bugfix age-class distribution

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '30453908'
+ValidationKey: '30512004'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package .* was built under R version'
@@ -8,3 +8,4 @@ AcceptedNotes:
 - includes the non-default packages
 allowLinterWarnings: no
 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           # gms, goxygen, GDPuc) will usually have an outdated binary version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: 'mrmagpie: madrat based MAgPIE Input Data Library'
-version: 1.52.3
-date-released: '2024-09-30'
+version: 1.52.4
+date-released: '2024-10-25'
 abstract: Provides functions for MAgPIE country and cellular input data generation.
 authors:
 - family-names: Karstens

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: mrmagpie
 Title: madrat based MAgPIE Input Data Library
-Version: 1.52.3
-Date: 2024-09-30
+Version: 1.52.4
+Date: 2024-10-25
 Authors@R: c(
     person("Kristine", "Karstens", , "[email protected]", role = c("aut", "cre")),
     person("Jan Philipp", "Dietrich", , "[email protected]", role = "aut"),

R/calcAgeClassDistribution.R

@@ -1,10 +1,10 @@
 #' @title calcAgeClassDistribution
-#' @description This function calculates the share of each age class in secondary forests in each
-#'              MAgPIE simulation cluster based on Global Forest Age Dataset from Poulter et al. 2019
+#' @description This function calculates forest area in 15 age classes based on the
+#' Global Forest Age Dataset (GFAD) from Poulter et al. 2019
 #' @param cells lpjcell for 67420 cells or magpiecell for 59199 cells
 #'
 #' @return magpie object in cluster resolution
-#' @author Abhijeet Mishra, Felicitas Beier
+#' @author Abhijeet Mishra, Felicitas Beier, Florian Humpenoeder
 #'
 #' @examples
 #' \dontrun{
@@ -23,26 +23,18 @@ calcAgeClassDistribution <- function(cells = "lpjcell") {
   cb <- toolGetMapping("LPJ_CellBelongingsToCountries.csv",
                        type = "cell", where = "mrcommons")
   cellArea <- (111e3 * 0.5) * (111e3 * 0.5) * cos(cb$lat / 180 * pi)
-  cellArea <- as.magpie(cellArea, spatial = 1)
+  cellArea <- as.magpie(cellArea, spatial = 1) /  1e10 # convert to Mha
   getItems(cellArea, dim = 1, raw = TRUE) <- paste(mapping$coords, mapping$iso, sep = ".")
   getSets(cellArea) <- c("x", "y", "iso", "year", "data")
 
   ######################
-  forestArea <- poulterDataset * cellArea
+  out <- poulterDataset * cellArea
 
-  forestArea <- dimSums(forestArea, dim = 3.1)
+  out <- dimSums(out, dim = 3.1)
 
-  getNames(forestArea) <- gsub(pattern = "X",
-                               replacement = "class",
-                               x = getNames(forestArea))
-
-  ## Set age classes to 0 where forest does not exist
-  ## Only checking where zero forest area exists
-  zeroForestArea <- dimSums(forestArea, dim = 3)
-  acDistribution <- forestArea / zeroForestArea
-  acDistribution[magclass::where((setYears(zeroForestArea, "y2000")) == 0)$true$regions, , ] <- 0
-
-  out <- acDistribution
+  getNames(out) <- gsub(pattern = "X",
+                        replacement = "class",
+                        x = getNames(out))
 
   if (cells == "magpiecell") {
     out      <- toolCoord2Isocell(out, cells = cells)
@@ -51,8 +43,8 @@ calcAgeClassDistribution <- function(cells = "lpjcell") {
 
   return(list(x = out,
               weight = cellArea,
-              unit = "1",
-              description = "Fraction of each age class in secondary forest from each spatially
-                             explicit cell as described in Poulter age classes",
+              unit = "Mha",
+              description = "Forest area in 15 age classes based the Global Forest Age
+                Dataset (GFAD) from Poulter et al. 2019",
               isocountries = FALSE))
 }

README.md

@@ -1,6 +1,6 @@
 # madrat based MAgPIE Input Data Library
 
-R package **mrmagpie**, version **1.52.3**
+R package **mrmagpie**, version **1.52.4**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/mrmagpie)](https://cran.r-project.org/package=mrmagpie) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4319612.svg)](https://doi.org/10.5281/zenodo.4319612) [![R build status](https://github.com/pik-piam/mrmagpie/workflows/check/badge.svg)](https://github.com/pik-piam/mrmagpie/actions) [![codecov](https://codecov.io/gh/pik-piam/mrmagpie/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/mrmagpie) [![r-universe](https://pik-piam.r-universe.dev/badges/mrmagpie)](https://pik-piam.r-universe.dev/builds)
 
@@ -39,7 +39,7 @@ In case of questions / problems please contact Kristine Karstens <karstens@pik-p
 
 To cite package **mrmagpie** in publications use:
 
-Karstens K, Dietrich J, Chen D, Windisch M, Alves M, Beier F, Köberle A, v. Jeetze P, Mishra A, Humpenoeder F, Sauer P (2024). _mrmagpie: madrat based MAgPIE Input Data Library_. doi:10.5281/zenodo.4319612 <https://doi.org/10.5281/zenodo.4319612>, R package version 1.52.3, <https://github.com/pik-piam/mrmagpie>.
+Karstens K, Dietrich J, Chen D, Windisch M, Alves M, Beier F, Köberle A, v. Jeetze P, Mishra A, Humpenoeder F, Sauer P (2024). _mrmagpie: madrat based MAgPIE Input Data Library_. doi:10.5281/zenodo.4319612 <https://doi.org/10.5281/zenodo.4319612>, R package version 1.52.4, <https://github.com/pik-piam/mrmagpie>.
 
 A BibTeX entry for LaTeX users is
 
@@ -48,7 +48,7 @@ A BibTeX entry for LaTeX users is
   title = {mrmagpie: madrat based MAgPIE Input Data Library},
   author = {Kristine Karstens and Jan Philipp Dietrich and David Chen and Michael Windisch and Marcos Alves and Felicitas Beier and Alexandre Köberle and Patrick {v. Jeetze} and Abhijeet Mishra and Florian Humpenoeder and Pascal Sauer},
   year = {2024},
-  note = {R package version 1.52.3},
+  note = {R package version 1.52.4},
   url = {https://github.com/pik-piam/mrmagpie},
   doi = {10.5281/zenodo.4319612},
 }