Merge branch 'fix_get_cellindex' into 'master'

Fix get cellindex

See merge request lpjml/lpjmlkit!94

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '2793210'
+ValidationKey: '2814724'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

.github/workflows/check.yaml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -23,7 +23,6 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
-            gamstransfer=?ignore
             any::lucode2
             any::covr
             any::madrat
@@ -36,7 +35,7 @@ jobs:
           # gms, goxygen, GDPuc) will usually have an outdated binary version
           # available; by using extra-packages we get the newest version
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3.9
 

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: 1.4.1
-date-released: '2024-03-28'
+version: 1.4.2
+date-released: '2024-04-09'
 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: 1.4.1
+Version: 1.4.2
 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")),
@@ -54,4 +54,4 @@ Suggests:
     sf
 Config/testthat/edition: 3
 VignetteBuilder: knitr
-Date: 2024-03-28
+Date: 2024-04-09

R/get_cellindex.R

@@ -9,9 +9,9 @@
 #' to correct it.
 #'
 #' @param grid_filename A string representing the grid file name.
-#' @param extent A numeric vector of length 4 representing the extent
-#' (lonmin, lonmax, latmin, latmax).
-#' @param coordinates A list of two numeric vectors representing the coordinates.
+#' @param extent A numeric vector (lonmin, lonmax, latmin, latmax) containing the
+#'  longitude and latitude boundaries between which values included in the subset.
+#' @param coordinates A list of two named (lon, lat) numeric vectors representing the coordinates.
 #'
 #'
 #' @return The cell index from the grid file based on the provided extent or
@@ -22,11 +22,11 @@
 #' \dontrun{
 #' get_cellindex(
 #'   grid_filename = "my_grid.bin.json",
-#'   extent = c(-123.25, -122.75, 49.25, 49.75)
+#'   extent = c(-123.25, -122.75, 49.25, 49.75) # (lonmin, lonmax, latmin, latmax)
 #' )
 #' get_cellindex(
 #'   grid_filename = "my_grid.bin.json",
-#'   coordinates = list(c(-123.25, -122.75), c(49.25, 49.75))
+#'   coordinates = list(lon = c(-123.25, -122.75), lat = c(49.25, 49.75))
 #' )
 #' }
 #' @details
@@ -64,7 +64,7 @@ get_cellindex <- function(grid_filename, extent = NULL, coordinates = NULL) {
     extent <- check_extent(extent) %>%
       correct_extent()
   } else if (!is.null(coordinates)) {
-    check_coordinates_length(coordinates)
+    coordinates <- check_coordinates(coordinates)
   }
 
   # Read the grid file and create a data frame
@@ -120,7 +120,7 @@ get_cellindex <- function(grid_filename, extent = NULL, coordinates = NULL) {
 
     grid_cell <- transform(grid_lonlat, "lon_lat")
 
-    grid_cell$subset(coordinates = coordinates)
+    grid_cell$subset(coordinates = lapply(X = coordinates, FUN = as.character))
 
     cells <- c(stats::na.omit(c(grid_cell$data + 1)))
 
@@ -165,7 +165,6 @@ check_extent <- function(extent) {
 }
 
 
-# Check if the coordinates are a list of two numeric vectors of equal length
 
 # Check if both extent and coordinates are provided
 check_extent_and_coordinates <- function(extent, coordinates) {
@@ -193,12 +192,30 @@ correct_extent <- function(extent) {
       warning("Swapped values of latmin and latmax.")
     }
   }
-  return(extent)
+
+  extent
 }
 
-# Check the length of coordinates
-check_coordinates_length <- function(coordinates) {
+# Check if the coordinates are a list of two numeric vectors and of equal length
+check_coordinates <- function(coordinates) {
+  if (!is.list(coordinates) || length(coordinates) != 2) {
+    stop("coordinates must be a list of two vectors.")
+  }
+
+  coordinates <- lapply(coordinates, function(coord) {
+    if (!is.numeric(coord)) {
+      warning("Non-numeric coordinates detected, attempting to convert to numeric.")
+      coord <- as.numeric(coord)
+      if (any(is.na(coord))) {
+        stop("Unable to convert all coordinates to numeric.")
+      }
+    }
+    coord
+  })
+
   if (length(coordinates[[1]]) != length(coordinates[[2]])) {
     stop("The two vectors in coordinates must have the same length.")
   }
+
+  coordinates
 }

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 **1.4.1**
+R package **lpjmlkit**, version **1.4.2**
 
 [![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 1.4.1, <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 1.4.2, <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 1.4.1},
+  note = {R package version 1.4.2},
   doi = {10.5281/zenodo.7773134},
   url = {https://github.com/PIK-LPJmL/lpjmlkit},
 }

tests/testthat/test-get_cellindex.R

@@ -40,12 +40,12 @@ test_that("get_cellindex handles extent values out of order", {
 })
 
 test_that("get_cellindex handles valid coordinates", {
-  expect_error(
+  expect_warning(
     get_cellindex(
       "../testdata/output/grid.bin.json",
-      coordinates = list(c(-87.25, -87.25), c(55.25, 55.75))
+      coordinates = list(lon = c("-87.25", -87.25), lat = c(55.25, 55.75))
     ),
-    "Values for coordinate pairs must be supplied as strings"
+    "Non-numeric coordinates detected"
   )
 })
 
@@ -58,7 +58,7 @@ test_that("get_cellindex returns correct cell index for given extent", {
 
 test_that("get_cellindex returns correct cell index for given coordinates", {
   result <- get_cellindex("../testdata/output/grid.bin.json",
-    coordinates = list(lon = c("-87.25", "-87.25"), lat = c("55.25", "55.75"))
+    coordinates = list(lon = c(-87.25, -87.25), lat = c(55.25, 55.75))
   )
   expect_true(length(result) == 2 && result[1] == 10001 && result[2] == 10002)
 })