Merge branch 'speed_up_get_cellindex' into 'master'

Avoid unnecesarry transfomrations of LPJmLData Object.

See merge request lpjml/lpjmlkit!103

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '3489222'
+ValidationKey: '3512075'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 exclude: '^tests/testthat/_snaps/.*$'
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 2c9f875913ee60ca25ce70243dc24d5b6415598c  # frozen: v4.6.0
+    rev: cef0300fd0fc4d2a87a85fa2093c6b283ea36f4b  # frozen: v5.0.0
     hooks:
     -   id: check-case-conflict
     -   id: check-json
@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: bae853d82da476eee0e0a57960ee6b741a3b3fb7  # frozen: v0.4.3
+    rev: 3b70240796cdccbe1474b0176560281aaded97e6  # frozen: v0.4.3.9003
     hooks:
     -   id: parsable-R
     -   id: deps-in-desc

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: 1.7.4
-date-released: '2024-11-26'
+version: 1.7.5
+date-released: '2024-12-12'
 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: 1.7.4
+Version: 1.7.5
 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: 2024-11-26
+Date: 2024-12-12

R/get_cellindex.R

@@ -87,7 +87,7 @@ get_cellindex <- function(grid_filename, extent = NULL, coordinates = NULL, shap
 
   # Check if extent values are within the longitude and latitude range in the cells
   if (!is.null(extent)) {
-    cells$cellindex <- as.numeric(row.names(cells))
+    cells$cellindex <- as.numeric(row.names(cells)) + 1
 
     out_of_bounds_lon <- extent[c(1, 2)][extent[c(1, 2)] < lon_range[1] |
                                            extent[c(1, 2)] > lon_range[2]]
@@ -107,12 +107,15 @@ get_cellindex <- function(grid_filename, extent = NULL, coordinates = NULL, shap
                      cells$lon <= extent[2] &
                      cells$lat >= extent[3] & cells$lat <= extent[4], ]
 
-    grid_cell <- transform(grid_lonlat, "lon_lat")
-
-    cells <- grid_cell$subset(coordinates = lapply(X = list(lon = cells$lon,
-                                                            lat = cells$lat),
-                                                   FUN = as.character))
+    if (!simplify) {
+      grid_cell <- transform(grid_lonlat, "lon_lat")
 
+      cells <- grid_cell$subset(coordinates = lapply(X = list(lon = cells$lon,
+                                                              lat = cells$lat),
+                                                     FUN = as.character))
+    } else {
+      cells <- cells$cellindex
+    }
   }
 
   # Check if coordinates are within the longitude and latitude range in the cells
@@ -149,18 +152,20 @@ get_cellindex <- function(grid_filename, extent = NULL, coordinates = NULL, shap
   }
 
   if (!is.null(shape)) {
+    grid_lonlat <- grid_lonlat$transform("lon_lat")
+
     cell_coords <- grid_lonlat |>
       as_terra() |>
       terra::mask(shape) |>
       terra::as.data.frame(xy = TRUE) |>
       dplyr::select("x", "y")
 
-    cells <- grid_lonlat$transform("lon_lat") |>
+    cells <- grid_lonlat |>
       subset(coordinates = lapply(list(lon = cell_coords$x, lat = cell_coords$y),
                                   FUN = as.character))
   }
 
-  if (simplify) {
+  if (simplify && is.null(extent)) {
     cells <- c(stats::na.omit(c(cells$data + 1)))
   }
 

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 **1.7.4**
+R package **lpjmlkit**, version **1.7.5**
 
 [![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 1.7.4, <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 1.7.5, <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 1.7.4},
+  note = {R package version 1.7.5},
   url = {https://github.com/PIK-LPJmL/lpjmlkit},
   doi = {10.5281/zenodo.7773134},
 }