Merge branch 'fix_split_time_names' into 'master'

Fix split_time_names to enable negative years

See merge request lpjml/lpjmlkit!102

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '3458270'
+ValidationKey: '3489222'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
@@ -7,3 +7,4 @@ allowLinterWarnings: no
 AddInReadme: inst/README.md
 AddLogoReadme: inst/img/logo.png
 enforceVersionUpdate: no
+skipCoverage: no

.github/workflows/check.yaml

@@ -23,14 +23,14 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
-            any::lucode2
-            any::covr
-            any::madrat
-            any::magclass
-            any::citation
-            any::gms
-            any::goxygen
-            any::GDPuc
+            lucode2
+            covr
+            madrat
+            magclass
+            citation
+            gms
+            goxygen
+            GDPuc
           # piam packages also available on CRAN (madrat, magclass, citation,
           # gms, goxygen, GDPuc) will usually have an outdated binary version
           # available; by using extra-packages we get the newest version
@@ -63,6 +63,6 @@ jobs:
         shell: Rscript {0}
         run: |
           nonDummyTests <- setdiff(list.files("./tests/testthat/"), c("test-dummy.R", "_snaps"))
-          if(length(nonDummyTests) > 0) covr::codecov(quiet = FALSE)
+          if(length(nonDummyTests) > 0 && !lucode2:::loadBuildLibraryConfig()[["skipCoverage"]]) covr::codecov(quiet = FALSE)
         env:
           NOT_CRAN: "true"

CITATION.cff

@@ -2,8 +2,8 @@ cff-version: 1.2.0
 message: If you use this software, please cite it using the metadata from this file.
 type: software
 title: 'lpjmlkit: Toolkit for Basic LPJmL Handling'
-version: 1.7.3
-date-released: '2024-09-24'
+version: 1.7.4
+date-released: '2024-11-26'
 abstract: A collection of basic functions to facilitate the work with the Dynamic
   Global Vegetation Model (DGVM) Lund-Potsdam-Jena managed Land (LPJmL) hosted at
   the Potsdam Institute for Climate Impact Research (PIK). It provides functions for

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: lpjmlkit
 Type: Package
 Title: Toolkit for Basic LPJmL Handling
-Version: 1.7.3
+Version: 1.7.4
 Authors@R: c(
     person("Jannes", "Breier", , "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-9055-6904")),
     person("Sebastian","Ostberg", , "[email protected]", role = "aut", comment = c(ORCID = "0000-0002-2368-7015")),
@@ -55,4 +55,4 @@ Suggests:
     sf
 Config/testthat/edition: 3
 VignetteBuilder: knitr
-Date: 2024-09-24
+Date: 2024-11-26

NAMESPACE

@@ -35,6 +35,7 @@ export(read_io)
 export(read_meta)
 export(run_lpjml)
 export(set_header_item)
+export(split_time_names)
 export(submit_lpjml)
 export(subset.LPJmLData)
 export(transform)

R/time_names.R

@@ -28,8 +28,8 @@ create_time_names <- function(
   mm <- {if (is.null(months)) seq_len(12) else months} %>% #nolint
     sprintf("%02d", .)
 
-  # Daily data: YYYY-MM-DD
   if (nstep == 365) {
+    # Daily data: YYYY-MM-DD
     d_mmdd <- paste(
       rep(x = mm, times = {
         # Cases of months or days being subsetted or not.
@@ -44,36 +44,63 @@ create_time_names <- function(
       ), dd, sep = "-"
     )
 
-    time_dimnames <- paste(rep(years, each = length(dd)),
-                        rep(d_mmdd, times = length(years)), sep = "-")
-
-  # Monthly data: YYYY-MM-LastDayOfMonth
+    time_dimnames <- paste(
+      rep(years, each = length(dd)),
+      rep(d_mmdd, times = length(years)),
+      sep = "-"
+    )
   } else if (nstep == 12) {
+    # Monthly data: YYYY-MM-LastDayOfMonth
     m_mmdd <- paste(mm, ndays_in_month, sep = "-")
 
     time_dimnames  <- paste(
       rep(years, each = length(ndays_in_month)),
       rep(m_mmdd, times = length(years)),
       sep = "-"
     )
-
-  # Annual data: YYYY-12-31
   } else if (nstep == 1) {
+    # Annual data: YYYY-12-31
     time_dimnames <- paste(years, 12, 31, sep = "-")
-
-  # Currently no support for other (special) nstep cases
   } else {
+    # Currently no support for other (special) nstep cases
     stop("Invalid nstep: ", nstep, "\nnstep has to be 1, 12 or 365")
   }
 
   return(time_dimnames)
 }
 
+#' Split date strings into years, months and days
+#'
+#' Splits one or several date strings into a list of unique days, months and
+#' years.
+#'
+#' @param time_names Character vector with one or several date strings in the
+#'   form YYYY-MM-DD.
+#'
+#' @return List containing unique `year`, `month` and `day` values included in
+#'   `time_names`.
+#'
+#' @examples
+#' \dontrun{
+#'  time_names <- split_time_names(c("2024-11-25", "2024-11-26"))
+#'  time_names
+#'  # $year
+#'  # [1] "2024"
+#'  # $month
+#'  # [1] "11"
+#'  # $day
+#'  # [1] "25" "26"
+#' }
+#'
+#' @md
+#' @export
 split_time_names <- function(time_names) {
 
   # Split time string "year-month-day" into year, month, day integer vector
-  time_split <- strsplit(time_names, "-") %>%
-    lapply(function(x) as.character(as.integer(x)))
+  time_split <- regmatches(
+    time_names,
+    regexec("([-]?[[:digit:]]+)-([[:digit:]]+)-([[:digit:]]+)", time_names)
+  ) %>% lapply(function(x) as.character(as.integer(x[-1])))
 
   # Create corresponding dimnames for disaggregated array by unique entry
   matrix(unlist(time_split),
@@ -83,5 +110,5 @@ split_time_names <- function(time_names) {
                          c("year", "month", "day"))) %>%
     apply(2, unique) %>%
     as.list() %>%
-  return()
+    return()
 }

README.md

@@ -1,6 +1,6 @@
 # <a href=''><img src='inst/img/logo.png' align='right' alt='logo' height=139 /></a> Toolkit for Basic LPJmL Handling
 
-R package **lpjmlkit**, version **1.7.3**
+R package **lpjmlkit**, version **1.7.4**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/lpjmlkit)](https://cran.r-project.org/package=lpjmlkit) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.7773134.svg)](https://doi.org/10.5281/zenodo.7773134) [![R build status](https://github.com/PIK-LPJmL/lpjmlkit/workflows/check/badge.svg)](https://github.com/PIK-LPJmL/lpjmlkit/actions) [![codecov](https://codecov.io/gh/PIK-LPJmL/lpjmlkit/branch/master/graph/badge.svg)](https://app.codecov.io/gh/PIK-LPJmL/lpjmlkit) [![r-universe](https://pik-piam.r-universe.dev/badges/lpjmlkit)](https://pik-piam.r-universe.dev/builds)
 
@@ -76,7 +76,7 @@ In case of questions / problems please contact Jannes Breier <jannesbr@pik-potsd
 
 To cite package **lpjmlkit** in publications use:
 
-Breier J, Ostberg S, Wirth S, Minoli S, Stenzel F, Hötten D, Müller C (2024). _lpjmlkit: Toolkit for Basic LPJmL Handling_. doi:10.5281/zenodo.7773134 <https://doi.org/10.5281/zenodo.7773134>, R package version 1.7.3, <https://github.com/PIK-LPJmL/lpjmlkit>.
+Breier J, Ostberg S, Wirth S, Minoli S, Stenzel F, Hötten D, Müller C (2024). _lpjmlkit: Toolkit for Basic LPJmL Handling_. doi:10.5281/zenodo.7773134 <https://doi.org/10.5281/zenodo.7773134>, R package version 1.7.4, <https://github.com/PIK-LPJmL/lpjmlkit>.
 
 A BibTeX entry for LaTeX users is
 
@@ -85,7 +85,7 @@ A BibTeX entry for LaTeX users is
   title = {lpjmlkit: Toolkit for Basic LPJmL Handling},
   author = {Jannes Breier and Sebastian Ostberg and Stephen Björn Wirth and Sara Minoli and Fabian Stenzel and David Hötten and Christoph Müller},
   year = {2024},
-  note = {R package version 1.7.3},
+  note = {R package version 1.7.4},
   url = {https://github.com/PIK-LPJmL/lpjmlkit},
   doi = {10.5281/zenodo.7773134},
 }