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bugfix forestry yields
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‎.buildlibrary

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ValidationKey: '2391914430'
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ValidationKey: '2392175504'
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AutocreateReadme: yes
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AcceptedWarnings:
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- 'Warning: package ''.*'' was built under R version'

‎CITATION.cff

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message: If you use this software, please cite it using the metadata from this file.
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type: software
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title: 'magpie4: MAgPIE outputs R package for MAgPIE version 4.x'
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version: 1.206.21
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date-released: '2024-04-17'
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version: 1.206.22
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date-released: '2024-04-19'
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abstract: Common output routines for extracting results from the MAgPIE framework
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(versions 4.x).
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authors:

‎DESCRIPTION

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Type: Package
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Package: magpie4
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Title: MAgPIE outputs R package for MAgPIE version 4.x
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Version: 1.206.21
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Date: 2024-04-17
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Version: 1.206.22
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Date: 2024-04-19
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Authors@R: c(
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person("Benjamin Leon", "Bodirsky", , "[email protected]", role = c("aut", "cre")),
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person("Florian", "Humpenoeder", , "[email protected]", role = "aut"),

‎R/ForestYield.R

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#' @title ForestYield
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#' @description reads timber yield out of a MAgPIE gdx file
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#'
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#' @description calculates timber yield out of a MAgPIE gdx file
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#'
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#' @export
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#'
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#' @param gdx GDX file
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#' @param file a file name the output should be written to using write.magpie
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#' @param level Level of regional aggregation; "cell", "reg" (regional), "glo" (global), "regglo" (regional and global) or any secdforest aggregation level defined in superAggregate
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#' @details Forest yield for timber production
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#' @return Forest yield for timber production
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#' @author Abhijeet Mishra
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#' @return Forest yield for timber production in tDM per ha per year
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#' @author Abhijeet Mishra, Florian Humpenoeder
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#' @importFrom gdx readGDX out
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#' @importFrom magclass clean_magpie dimSums collapseNames setYears write.magpie
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#' @importFrom luscale superAggregate
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#' @examples
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#'
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#'
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#' \dontrun{
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#' x <- ForestYield(gdx)
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#' }
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ForestYield <- function(gdx, file=NULL, level="cell"){
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a <- NULL
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if(as.numeric(readGDX(gdx, "s32_hvarea")) > 0 & as.numeric(readGDX(gdx, "s35_hvarea")) > 0) {
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if (level == "cell") {
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#### Production and harvest area calculations
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ov73_prod_forestry <-dimSums(readGDX(gdx,"ov_prod_forestry","ov73_prod_forestry",select = list(type="level")),dim=3)
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ov73_hvarea_forestry <- dimSums(readGDX(gdx,"ov32_hvarea_forestry","ov73_hvarea_forestry","ov_hvarea_forestry",react = "silent",select = list(type="level")),dim=3)
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ov73_prod_natveg_secdf <- dimSums(readGDX(gdx,"ov_prod_natveg","ov73_prod_natveg",select = list(type="level"))[,,"secdforest"],dim=3)
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ov_hvarea_secdf <- dimSums(readGDX(gdx,"ov35_hvarea_secdforest","ov_hvarea_secdforest",select = list(type="level")),dim=3)
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ov73_prod_natveg_primf <- dimSums(readGDX(gdx,"ov_prod_natveg","ov73_prod_natveg",select = list(type="level"))[,,"primforest"],dim=3)
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ov_hvarea_primf <- dimSums(readGDX(gdx,"ov35_hvarea_primforest","ov_hvarea_primforest",select = list(type="level")),dim=3)
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ov73_prod_natveg_other <- dimSums(readGDX(gdx,"ov_prod_natveg","ov73_prod_natveg",select = list(type="level"))[,,"other"],dim=3)
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ov_hvarea_other <- dimSums(readGDX(gdx,"ov35_hvarea_other","ov73_hvarea_other","ov_hvarea_other",react = "silent",select = list(type="level")),dim=3)
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#### Yield calculations
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## Plantations
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yield_forestry <- ov73_prod_forestry/ov73_hvarea_forestry
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if(any(is.na(range(yield_forestry)))){
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yield_forestry[is.na(yield_forestry)] <- 0
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}
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if(any(is.infinite(range(yield_forestry)))){
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div0 <- where(ov73_prod_forestry != 0 & ov73_hvarea_forestry == 0)$true$regions
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yield_forestry[is.infinite(yield_forestry)] <- 0
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}
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## Secondary forest
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yield_secdf <- ov73_prod_natveg_secdf/ov_hvarea_secdf
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if(any(is.na(range(yield_secdf)))){
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yield_secdf[is.na(yield_secdf)] <- 0
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}
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if(any(is.infinite(range(yield_secdf)))){
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div0 <- where(ov73_prod_natveg_secdf != 0 & ov_hvarea_secdf == 0)$true$regions
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yield_secdf[is.infinite(yield_secdf)] <- 0
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}
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## Primary forest
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yield_primf <- ov73_prod_natveg_primf/ov_hvarea_primf
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if(any(is.na(range(yield_primf)))){
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yield_primf[is.na(yield_primf)] <- 0
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}
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if(any(is.infinite(range(yield_primf)))){
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div0 <- where(ov73_prod_natveg_primf != 0 & ov_hvarea_primf == 0)$true$regions
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yield_primf[is.infinite(yield_primf)] <- 0
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}
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## Other land
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yield_other <- ov73_prod_natveg_other/ov_hvarea_other
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if(any(is.na(range(yield_other)))){
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yield_other[is.na(yield_other)] <- 0
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}
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if(any(is.infinite(range(yield_other)))){
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div0 <- where(ov73_prod_natveg_other != 0 & ov_hvarea_other == 0)$true$regions
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yield_other[is.infinite(yield_other)] <- 0
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}
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a <- mbind(setNames(yield_forestry,"Forestry"),
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setNames(yield_secdf,"Secondary forest"),
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setNames(yield_primf,"Primary forest"),
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setNames(yield_other,"Other land"))
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} else if (level == "regglo" | level == "reg"){
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#### Production and harvest area calculations
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ov73_prod_forestry <- dimSums(readGDX(gdx,"ov_prod_forestry","ov73_prod_forestry",select = list(type="level")),dim=3)
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ov73_prod_forestry <- superAggregate(data = ov73_prod_forestry,aggr_type = "sum",level = level)
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ov73_hvarea_forestry <- dimSums(readGDX(gdx,"ov32_hvarea_forestry","ov73_hvarea_forestry","ov_hvarea_forestry",react = "silent",select = list(type="level")),dim=3)
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ov73_hvarea_forestry <- superAggregate(data = ov73_hvarea_forestry ,aggr_type = "sum",level = level)
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ov73_prod_natveg_secdf <- dimSums(readGDX(gdx,"ov_prod_natveg","ov73_prod_natveg",select = list(type="level"))[,,"secdforest"],dim=3)
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ov73_prod_natveg_secdf <- superAggregate(data = ov73_prod_natveg_secdf,aggr_type = "sum",level = level)
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ov_hvarea_secdf <- dimSums(readGDX(gdx,"ov35_hvarea_secdforest","ov_hvarea_secdforest",select = list(type="level")),dim=3)
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ov_hvarea_secdf <- superAggregate(data = ov_hvarea_secdf ,aggr_type = "sum",level = level)
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ov73_prod_natveg_primf <- dimSums(readGDX(gdx,"ov_prod_natveg","ov73_prod_natveg",select = list(type="level"))[,,"primforest"],dim=3)
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ov73_prod_natveg_primf <- superAggregate(data = ov73_prod_natveg_primf,aggr_type = "sum",level = level)
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ov_hvarea_primf <- dimSums(readGDX(gdx,"ov35_hvarea_primforest","ov_hvarea_primforest",select = list(type="level")),dim=3)
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ov_hvarea_primf <- superAggregate(data = ov_hvarea_primf ,aggr_type = "sum",level = level)
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ov73_prod_natveg_other <- dimSums(readGDX(gdx,"ov_prod_natveg","ov73_prod_natveg",select = list(type="level"))[,,"other"],dim=3)
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ov73_prod_natveg_other <- superAggregate(data = ov73_prod_natveg_other,aggr_type = "sum",level = level)
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ov_hvarea_other <- dimSums(readGDX(gdx,"ov35_hvarea_other","ov73_hvarea_other","ov_hvarea_other",react = "silent",select = list(type="level")),dim=3)
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ov_hvarea_other <- superAggregate(data = ov_hvarea_other ,aggr_type = "sum",level = level)
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#### Yield calculations
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## Plantations
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yield_forestry <- ov73_prod_forestry/ov73_hvarea_forestry
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if(any(is.na(range(yield_forestry)))){
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yield_forestry[is.na(yield_forestry)] <- 0
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}
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if(any(is.infinite(range(yield_forestry)))){
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div0 <- where(ov73_prod_forestry != 0 & ov73_hvarea_forestry == 0)$true$regions
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yield_forestry[is.infinite(yield_forestry)] <- 0
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}
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## Secondary forest
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yield_secdf <- ov73_prod_natveg_secdf/ov_hvarea_secdf
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if(any(is.na(range(yield_secdf)))){
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yield_secdf[is.na(yield_secdf)] <- 0
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}
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if(any(is.infinite(range(yield_secdf)))){
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div0 <- where(ov73_prod_natveg_secdf != 0 & ov_hvarea_secdf == 0)$true$regions
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yield_secdf[is.infinite(yield_secdf)] <- 0
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}
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## Primary forest
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yield_primf <- ov73_prod_natveg_primf/ov_hvarea_primf
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if(any(is.na(range(yield_primf)))){
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yield_primf[is.na(yield_primf)] <- 0
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}
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if(any(is.infinite(range(yield_primf)))){
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div0 <- where(ov73_prod_natveg_primf != 0 & ov_hvarea_primf == 0)$true$regions
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yield_primf[is.infinite(yield_primf)] <- 0
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}
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## Other land
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yield_other <- ov73_prod_natveg_other/ov_hvarea_other
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if(any(is.na(range(yield_other)))){
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yield_other[is.na(yield_other)] <- 0
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}
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if(any(is.infinite(range(yield_other)))){
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div0 <- where(ov73_prod_natveg_other != 0 & ov_hvarea_other == 0)$true$regions
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yield_other[is.infinite(yield_other)] <- 0
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}
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a <- mbind(setNames(yield_forestry,"Forestry"),
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setNames(yield_secdf,"Secondary forest"),
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setNames(yield_primf,"Primary forest"),
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setNames(yield_other,"Other land"))
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} else {stop("Resolution not recognized. Select cell or reg or regglo as level. NULL returned.")}
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#### get annual production and annual harvested area
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ov73_prod_forestry <- setNames(dimSums(readGDX(gdx,"ov_prod_forestry","ov73_prod_forestry",select = list(type="level")),dim=3), "Forestry")
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ov73_prod_natveg <- dimSums(readGDX(gdx,"ov_prod_natveg","ov73_prod_natveg",select = list(type="level")),dim="kforestry")
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ov73_prod_natveg <- setNames(ov73_prod_natveg,c("Primary forest","Secondary forest","Other land"))
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ov73_prod <- mbind(ov73_prod_forestry, ov73_prod_natveg)
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ov73_prod <- gdxAggregate(gdx, ov73_prod, to = level)
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ov73_hvarea <- harvested_area_timber(gdx, level = level)
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#### Yield calculations
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yield <- ov73_prod / ov73_hvarea
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if(any(is.na(range(yield)))){
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yield[is.na(yield)] <- 0
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}
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if(any(is.infinite(range(yield)))){
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div0 <- where(ov73_prod != 0 & ov73_hvarea == 0)$true$regions
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yield[is.infinite(yield)] <- 0
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}
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a <- yield
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} else {message("Disabled (no dynamic forestry) ", appendLF = FALSE)}
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out(a,file)
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}
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}

‎README.md

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# MAgPIE outputs R package for MAgPIE version 4.x
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R package **magpie4**, version **1.206.21**
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R package **magpie4**, version **1.206.22**
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[![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)
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@@ -39,7 +39,7 @@ In case of questions / problems please contact Benjamin Leon Bodirsky <bodirsky@
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To cite package **magpie4** in publications use:
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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 1.206.21, <https://github.com/pik-piam/magpie4>.
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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 1.206.22, <https://github.com/pik-piam/magpie4>.
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A BibTeX entry for LaTeX users is
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title = {magpie4: MAgPIE outputs R package for MAgPIE version 4.x},
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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},
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year = {2024},
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note = {R package version 1.206.21},
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note = {R package version 1.206.22},
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doi = {10.5281/zenodo.1158582},
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url = {https://github.com/pik-piam/magpie4},
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}

‎man/ForestYield.Rd

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