarded to the `startR::Start` 
 #'  function. See details in `?startR::Start`.

R/CST_Subset.R

@@ -79,15 +79,15 @@ CST_Subset <- function(x, along, indices, drop = FALSE, var_dim = NULL,
   }
 
   # Subset data
-  x$data <- ClimProjDiags::Subset(x$data, along = along,
-                                  indices = indices,
-                                  drop = drop)
+  x$data <- Subset(x$data, along = along,
+                   indices = indices,
+                   drop = drop)
   # Adjust dimensions
   x$dims <- dim(x$data)
   # Adjust coordinates
   for (dimension in 1:length(along)) {
     dim_name <- along[dimension]
-    index <- indices[[dimension]]
+    index <- indices[dimension]
     # Only rename coordinates that have not been dropped
     if (dim_name %in% names(x$dims)) {
       # Subset coordinate by indices
@@ -113,10 +113,10 @@ CST_Subset <- function(x, along, indices, drop = FALSE, var_dim = NULL,
     }
     if ((!is.null(x$attrs$source_files)) &&
 	      (dim_name %in% names(dim(x$attrs$source_files)))) {
-      x$attrs$source_files <- ClimProjDiags::Subset(x$attrs$source_files,
-                                                    along = dim_name,
-                                                    indices = index,
-                                                    drop = drop)
+      x$attrs$source_files <- Subset(x$attrs$source_files,
+                                     along = dim_name,
+                                     indices = index,
+                                     drop = drop)
     }
   }
   # Remove metadata from variables that were dropped
@@ -128,10 +128,10 @@ CST_Subset <- function(x, along, indices, drop = FALSE, var_dim = NULL,
   if (!(length(time_along) == 0)) {
     time_indices <- indices[match(time_along, along)]
     original_dates <- x$attrs$Dates
-    x$attrs$Dates <- ClimProjDiags::Subset(x$attrs$Dates,
-                                           along = time_along,
-                                           indices = time_indices,
-                                           drop = drop)
+    x$attrs$Dates <- Subset(x$attrs$Dates,
+                            along = time_along,
+                            indices = time_indices,
+                            drop = drop)
   }
   # Subset metadata
   for (variable in 1:length(names(x$attrs$Variable$metadata))) {
@@ -150,12 +150,12 @@ CST_Subset <- function(x, along, indices, drop = FALSE, var_dim = NULL,
 # Function to subset with attributes
 .subset_with_attrs <- function(x, ...) {
   args_subset <- list(...)
-  if (is.null(dim(x)) | length(dim(x)) == 1) {
-    l <- x[args_subset[['indices']]]
+  if (any(is.null(dim(x)), length(dim(x)) == 1)) {
+    l <- x[args_subset[['indices']][[1]]]
   } else {
-    l <- ClimProjDiags::Subset(x, along = args_subset[['along']], 
-                               indices = args_subset[['indices']],
-                               drop = args_subset[['drop']])
+    l <- Subset(x, along = args_subset[['along']], 
+                indices = args_subset[['indices']],
+                drop = args_subset[['drop']])
   }
   attr.names <- names(attributes(x))
   attr.names <- attr.names[attr.names != 'names']

R/CST_WeatherRegimes.R

@@ -72,8 +72,7 @@ CST_WeatherRegimes <- function(data, ncenters = NULL,
                                ncores = NULL)  {
   # Check 's2dv_cube'
   if (!inherits(data, 's2dv_cube')) {
-    stop("Parameter 'data' must be of the class 's2dv_cube', ",
-         "as output by CSTools::CST_Load.")
+    stop("Parameter 'data' must be of the class 's2dv_cube'.")
   }
   # Check 'exp' object structure
   if (!all(c('data', 'coords') %in% names(data))) {

R/PlotCombinedMap.R

@@ -35,6 +35,35 @@
 #'  colour bar will be automatically interpolated to match the number of breaks. 
 #'  Each item in this list can be named, and the name will be used as title for 
 #'  the corresponding colour bar (equivalent to the parameter 'bar_titles').
+#'@param bar_limits Parameter from s2dv::ColorBar. Vector of two numeric values 
+#'  with the extremes of the range of values represented in the colour bar. If 
+#'  'var_limits' go beyond this interval, the drawing of triangle extremes is 
+#'  triggered at the corresponding sides, painted in 'col_inf' and 'col_sup'. 
+#'  Either of them can be set as NA and will then take as value the 
+#'  corresponding extreme in 'var_limits' (hence a triangle end won't be 
+#'  triggered for these sides). Takes as default the extremes of 'brks' if 
+#'  available, else the same values as 'var_limits'.
+#'@param triangle_ends Parameter from s2dv::ColorBar. Vector of two logical 
+#'  elements, indicating whether to force the drawing of triangle ends at each 
+#'  of the extremes of the colour bar. This choice is automatically made from 
+#'  the provided 'brks', 'bar_limits', 'var_limits', 'col_inf' and 'col_sup', 
+#'  but the behaviour can be manually forced to draw or not to draw the triangle 
+#'  ends with this parameter. If 'cols' is provided, 'col_inf' and 'col_sup' 
+#'  will take priority over 'triangle_ends' when deciding whether to draw the 
+#'  triangle ends or not.
+#'@param col_inf Parameter from s2dv::ColorBar. Colour to fill the inferior 
+#'  triangle end with. Useful if specifying colours manually with parameter 
+#'  'cols', to specify the colour and to trigger the drawing of the lower 
+#'  extreme triangle, or if 'cols' is not specified, to replace the colour 
+#'  automatically generated by ColorBar().
+#'@param col_sup Parameter from s2dv::ColorBar. Colour to fill the superior 
+#'  triangle end with. Useful if specifying colours manually with parameter 
+#'  'cols', to specify the colour and to trigger the drawing of the upper 
+#'  extreme triangle, or if 'cols' is not specified, to replace the colour 
+#'  automatically generated by ColorBar().
+#'@param bar_extra_margin Parameter from s2dv::ColorBar. Extra margins to be 
+#'  added around the colour bar, in the format c(y1, x1, y2, x2). The units are 
+#'  margin lines. Takes rep(0, 4) by default.
 #'@param col_unknown_map Colour to use to paint the grid cells for which a map 
 #'  is not possible to be chosen according to 'map_select_fun' or for those 
 #'  values that go beyond 'display_range'. Takes the value 'white' by default.