.Rbuildignore

@@ -6,6 +6,7 @@
 ./.nc$
 .*^(?!data)\.RData$
 .*\.gitlab-ci.yml$
+.lintr
 ^tests$
 ./.nfs*
 ^cran-comments\.md$

.gitlab-ci.yml

 stages:
   - build
+
 build:
   stage: build
   script:
@@ -7,3 +8,11 @@ build:
     - R CMD build --resave-data .
     - R CMD check --as-cran --no-manual --run-donttest CSIndicators_*.tar.gz
     - R -e 'covr::package_coverage()'
+
+lint-check:
+  stage: build
+  script:
+    - module load R/4.1.2-foss-2015a-bare
+    - module load CDO/1.9.8-foss-2015a
+    - 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",
+    "tests/testthat/",
+    "tests/testthat.R"
+  )

DESCRIPTION

 Package: CSIndicators
 Title: Climate Services' Indicators Based on Sub-Seasonal to Decadal Predictions
-Version: 1.1.0
+Version: 1.1.1
 Authors@R: c(
-  person("Eva", "Rifà", , "eva.rifarovira@bsc.es", role = c("cre")),
+  person("Victòria", "Agudetse", , "victoria.agudetse@bsc.es", role = c("cre")),
+  person("Eva", "Rifà", , "eva.rifarovira@bsc.es", role = c("ctb")),
   person("Nuria", "Perez-Zanon", , "nuria.perez@bsc.es", role = c("aut"), comment = c(ORCID = "0000-0001-8568-3071")),
   person("Chou", "Chihchung", ,"chihchung.chou@bsc.es", role = "aut"),
   person("Llorenç", "Lledó", , "llorenc.lledo@bsc.es", role = "aut"),
@@ -36,7 +37,8 @@ Imports:
     SPEI,
     lmom,
     lmomco,
-    zoo
+    zoo,
+    s2dv
 Suggests:
     testthat,
     knitr,
@@ -47,5 +49,5 @@ License: GPL-3
 URL: https://earth.bsc.es/gitlab/es/csindicators/
 BugReports: https://earth.bsc.es/gitlab/es/csindicators/-/issues
 Encoding: UTF-8
-RoxygenNote: 7.2.0
+RoxygenNote: 7.2.3
 Config/testthat/edition: 3

NAMESPACE

@@ -54,6 +54,7 @@ importFrom(lmomco,parpe3)
 importFrom(lmomco,pwm.pp)
 importFrom(lmomco,pwm.ub)
 importFrom(lmomco,pwm2lmom)
+importFrom(s2dv,Reorder)
 importFrom(stats,approxfun)
 importFrom(stats,ecdf)
 importFrom(stats,qnorm)

NEWS.md

+# CSIndicators 1.1.1 (Release date: 2024-01-24)  
+
+### Fixes
+- Corrected error in SelectPeriodOnDates to allow dates to be transposed
+
+### Other
+- Included CITATION file in the pacakge
+
 # CSIndicators 1.1.0 (Release date: 2023-11-20)  
 
 ### Fixes  

R/SelectPeriodOnData.R

@@ -101,6 +101,7 @@ CST_SelectPeriodOnData <- function(data, start, end, time_dim = 'time',
 #'Period <- SelectPeriodOnData(data, Dates, start = list(21, 6), end = list(21, 9))
 #'@import multiApply
 #'@importFrom ClimProjDiags Subset
+#'@importFrom s2dv Reorder
 #'@export
 SelectPeriodOnData <- function(data, dates, start, end, 
                                time_dim = 'time', ncores = NULL) {
@@ -153,7 +154,8 @@ SelectPeriodOnData <- function(data, dates, start, end,
     indices <- as.list(rep(1, length(dim_remove)))
     res <- Subset(res, along = dim_remove, indices, drop = 'selected')
   }
-  pos <- match(names(dim(data)), names(dim(res)))
-  res <- aperm(res, pos)
+  if (any(names(dims) != names(dim(res)))) {
+    res <- Reorder(res, names(dims))
+  }
   return(res)
 }

R/SelectPeriodOnDates.R

@@ -19,8 +19,6 @@
 #'@return A multidimensional array with named dimensions containing the subset of 
 #'the vector dates during the period requested from \code{start} to \code{end}.
 #'
-#'@import multiApply
-#'
 #'@examples
 #'Dates <- c(seq(as.Date("01-05-2000", format = "%d-%m-%Y"), 
 #'               as.Date("30-11-2000", format = "%d-%m-%Y"), by = 'day'),
@@ -30,6 +28,8 @@
 #'               as.Date("30-11-2002", format = "%d-%m-%Y"), by = 'day'))
 #'dim(Dates) <- c(time = 214, sdate = 3)
 #'Period <- SelectPeriodOnDates(Dates, start = list(21, 6), end = list(21, 9))
+#'@import multiApply
+#'@importFrom s2dv Reorder
 #'@export
 SelectPeriodOnDates <- function(dates, start, end,
                                 time_dim = 'time', ncores = NULL) {
@@ -45,6 +45,12 @@ SelectPeriodOnDates <- function(dates, start, end,
                ini_day = start[[1]], ini_month = start[[2]],
                end_day = end[[1]], end_month = end[[2]],
                ncores = ncores)$output1
+  reorder <- FALSE
+  if (which(names(dim(dates)) == time_dim) != 1) {
+    dimdates <- names(dim(dates))
+    dates <- Reorder(dates, c(time_dim, names(dim(dates))[which(names(dim(dates)) != time_dim)]))
+    reorder <- TRUE
+  }
   # when 29Feb is included the length of the output changes:
   regular <- Apply(list(res), target_dims = time_dim,
                    fun = sum, ncores = ncores)$output1
@@ -64,12 +70,11 @@ SelectPeriodOnDates <- function(dates, start, end,
                      }, ncores = ncores)$output1
     res <- as.POSIXct(res, origin = '1970-01-01', tz = 'UTC')  
   } else {
-    if (!all(names(dim(res)) == names(dim(dates)))) {
-      pos <- match(names(dim(dates)), names(dim(res)))
-      res <- aperm(res, pos)
-    }  
     res <- dates[res]
     dim(res) <- dims
+    if (reorder) {
+      res <- Reorder(res, dimdates)
+    }
   }
   return(res)
 }

README.md

@@ -41,61 +41,76 @@ Functions documentation can be found [here](https://CRAN.R-project.org/package=C
 
 | Function                       | CST version                        | Indicators                      |
 |--------------------------------|------------------------------------|---------------------------------|
-|PeriodMean                      |CST_PeriodMean                      |GST, SprTX, DTR                  |
-|PeriodAccumulation              |CST_PeriodAccumulation              |SprR, HarR, PRCPTOT              | 
-|AccumulationExceedingThreshold  |CST_AccumulationExceedingThreshold  |GDD, R95pTOT, R99pTOT            |
-|TotalTimeExceedingThreshold     |CST_TotalTimeExceedingThreshold     |SU35, SU, FD, ID, TR, R10mm, Rnmm|
-|TotalSpellTimeExceedingThreshold|CST_TotalSpellTimeExceedingThreshold|WSDI, CSDI                       |
-|WindCapacityFactor              |CST_WindCapacityFactor              |Wind Capacity Factor             |
-|WindPowerDensity                |CST_WindPowerDensity                |Wind Power Density               |
+|[PeriodMean](R/PeriodMean.R)    |CST_PeriodMean                      |GST, SprTX, DTR, BIO1, BIO2      |
+|[PeriodMax](R/PeriodMax.R)      |CST_PeriodMax                       |BIO5, BIO13                      |
+|[PeriodMin](R/PeriodMin.R)      |PeriodMin                           |BIO6, BIO14                      |
+|[PeriodVariance](R/PeriodVariance.R) |CST_PeriodVariance             |BIO4, BIO15                      |
+|[PeriodAccumulation](R/PeriodAccumulation.R) |CST_PeriodAccumulation |SprR, HarR, PRCPTOT, BIO16, ...  | 
+|[PeriodPET](R/PeriodPET.R)      |CST_PeriodPET                       |PET, SPEI                        | 
+|[PeriodStandardization](R/PeriodStandardization.R)    |CST_PeriodStandardization           |SPEI, SPI                        | 
+|[AccumulationExceedingThreshold](R/AccumulationExceedingThreshold.R)  |CST_AccumulationExceedingThreshold  |GDD, R95pTOT, R99pTOT            |
+|[TotalTimeExceedingThreshold](R/TotalTimeExceedingThreshold.R)     |CST_TotalTimeExceedingThreshold     |SU35, SU, FD, ID, TR, R10mm, Rnmm|
+|[TotalSpellTimeExceedingThreshold](R/TotalSpellTimeExceedingThreshold.R)|CST_TotalSpellTimeExceedingThreshold|WSDI, CSDI                       |
+|[WindCapacityFactor](R/WindCapacityFactor.R)              |CST_WindCapacityFactor              |Wind Capacity Factor             |
+|[WindPowerDensity](R/WindPowerDensity.R)                |CST_WindPowerDensity                |Wind Power Density               |
  
   	
 | Auxiliar function | CST version          |
 |-------------------|----------------------|
-|AbsToProbs         |CST_AbsToProbs        |
-|QThreshold         |CST_QThreshold        |
-|Threshold          |CST_Threshold         |
-|MergeRefToExp      |CST_MergeRefToExp     |
-|SelectPeriodOnData |CST_SelectPeriodOnData|
-|SelectPeriodOnDates|                      |
+|[AbsToProbs](R/AbsToProbs.R)         |CST_AbsToProbs        |
+|[QThreshold](R/QThreshold.R)         |CST_QThreshold        |
+|[Threshold](R/Threshold.R)          |CST_Threshold         |
+|[MergeRefToExp](R/MergeRefToExp.R)      |CST_MergeRefToExp     |
+|[SelectPeriodOnData](R/SelectPeriodOnData.R) |CST_SelectPeriodOnData|
+|[SelectPeriodOnDates](R/SelectPeriodOnDates.R)|                      |
 
 Find the current status of each function in [this link](https://docs.google.com/spreadsheets/d/1arqgw-etNPs-XRyMTJ4ekF5YjQxAZBzssxxr2GMXp3c/edit#gid=0).
 
-*Note: the CST version uses 's2dv_cube' objects as inputs and outputs while the former version uses multidimensional arrays with named dimensions as inputs and outputs*
+> **Note I:** the CST version uses 's2dv_cube' objects as inputs and outputs while the former version uses multidimensional arrays with named dimensions as inputs and outputs.
 
-*Note: All functions computing indicators allows to subset a time period if required, although this temporal subsetting can also be done with functions `SelectPeriodOnData` in a separated step.* 
+> **Note II:** All functions computing indicators allows to subset a time period if required, although this temporal subsetting can also be done with functions `SelectPeriodOnData` in a separated step. 
 
-#### Object class 's2dv_cube'
+#### Object class s2dv_cube
 
-This package is designed to be compatible with other R packages such as [CSTools](https://CRAN.R-project.org/package=CSTools) through a common object: the `s2dv_cube` object class, used in functions with the prefix **CST_**. This object can be created from Start ([startR](https://CRAN.R-project.org/package=startR) package) and from Load ([s2dv](https://CRAN.R-project.org/package=s2dv) package) directly.  
+This package is designed to be compatible with other R packages such as [CSTools](https://CRAN.R-project.org/package=CSTools) through a common object: the `s2dv_cube`, used in functions with the prefix **CST**. 
 
-The class `s2dv_cube` is mainly a list of named elements to keep data and metadata in a single object. Basic structure of the object:
+An `s2dv_cube` is an object to store ordered multidimensional array with named dimensions, specific coordinates and stored metadata. As an example, this is how it looks like (see `CSTools::lonlat_temp_st$exp`): 
 
 ```r
-$ data: [data array]
-$ dims: [dimensions vector]
-$ coords: [List of coordinates vectors]
-  $ sdate
-  $ time
-  $ lon
-  [...]
-$ attrs: [List of the attributes]
-  $ Variable:
-    $ varName
-    $ metadata 
-  $ Datasets
-  $ Dates
-  $ source_files
-  $ when
-  $ load_parameters
+'s2dv_cube'
+Data          [ 279.99, 280.34, 279.45, 281.99, 280.92,  ... ] 
+Dimensions    ( dataset = 1, var = 1, member = 15, sdate = 6, ftime = 3, lat = 22, lon = 53 ) 
+Coordinates  
+ * dataset : dat1 
+ * var : tas 
+   member : 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15 
+ * sdate : 20001101, 20011101, 20021101, 20031101, 20041101, 20051101 
+   ftime : 1, 2, 3 
+ * lat : 48, 47, 46, 45, 44, 43, 42, 41, 40, 39, 38, 37, 36, 35, 34, ...
+ * lon : 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, ...
+Attributes   
+   Dates  : 2000-11-01 2001-11-01 2002-11-01 2003-11-01 2004-11-01 ... 
+   varName  : tas 
+   metadata :  
+      lat 
+        units : degrees_north 
+        long name : latitude 
+      lon 
+        units : degrees_east 
+        long name : longitude 
+      ftime 
+        units : hours since 2000-11-01 00:00:00 
+      tas 
+        units : K 
+        long name : 2 metre temperature 
+   Datasets  : dat1 
+   when  : 2023-10-02 10:11:06 
+   source_files  : "/ecmwf/system5c3s/monthly_mean/tas_f6h/tas_20001101.nc" ... 
+   load_parameters  : 
+       ( dat1 )  : dataset = dat1, var = tas, sdate = 20001101 ... 
 ```
 
-More information about the `s2dv_cube` object class can be found here: [description of the s2dv_cube object structure document](https://docs.google.com/document/d/1ko37JFl_h6mOjDKM5QSQGikfLBKZq1naL11RkJIwtMM/edit?usp=sharing).
-
-The current `s2dv_cube` object (CSIndicators 1.0.0 and CSTools 5.0.0) differs from the original object used in the previous versions of the packages. If you have **questions** on this change you can follow some of the points below:
-
-- [New s2dv_cube object discussion in CSTools](https://earth.bsc.es/gitlab/external/cstools/-/issues/94)
-- [How to deal with the compatibility break in CSIndicators](https://earth.bsc.es/gitlab/es/csindicators/-/issues/25)
+> **Note:** The current `s2dv_cube` object (CSIndicators > 0.0.2 and CSTools > 4.1.1) differs from the original object used in the previous versions of the packages. More information about the `s2dv_cube` object class can be found here: [description of the s2dv_cube object structure document](https://docs.google.com/document/d/1ko37JFl_h6mOjDKM5QSQGikfLBKZq1naL11RkJIwtMM/edit?usp=sharing).
 
 Contribute
 ----------
@@ -105,7 +120,7 @@ Contribute
 3. Create a new branch from master with a meaningful name
 4. Once the development is finished, open a merge request to merge the branch on master
 
-*Note: Remember to work with multidimensionals arrays with named dimensions when possible and use [multiApply](https://earth.bsc.es/gitlab/ces/multiApply).*
+> **Note:** Remember to work with multidimensionals arrays with named dimensions when possible and use [multiApply](https://earth.bsc.es/gitlab/ces/multiApply).
 
 #### Add a function
 

inst/CITATION

+citHeader("To cite package 'CSTools' in publications use:")
+
+yr <- sub('.*(2[[:digit:]]{3})-.*', '\\1', meta$Date, perl = TRUE)
+if (length(yr) == 0) yr <- format(Sys.Date(), '%Y')
+
+bibentry(
+  bibtype = 'Manual',
+  title = paste0(meta$Package, ': ', meta$Title),
+  author = Filter(function(p) 'aut' %in% p$role, as.person(meta$Author)),
+  year = yr,
+  note = paste('R package version', meta$Version),
+  url = meta$URL
+)
+
+bibentry(
+  bibtype = "Article",
+  author = c(person("Núria", "Pérez-Zanón", email = "nuria.perez@bsc.es"), person("", "et al.")),
+  title = "CSIndicators: Get tailored climate indicators for applications in your sector",
+  doi = "10.1016/j.cliser.2023.100393",
+  url = "https://www.sciencedirect.com/science/article/pii/S2405880723000547",
+  journal = "Climate Services",
+  publisher = "Elsevier",
+  year = "2023"
+)

tests/testthat/test-SelectPeriod.R

@@ -56,7 +56,6 @@ test_that("2. Output checks", {
     dim(res),
     c(time = 52)
   )
-
 })
 
 ##############################################
@@ -250,3 +249,49 @@ test_that("4. Seasonal", {
     )
 })
 
+##############################################
+
+test_that("5. Test sample data", {
+  dates <- c(seq(as.POSIXct("10-03-2011", format = "%d-%m-%Y", tz = "UTC"),
+                 as.POSIXct("20-03-2011", format = "%d-%m-%Y", tz = "UTC"), by = 'day'),
+             seq(as.POSIXct("10-03-2012", format = "%d-%m-%Y", tz = "UTC"),
+                 as.POSIXct("20-03-2012", format = "%d-%m-%Y", tz = "UTC"), by = 'day'),
+             seq(as.POSIXct("10-03-2013", format = "%d-%m-%Y", tz = "UTC"),
+                 as.POSIXct("20-03-2013", format = "%d-%m-%Y", tz = "UTC"), by = 'day'))
+  dim(dates) <- c(ftime = 11, sdate = 3)
+  expect_equal(
+    SelectPeriodOnDates(dates = lonlat_prec$attrs$Dates, start = list(10, 03), 
+                        end = list(20, 03),  time_dim = 'ftime'),
+    dates
+  )
+  dates_lonlat <- lonlat_prec_st$attrs$Dates
+  dates_lonlat <- Reorder(dates_lonlat-12*3600, c(2,1))
+  expect_equal(
+    SelectPeriodOnDates(dates = dates_lonlat, start = list(10, 03), 
+                        end = list(20, 03),  time_dim = 'ftime'),
+    dates
+  )
+  # test error
+  dates <- CSTools::lonlat_prec_st$attrs$Dates
+  out_sdates <- c(as.POSIXct("10-03-2011", format = "%d-%m-%Y", tz = "UTC"),
+                  as.POSIXct("10-03-2012", format = "%d-%m-%Y", tz = "UTC"),
+                  as.POSIXct("10-03-2013", format = "%d-%m-%Y", tz = "UTC"))
+  dim(dates) <- c(a = 3, len = 31)
+  expect_error(
+    SelectPeriodOnDates(dates = dates, start = list(10, 03), 
+                        end = list(20, 03), time_dim = 'ftime'),
+    "Could not find dimension 'ftime' in 1th object provided in 'data'."
+  )
+  dim(dates) <- c(sdate = 3, ftime = 31)
+  expect_equal(
+    SelectPeriodOnDates(dates = dates-12*3600, start = list(10, 03), 
+                        end = list(20, 03), time_dim = 'ftime')[, 1],
+    out_sdates
+  )
+  dates <- Reorder(dates, c(2,1))
+  expect_equal(
+    SelectPeriodOnDates(dates = dates-12*3600, start = list(10, 03), 
+                        end = list(20, 03), time_dim = 'ftime')[1, ],
+    out_sdates
+  )
+})