add SOC valitation

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '51377672'
+ValidationKey: '51515100'
 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: 'mrvalidation: madrat data preparation for validation purposes'
-version: 2.58.4
-date-released: '2024-06-09'
+version: 2.59.0
+date-released: '2024-06-16'
 abstract: Package contains routines to prepare data for validation exercises.
 authors:
 - family-names: Bodirsky

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: mrvalidation
 Title: madrat data preparation for validation purposes
-Version: 2.58.4
-Date: 2024-06-09
+Version: 2.59.0
+Date: 2024-06-16
 Authors@R: c(
     person("Benjamin Leon", "Bodirsky", , "[email protected]", role = c("aut", "cre")),
     person("Stephen", "Wirth", role = "aut"),

R/calcValidSOCShare.R

@@ -0,0 +1,78 @@
+#' @title calcValidSOCShare
+#' @description calculates the validation data for the soil carbon shares
+#'
+#' @param datasource Datasources only "histSOCbudget"
+#'
+#' @return List of magpie objects with results on country level, weight on country level, unit and description.
+#' @author Kristine Karstens
+#'
+#' @examples
+#' \dontrun{
+#' calcOutput("ValidSOCShare")
+#' }
+#'
+#' @importFrom magclass mbind getYears setYears
+
+calcValidSOCShare <- function(datasource = "histSOCbudget") {
+
+  if (datasource == "histSOCbudget") {
+
+    steadyState  <- calcOutput("SteadyState", aggregate = FALSE)
+    landuse      <- calcOutput("Landuse", aggregate = FALSE)[, getYears(steadyState), ]
+    somStock     <- calcOutput("SoilCarbon", aggregate = FALSE, output = "actualstate")[, getYears(steadyState), ]
+    natStock     <- calcOutput("SoilCarbon", aggregate = FALSE, output = "naturalstate")[, getYears(steadyState), ]
+
+    somStock  <- mstools::toolConv2CountryByCelltype(dimSums(somStock, dim = 3.1), cells = "lpjcell")
+    natStock  <- mstools::toolConv2CountryByCelltype(dimSums(natStock, dim = 3.1), cells = "lpjcell")
+    equStock  <- mstools::toolConv2CountryByCelltype(dimSums(steadyState * landuse, dim = 3.1), cells = "lpjcell")
+    pEquStock <- mstools::toolConv2CountryByCelltype(dimSums(steadyState[, , "natveg"] * landuse,
+                                                             dim = 3.1), cells = "lpjcell")
+    pEquStock <- collapseNames(pEquStock)
+
+    somStock  <- mbind(somStock, add_dimension(dimSums(somStock, dim = 3.1), add = "landuse", nm = "total"))
+    natStock  <- mbind(natStock, add_dimension(dimSums(natStock, dim = 3.1), add = "landuse", nm = "total"))
+    equStock  <- mbind(equStock, add_dimension(dimSums(equStock, dim = 3.1), add = "landuse", nm = "total"))
+    pEquStock <- mbind(pEquStock, add_dimension(dimSums(pEquStock, dim = 3.1), add = "landuse", nm = "total"))
+
+    somShare <- somStock / natStock
+    unit          <- "(tC/tC)"
+    zeroOrderName <- "Resources|Soil Carbon|Actual|Carbon Share|SOC in top 30 cm"
+    out <- mbind(setNames(somShare[, , "total"],  paste0(zeroOrderName, " ", unit)),
+                 setNames(somShare[, , "crop"],   paste0(zeroOrderName, "|+|Cropland Soils ", unit)),
+                 setNames(somShare[, , "natveg"], paste0(zeroOrderName, "|+|Noncropland Soils ", unit)))
+
+    weight <- mbind(setNames(natStock[, , "total"],  paste0(zeroOrderName, " ", unit)),
+                    setNames(natStock[, , "crop"],   paste0(zeroOrderName, "|+|Cropland Soils ", unit)),
+                    setNames(natStock[, , "natveg"], paste0(zeroOrderName, "|+|Noncropland Soils ", unit)))
+
+    zeroOrderName <- "Resources|Soil Carbon|Target|Carbon Share|SOC in top 30 cm"
+    equSomShare   <- equStock / pEquStock
+    out <- mbind(out,
+                 setNames(equSomShare[, , "total"],  paste0(zeroOrderName, " ", unit)),
+                 setNames(equSomShare[, , "crop"],   paste0(zeroOrderName, "|+|Cropland Soils ", unit)),
+                 setNames(equSomShare[, , "natveg"], paste0(zeroOrderName, "|+|Noncropland Soils ", unit)))
+
+    weight <- mbind(weight,
+                    setNames(pEquStock[, , "total"],  paste0(zeroOrderName, " ", unit)),
+                    setNames(pEquStock[, , "crop"],   paste0(zeroOrderName, "|+|Cropland Soils ", unit)),
+                    setNames(pEquStock[, , "natveg"], paste0(zeroOrderName, "|+|Noncropland Soils ", unit)))
+
+    out <- add_dimension(out, dim = 3.1, add = "scenario", nm = "historical")
+    out <- add_dimension(out, dim = 3.2, add = "model", nm = datasource)
+
+    weight <- add_dimension(weight, dim = 3.1, add = "scenario", nm = "historical")
+    weight <- add_dimension(weight, dim = 3.2, add = "model", nm = datasource)
+
+  } else {
+    stop("No data exist for the given datasource!")
+  }
+
+  names(dimnames(out))[3]    <- "scenario.model.variable"
+  names(dimnames(weight))[3] <- "scenario.model.variable"
+
+  return(list(x           = out,
+              weight      = weight,
+              unit        = "tC per tC",
+              description = "Soil Carbon Share")
+  )
+}

R/calcValidSOCStocks.R

@@ -18,9 +18,55 @@
 #' @importFrom magclass mbind getYears setYears nregions
 #' @importFrom mstools toolCoord2Isocell
 
-calcValidSOCStocks <- function(datasource = "LPJ_IPCC2006", baseyear = 1995) {
+calcValidSOCStocks <- function(datasource = "histSOCbudget", baseyear = 1995) {
 
-  if (datasource == "LPJ_IPCC2006") {
+  if (datasource == "histSOCbudget") {
+
+    steadyState  <- calcOutput("SteadyState", aggregate = FALSE)
+    landuse      <- calcOutput("Landuse", aggregate = FALSE)[, getYears(steadyState), ]
+    somStock     <- calcOutput("SoilCarbon", aggregate = FALSE, output = "actualstate")[, getYears(steadyState), ]
+    natStock     <- calcOutput("SoilCarbon", aggregate = FALSE, output = "naturalstate")[, getYears(steadyState), ]
+
+    somStock  <- mstools::toolConv2CountryByCelltype(dimSums(somStock, dim = 3.1), cells = "lpjcell")
+    natStock  <- mstools::toolConv2CountryByCelltype(dimSums(natStock, dim = 3.1), cells = "lpjcell")
+    equStock  <- mstools::toolConv2CountryByCelltype(dimSums(steadyState * landuse, dim = 3.1), cells = "lpjcell")
+
+    somStock  <- mbind(somStock, add_dimension(dimSums(somStock, dim = 3.1), add = "landuse", nm = "total"))
+    natStock  <- mbind(natStock, add_dimension(dimSums(natStock, dim = 3.1), add = "landuse", nm = "total"))
+    equStock  <- mbind(equStock, add_dimension(dimSums(equStock, dim = 3.1), add = "landuse", nm = "total"))
+
+    unit          <- "(Mt C)"
+    zeroOrderName <- "Resources|Soil Carbon|Actual|Stock|SOC in top 30 cm"
+    out <- mbind(setNames(somStock[, , "total"],  paste0(zeroOrderName, " ", unit)),
+                 setNames(somStock[, , "crop"],   paste0(zeroOrderName, "|+|Cropland Soils ", unit)),
+                 setNames(somStock[, , "natveg"], paste0(zeroOrderName, "|+|Noncropland Soils ", unit)))
+
+    zeroOrderName <- "Resources|Soil Carbon|Target|Stock|SOC in top 30 cm"
+    out <- mbind(out,
+                 setNames(equStock[, , "total"],  paste0(zeroOrderName, " ", unit)),
+                 setNames(equStock[, , "crop"],   paste0(zeroOrderName, "|+|Cropland Soils ", unit)),
+                 setNames(equStock[, , "natveg"], paste0(zeroOrderName, "|+|Noncropland Soils ", unit)))
+
+    somChang <- somStock - setYears(somStock[, baseyear, ], NULL)
+    unit     <- paste0("Mt C wrt ", baseyear)
+    zeroOrderName <- "Resources|Soil Carbon|Actual|Stock Change|SOC in top 30 cm"
+    out <- mbind(out,
+                 setNames(somChang[, , "total"],  paste0(zeroOrderName, " ", unit)),
+                 setNames(somChang[, , "crop"],   paste0(zeroOrderName, "|+|Cropland Soils ", unit)),
+                 setNames(somChang[, , "natveg"], paste0(zeroOrderName, "|+|Noncropland Soils ", unit)))
+
+    somDebt <- natStock - somStock
+    unit          <- "(Mt C)"
+    zeroOrderName <- "Resources|Soil Carbon|Actual|Debt|SOC in top 30 cm"
+    out <- mbind(out,
+                 setNames(somDebt[, , "total"],  paste0(zeroOrderName, " ", unit)),
+                 setNames(somDebt[, , "crop"],   paste0(zeroOrderName, "|+|Cropland Soils ", unit)),
+                 setNames(somDebt[, , "natveg"], paste0(zeroOrderName, "|+|Noncropland Soils ", unit)))
+
+    out <- add_dimension(out, dim = 3.1, add = "scenario", nm = "historical")
+    out <- add_dimension(out, dim = 3.2, add = "model", nm = datasource)
+
+  } else if (datasource == "LPJ_IPCC2006") {
 
     mapping    <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell", where = "mappingfolder")
     somStock  <- calcOutput("SOM", subtype = "stock",   aggregate = FALSE)
@@ -51,7 +97,6 @@ calcValidSOCStocks <- function(datasource = "LPJ_IPCC2006", baseyear = 1995) {
                paste0("Resources|Soil Carbon|Actual|Stock Change|",
                       "SOC in top 30 cm|+|Noncropland Soils (Mt C wrt ", baseyear, ")"))
     )
-
     out <- mbind(out,
       setNames(somStock[, , "total"][, , "target_soilc"],
                "Resources|Soil Carbon|Target|Stock|SOC in top 30 cm (Mt C)"),

R/fullVALIDATION.R

@@ -205,6 +205,10 @@ fullVALIDATION <- function(rev = 0.1) {
 
   # Carbon
   calcOutput("ValidResidues", aggregate = "REG+GLO", file = valfile, append = TRUE, try = TRUE)
+  calcOutput("ValidSOCStocks", datasource = "histSOCbudget", aggregate = "REG+GLO",
+             file = valfile, append = TRUE, try = TRUE)
+  calcOutput("ValidSOCShare", datasource = "histSOCbudget", aggregate = "REG+GLO",
+             file = valfile, append = TRUE, try = TRUE)
 
   # Carbon Stocks
   calcOutput("ValidCarbon", datasource = "LPJmL4_for_MAgPIE_44ac93de:GSWP3-W5E5:historical", aggregate = "REG+GLO",

README.md

@@ -1,6 +1,6 @@
 # madrat data preparation for validation purposes
 
-R package **mrvalidation**, version **2.58.4**
+R package **mrvalidation**, version **2.59.0**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/mrvalidation)](https://cran.r-project.org/package=mrvalidation) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4317826.svg)](https://doi.org/10.5281/zenodo.4317826) [![R build status](https://github.com/pik-piam/mrvalidation/workflows/check/badge.svg)](https://github.com/pik-piam/mrvalidation/actions) [![codecov](https://codecov.io/gh/pik-piam/mrvalidation/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/mrvalidation) [![r-universe](https://pik-piam.r-universe.dev/badges/mrvalidation)](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 **mrvalidation** in publications use:
 
-Bodirsky B, Wirth S, Karstens K, Humpenoeder F, Stevanovic M, Mishra A, Biewald A, Weindl I, Beier F, Chen D, Crawford M, Leip D, Molina Bacca E, Kreidenweis U, W. Yalew A, von Jeetze P, Wang X, Dietrich J, Alves M (2024). _mrvalidation: madrat data preparation for validation purposes_. doi:10.5281/zenodo.4317826 <https://doi.org/10.5281/zenodo.4317826>, R package version 2.58.4, <https://github.com/pik-piam/mrvalidation>.
+Bodirsky B, Wirth S, Karstens K, Humpenoeder F, Stevanovic M, Mishra A, Biewald A, Weindl I, Beier F, Chen D, Crawford M, Leip D, Molina Bacca E, Kreidenweis U, W. Yalew A, von Jeetze P, Wang X, Dietrich J, Alves M (2024). _mrvalidation: madrat data preparation for validation purposes_. doi:10.5281/zenodo.4317826 <https://doi.org/10.5281/zenodo.4317826>, R package version 2.59.0, <https://github.com/pik-piam/mrvalidation>.
 
 A BibTeX entry for LaTeX users is
 
@@ -48,7 +48,7 @@ A BibTeX entry for LaTeX users is
   title = {mrvalidation: madrat data preparation for validation purposes},
   author = {Benjamin Leon Bodirsky and Stephen Wirth and Kristine Karstens and Florian Humpenoeder and Mishko Stevanovic and Abhijeet Mishra and Anne Biewald and Isabelle Weindl and Felicitas Beier and David Chen and Michael Crawford and Debbora Leip and Edna {Molina Bacca} and Ulrich Kreidenweis and Amsalu {W. Yalew} and Patrick {von Jeetze} and Xiaoxi Wang and Jan Philipp Dietrich and Marcos Alves},
   year = {2024},
-  note = {R package version 2.58.4},
+  note = {R package version 2.59.0},
   doi = {10.5281/zenodo.4317826},
   url = {https://github.com/pik-piam/mrvalidation},
 }