added disaggregation of other land to reporting

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '426562270'
+ValidationKey: '426603598'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

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: 'magpie4: MAgPIE outputs R package for MAgPIE version 4.x'
-version: 2.13.10
-date-released: '2024-10-21'
+version: 2.13.11
+date-released: '2024-10-22'
 abstract: Common output routines for extracting results from the MAgPIE framework
   (versions 4.x).
 authors:

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: magpie4
 Title: MAgPIE outputs R package for MAgPIE version 4.x
-Version: 2.13.10
-Date: 2024-10-21
+Version: 2.13.11
+Date: 2024-10-22
 Authors@R: c(
     person("Benjamin Leon", "Bodirsky", , "[email protected]", role = c("aut", "cre")),
     person("Florian", "Humpenoeder", , "[email protected]", role = "aut"),

NAMESPACE

@@ -31,6 +31,7 @@ export(NitrogenBudget)
 export(NitrogenBudgetNonagland)
 export(NitrogenBudgetPasture)
 export(NitrogenBudgetWithdrawals)
+export(OtherLand)
 export(PeatlandArea)
 export(PeatlandEmissions)
 export(PlantationEstablishment)

R/OtherLand.R

@@ -0,0 +1,50 @@
+#' @title OtherLand
+#' @description Disaggregation of other land into initial, restored and recovered land based on a MAgPIE gdx file
+#'
+#' @export
+#'
+#' @param gdx GDX file
+#' @param level Level of regional aggregation; "cell", "reg" (regional), "glo" (global), "regglo" (regional and global) or any aggregation level defined in superAggregate. In addition "climate" for the 3 climate regions tropical, temperate and boreal is available.
+#' @details initial, restored and recovered land
+#' @return Other land area in Mha
+#' @author Florian Humpenoeder
+#' @importFrom magclass dimSums collapseNames
+#' @importFrom luscale superAggregate
+#' @examples
+#'
+#'   \dontrun{
+#'     x <- PeatlandArea(gdx)
+#'   }
+
+OtherLand <- function(gdx, level="reg"){
+
+  a <- dimSums(readGDX(gdx,"ov_land_other",select=list(type="level"),react = "silent"),dim="othertype35")
+  b <- readGDX(gdx,"pm_land_conservation",react = "silent")
+  x <- m_yeardiff(gdx)
+  x[,1,] <- 5
+  ac <- readGDX(gdx,"ac")
+  ac_est <- new.magpie("GLO",getYears(x),ac,fill=0)
+  for(t in getYears(x)) {
+    ac_est[,t,getNames(ac_est[,t,])[1:(x[,t,]/5)]] <- 1
+  }
+  ac_sub <- 1 - ac_est
+  ac_sub[,,"acx"] <- 0
+
+  restoredEst <- collapseDim(b[,,"other.restore"])
+  restoredSub <- collapseDim(as.magpie(apply(b[, , "other.restore"], c(1, 3), cumsum)))
+  recoveredEst <- dimSums(a*ac_est,dim=3) - restoredEst
+  recoveredSub <- dimSums(a*ac_sub,dim=3) - restoredSub
+
+  initial <- setNames(collapseDim(a[,,"acx"]), "other_initial")
+  recovered <- setNames(recoveredEst+recoveredSub, "other_recovered")
+  restored <- setNames(restoredEst+restoredSub, "other_restored")
+  z <- mbind(initial, recovered, restored)
+
+  #check
+  indicator <- sum(dimSums(a,dim=3) - dimSums(z,dim=3))
+  if(abs(indicator) > 1e-6) warning("Other land sub-categories don't add-up to total. Check OtherLand.R function")
+
+  if (level != "cell") z <- superAggregate(z, aggr_type = "sum", level = level,na.rm = FALSE)
+
+  return(z)
+}

R/reportLandUse.R

@@ -19,6 +19,9 @@ reportLandUse <- function(gdx) {
   #read in regional data
   a <- land(gdx,level = "reg",types = NULL,subcategories = c("crop","forestry"),sum = FALSE)
   a <- setNames(a,gsub("indc","ndc",getNames(a)))
+  a <- a[,,"other",invert=TRUE]
+  b <- OtherLand(gdx)
+  a <- mbind(b,a)
 
   #add global
   a <- mbind(a, setItems(dimSums(a,dim=1), dim = 1, "GLO"))
@@ -32,7 +35,10 @@ reportLandUse <- function(gdx) {
   x <- mbind(x,setNames(a[,,"crop_treecover"],paste0("Resources|Land Cover|Cropland|+|", reportingnames("crop_treecover")," (million ha)")))
   x <- mbind(x,setNames(a[,,"past"],paste0("Resources|Land Cover|+|", reportingnames("past")," (million ha)")))
   x <- mbind(x,setNames(a[,,"urban"],paste0("Resources|Land Cover|+|", reportingnames("urban")," (million ha)")))
-  x <- mbind(x,setNames(a[,,"other"],paste0("Resources|Land Cover|+|", reportingnames("other")," (million ha)")))
+  x <- mbind(x,setNames(dimSums(a[,,c("other_initial","other_recovered","other_restored")],dim=3),paste0("Resources|Land Cover|+|", reportingnames("other")," (million ha)")))
+  x <- mbind(x,setNames(a[,,"other_initial"],paste0("Resources|Land Cover|", reportingnames("other"),"|Initial (million ha)")))
+  x <- mbind(x,setNames(a[,,"recovered"],paste0("Resources|Land Cover|", reportingnames("other"),"|Recovered (million ha)")))
+  x <- mbind(x,setNames(a[,,"other_restored"],paste0("Resources|Land Cover|", reportingnames("other"),"|Restored (million ha)")))
   x <- mbind(x,setNames(dimSums(a[,,c("primforest","secdforest","forestry_aff","forestry_ndc","forestry_plant")],dim=3),paste0("Resources|Land Cover|+|", reportingnames("forest")," (million ha)")))
   x <- mbind(x,setNames(dimSums(a[,,c("primforest","secdforest")],dim=3),    paste0("Resources|Land Cover|Forest|+|", reportingnames("natrforest")," (million ha)")))
   x <- mbind(x,setNames(dimSums(a[,,"primforest"],dim=3),    paste0("Resources|Land Cover|Forest|Natural Forest|+|", reportingnames("primforest")," (million ha)")))

README.md

@@ -1,6 +1,6 @@
 # MAgPIE outputs R package for MAgPIE version 4.x
 
-R package **magpie4**, version **2.13.10**
+R package **magpie4**, version **2.13.11**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/magpie4)](https://cran.r-project.org/package=magpie4) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1158582.svg)](https://doi.org/10.5281/zenodo.1158582) [![R build status](https://github.com/pik-piam/magpie4/workflows/check/badge.svg)](https://github.com/pik-piam/magpie4/actions) [![codecov](https://codecov.io/gh/pik-piam/magpie4/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/magpie4) [![r-universe](https://pik-piam.r-universe.dev/badges/magpie4)](https://pik-piam.r-universe.dev/builds)
 
@@ -39,7 +39,7 @@ In case of questions / problems please contact Benjamin Leon Bodirsky <bodirsky@
 
 To cite package **magpie4** in publications use:
 
-Bodirsky B, Humpenoeder F, Dietrich J, Stevanovic M, Weindl I, Karstens K, Wang X, Mishra A, Beier F, Breier J, Yalew A, Chen D, Biewald A, Wirth S, von Jeetze P, Leip D, Crawford M, Alves M (2024). _magpie4: MAgPIE outputs R package for MAgPIE version 4.x_. doi:10.5281/zenodo.1158582 <https://doi.org/10.5281/zenodo.1158582>, R package version 2.13.10, <https://github.com/pik-piam/magpie4>.
+Bodirsky B, Humpenoeder F, Dietrich J, Stevanovic M, Weindl I, Karstens K, Wang X, Mishra A, Beier F, Breier J, Yalew A, Chen D, Biewald A, Wirth S, von Jeetze P, Leip D, Crawford M, Alves M (2024). _magpie4: MAgPIE outputs R package for MAgPIE version 4.x_. doi:10.5281/zenodo.1158582 <https://doi.org/10.5281/zenodo.1158582>, R package version 2.13.11, <https://github.com/pik-piam/magpie4>.
 
 A BibTeX entry for LaTeX users is
 
@@ -48,7 +48,7 @@ A BibTeX entry for LaTeX users is
   title = {magpie4: MAgPIE outputs R package for MAgPIE version 4.x},
   author = {Benjamin Leon Bodirsky and Florian Humpenoeder and Jan Philipp Dietrich and Miodrag Stevanovic and Isabelle Weindl and Kristine Karstens and Xiaoxi Wang and Abhijeet Mishra and Felicitas Beier and Jannes Breier and Amsalu Woldie Yalew and David Chen and Anne Biewald and Stephen Wirth and Patrick {von Jeetze} and Debbora Leip and Michael Crawford and Marcos Alves},
   year = {2024},
-  note = {R package version 2.13.10},
+  note = {R package version 2.13.11},
   url = {https://github.com/pik-piam/magpie4},
   doi = {10.5281/zenodo.1158582},
 }