Merge branch 'fix_subsetting' into 'master'

bugfix for subsetting via indices for time(year, month, day) dimensions

See merge request lpjml/lpjmlkit!88

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '2593407'
+ValidationKey: '2613204'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

CITATION.cff

@@ -2,7 +2,7 @@ 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: 1.3.1
+version: 1.3.2
 date-released: '2024-03-15'
 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

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: lpjmlkit
 Type: Package
 Title: Toolkit for Basic LPJmL Handling
-Version: 1.3.1
+Version: 1.3.2
 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")),

R/LPJmLData_subset.R

@@ -186,7 +186,7 @@ LPJmLData$set(
 create_year_dimnames <- function(subset_list, data) {
 
   if ("year" %in% names(subset_list) && is.numeric(subset_list[["year"]])) {
-    year_dimnames <- data$dimnames()$year
+    year_dimnames <- dimnames(data)$year
   } else {
     year_dimnames <- NULL
   }

README.md

@@ -1,6 +1,6 @@
 # Toolkit for Basic LPJmL Handling <a href=''><img src='inst/img/logo.png' align='right' height='139' /></a>
 
-R package **lpjmlkit**, version **1.3.1**
+R package **lpjmlkit**, version **1.3.2**
 
 [![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, Müller C (2024). _lpjmlkit: Toolkit for Basic LPJmL Handling_. doi: 10.5281/zenodo.7773134 (URL: https://doi.org/10.5281/zenodo.7773134), R package version 1.3.1, <URL: https://github.com/PIK-LPJmL/lpjmlkit>.
+Breier J, Ostberg S, Wirth S, Minoli S, Stenzel F, Müller C (2024). _lpjmlkit: Toolkit for Basic LPJmL Handling_. doi: 10.5281/zenodo.7773134 (URL: https://doi.org/10.5281/zenodo.7773134), R package version 1.3.2, <URL: 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 Christoph Müller},
   year = {2024},
-  note = {R package version 1.3.1},
+  note = {R package version 1.3.2},
   doi = {10.5281/zenodo.7773134},
   url = {https://github.com/PIK-LPJmL/lpjmlkit},
 }

tests/testthat/test-LPJmLData_subset_transform.R

@@ -23,16 +23,16 @@ test_integrity <- function(output) {
   } else {
     # Test for equal dimnames of lat, lon in data and those of underlying grid
     expect_equal(dimnames_data$lat,
-                           dimnames(output$grid)$lat)
+                 dimnames(output$grid)$lat)
     expect_equal(dimnames_data$lon,
-                           dimnames(output$grid)$lon)
+                 dimnames(output$grid)$lon)
   }
 
   # Check for two cases "time" or "year_month_day"
   if ("time" %in% names(dim_data)) {
     # Test for equal length of time steps in data and meta data (nyear * nstep)
     expect_equal(dim_data[["time"]],
-                           output$meta$nyear * output$meta$nstep)
+                 output$meta$nyear * output$meta$nstep)
     # Test for equal dimnames of time steps in data and those constructed by
     #   meta data with create_time_names function (nstep, firstyear, nyear)
     expect_equal(
@@ -96,7 +96,7 @@ test_integrity <- function(output) {
       #   by meta data of output
       expect_true(
         all(as.vector(stats::na.omit(output$grid$data)) %in%
-            seq(output$meta$firstcell, length.out = output$meta$ncell))
+              seq(output$meta$firstcell, length.out = output$meta$ncell))
       )
     }
   }
@@ -208,7 +208,7 @@ test_that("test transform (space) method", {
   # Explicitly load grid
   output$add_grid("../testdata/output/grid.bin.json")
   output$transform(to = c("year_month_day", "lon_lat"))
-  output$subset(year = as.character(2005:2008),
+  output$subset(year = 5:8,
                 month = 6:9,
                 lat = c("55.25", "55.75", "56.25", "56.75"))
   output$transform(to = "cell")
@@ -221,7 +221,7 @@ test_that("test transform (space) method", {
   output2$add_grid("../testdata/output/grid.bin.json")
   output2$transform(to = c("year_month_day", "lon_lat"))
   output2$subset(year = as.character(2005:2008),
-                 month = 6:9,
+                 month = as.character(6:9),
                  lat = c("55.25", "55.75", "56.25", "56.75"))
   output2$transform(to = "cell")
   test_integrity(output2)