fix units for soil carbon

Author: k4rst3ns

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '4380441'
+ValidationKey: '4574470'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 exclude: '^tests/testthat/_snaps/.*$'
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.5.0
+    rev: 2c9f875913ee60ca25ce70243dc24d5b6415598c  # frozen: v4.6.0
     hooks:
     -   id: check-case-conflict
     -   id: check-json
@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.4.0
+    rev: 7910e0323d7213f34275a7a562b9ef0fde8ce1b9  # frozen: v0.4.2
     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: 'mrsoil: MadRat Soil Organic Carbon Budget Library'
-version: 2.2.1
-date-released: '2024-04-08'
+version: 2.3.0
+date-released: '2024-06-15'
 abstract: This packages provides functions for soil organic carbon budget for mineral
   soils using the steady-state method (Tier 2) of the 2019 Refinement to the 2006
   IPP Guidelines for National Greenhouse Gas Inventories.

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: mrsoil
 Type: Package
 Title: MadRat Soil Organic Carbon Budget Library
-Version: 2.2.1
-Date: 2024-04-08
+Version: 2.3.0
+Date: 2024-06-15
 Authors@R: c(person("Kristine", "Karstens", email = "karstens@pik-potsdam.de", role = c("aut","cre")),
              person("Jan Philipp", "Dietrich", email = "dietrich@pik-potsdam.de", role = "aut"))
 Description: This packages provides functions for soil organic carbon budget for mineral soils using the steady-state method (Tier 2) of the 2019 Refinement to the 2006 IPP Guidelines for National Greenhouse Gas Inventories.
@@ -11,9 +11,11 @@ Depends:
     magclass(>= 5.15.4),
     madrat(>= 1.86.0),
     mrcommons(>= 0.11.9),
+    mrlandcore (>= 1.0.0),
     mrdrivers(>= 1.0.0)
 Imports:
     magpiesets,
+    mstools (>= 0.6.0),
     readxl,
     lpjclass,
     utils,

NAMESPACE

@@ -6,6 +6,7 @@ import(madrat)
 import(magclass)
 import(mrcommons)
 import(mrdrivers)
+import(mrlandcore)
 importFrom(jsonlite,fromJSON)
 importFrom(lpjclass,read.LPJ_input)
 importFrom(madrat,toolSubtypeSelect)
@@ -15,6 +16,9 @@ importFrom(magclass,dimCode)
 importFrom(magclass,setNames)
 importFrom(magpiesets,addLocation)
 importFrom(magpiesets,findset)
+importFrom(mstools,toolGetMappingCoord2Country)
+importFrom(mstools,toolHarmonize2Baseline)
+importFrom(mstools,toolSmooth)
 importFrom(readxl,read_excel)
 importFrom(stats,quantile)
 importFrom(utils,download.file)

R/calcDecayFuture.R

@@ -22,6 +22,7 @@
 #'
 #' @import madrat
 #' @import magclass
+#' @importFrom mstools toolSmooth toolHarmonize2Baseline
 
 calcDecayFuture <- function(lpjmlNatveg = "LPJmL4_for_MAgPIE_44ac93de",
                             climatetype = "GSWP3-W5E5:historical") {

R/calcSoilCarbon.R

@@ -4,7 +4,7 @@
 #' @return magpie object in cellular resolution
 #' @author Kristine Karstens
 #'
-#' @param output "actualstate" (default), "carbontransfer", "interstate", "naturalstate"
+#' @param output "all" (default), "actualstate", "carbontransfer", "interstate", "naturalstate"
 #' @param lpjmlNatveg Switch between LPJmL natveg versionstop
 #' @param climatetype Switch between different climate scenarios
 #'
@@ -15,36 +15,55 @@
 #' @importFrom magclass setNames
 #' @importFrom magpiesets findset
 
-calcSoilCarbon <- function(output      = "actualstate",
+calcSoilCarbon <- function(output      = "all",
                            lpjmlNatveg = "LPJmL4_for_MAgPIE_44ac93de",
                            climatetype = "GSWP3-W5E5:historical") {
-  #######################
-  ### Load Data & Ini ###
-  #######################
-
-  # Load Landuse data
-  landuse               <- calcOutput("Landuse", aggregate = FALSE)
-  soilCarbonSteadyState <- calcOutput("SteadyState", lpjmlNatveg = lpjmlNatveg,
-                                      climatetype = climatetype, aggregate = FALSE)
-  decay                 <- calcOutput("DecayRaw",    lpjmlNatveg = lpjmlNatveg,
-                                      climatetype = climatetype, aggregate = FALSE)
-  soilCarbonInit        <- calcOutput("SoilCarbonSpinup", aggregate = FALSE)
-
-  ######################
-  ### Carbon Cycling ###
-  ######################
-
-  out <- toolSoilCarbonCycling(soilCarbonInit,
-                               soilCarbonSteadyState,
-                               decay,
-                               landuse)[, , output]
-
-  getSets(out, fulldim = FALSE)[1] <- "x.y.iso"
-  out <- collapseDim(out)
+
+  if (output ==  "all") {
+    #######################
+    ### Load Data & Ini ###
+    #######################
+
+    # Load Landuse data
+    landuse               <- calcOutput("Landuse", aggregate = FALSE)
+    soilCarbonSteadyState <- calcOutput("SteadyState", lpjmlNatveg = lpjmlNatveg,
+                                        climatetype = climatetype, aggregate = FALSE)
+    decay                 <- calcOutput("DecayRaw",    lpjmlNatveg = lpjmlNatveg,
+                                        climatetype = climatetype, aggregate = FALSE)
+    soilCarbonInit        <- calcOutput("SoilCarbonSpinup", aggregate = FALSE)
+
+    ######################
+    ### Carbon Cycling ###
+    ######################
+
+    out <- toolSoilCarbonCycling(soilCarbonInit,
+                                 soilCarbonSteadyState,
+                                 decay,
+                                 landuse)
+
+
+    getSets(out, fulldim = FALSE)[1] <- "x.y.iso"
+    out <- collapseDim(out)
+
+  } else if (output %in% c("actualstate", "interstate", "naturalstate")) {
+
+    out      <- calcOutput("SoilCarbon", aggregate = FALSE, output = "all",
+                           lpjmlNatveg = lpjmlNatveg, climatetype = climatetype)[, , "output"]
+    landuse  <- calcOutput("Landuse", aggregate = FALSE)[, getYears(out), ]
+    out      <- out * landuse
+
+  } else if (output == "carbontransfer") {
+
+    out <- calcOutput("SoilCarbon", aggregate = FALSE, output = "all",
+                      lpjmlNatveg = lpjmlNatveg, climatetype = climatetype)[, , "output"]
+
+  } else {
+    stop("'output' unknown.")
+  }
 
   return(list(x            = out,
               weight       = NULL,
-              unit         = "Mt C",
+              unit         = ifelse(output == "all", "tC per ha", "Mt C"),
               description  = "Carbon budget on croplands for historical period",
               isocountries = FALSE)
   )

R/calcSoilCarbonSpinup.R

@@ -56,7 +56,7 @@ calcSoilCarbonSpinup <- function(lpjmlNatveg = "LPJmL4_for_MAgPIE_44ac93de",
 
   return(list(x            = soilCarbonInit,
               weight       = NULL,
-              unit         = "Mt C",
+              unit         = "tC per ha",
               min          = 0,
               description  = "Soil carbon stocks on croplands for starting of the modelling period",
               isocountries = FALSE)

R/calcWaterEffectDecomposition.R

@@ -19,6 +19,7 @@
 #' }
 #'
 #' @importFrom magpiesets findset
+#' @importFrom mstools toolGetMappingCoord2Country
 
 calcWaterEffectDecomposition <- function(irrigation  = "mixedirrig",
                                          lpjmlNatveg = "LPJmL4_for_MAgPIE_44ac93de",

R/correctPorwolliksGriddedTillage.R

@@ -4,7 +4,7 @@
 #' @return List of magpie objects with results on cellular level, weight, unit and description.
 #' @author Kristine Karstens
 #' @seealso
-#' \code{\link[mrcommons]{readLPJmL}},
+#' \code{\link[mrlandcore]{readLPJmL_new}},
 #' \code{\link[lpjclass]{read.LPJ_input}}
 #' @examples
 #' \dontrun{

R/imports.R

@@ -1,4 +1,4 @@
 # Generated by lucode2: do not edit by hand
 
-#' @import magclass madrat mrcommons mrdrivers
+#' @import magclass madrat mrcommons mrlandcore mrdrivers
 NULL

R/readPorwolliksGriddedTillage.R

@@ -3,7 +3,7 @@
 #' @return List of magpie objects with results on cellular level, weight, unit and description.
 #' @author Kristine Karstens
 #' @seealso
-#' \code{\link[mrcommons]{readLPJmL}},
+#' \code{\link[mrlandcore]{readLPJmL_new}},
 #' \code{\link[lpjclass]{read.LPJ_input}}
 #' @examples
 #' \dontrun{

R/toolSoilCarbonCycling.R

@@ -29,10 +29,12 @@ toolSoilCarbonCycling <- function(soilCarbonInit, soilCarbonSteadyState, decay,
   # cut decay rates above 1
   decay[decay > 1]        <- 1
 
-  # Initialize outputs
+  # Initialize outputs (by binding 0. year with an object that runs over the full period of years.
+  # steadystate is here just a place holder for structure, so teh values are set to zero)
   soilCarbon             <- mbind(collapseDim(soilCarbonInit[, , "actualstate"],  dim = 3.1), soilCarbonSteadyState)
   soilCarbonNatural      <- mbind(collapseDim(soilCarbonInit[, , "naturalstate"], dim = 3.1), soilCarbonSteadyState)
-  soilCarbon[, years, ]    <- 0
+  soilCarbon[, years, ]           <- 0
+  soilCarbonNatural[, years, ]    <- 0
   soilCarbonTransfer     <- soilCarbonInter   <- soilCarbon
   soilCarbonTransfer[]   <- soilCarbonInter[] <- 0
 
@@ -55,10 +57,13 @@ toolSoilCarbonCycling <- function(soilCarbonInit, soilCarbonSteadyState, decay,
                                     (soilCarbonSteadyState[, t, ] - soilCarbonInter[, t, ]) * decay[, t, ])
 
     # Calculate counterfactual potential natural vegetation stocks
-    soilCarbonNatural[, t, ]  <- (setYears(soilCarbonNatural[, t - 1, ], t) +
-                                    (soilCarbonSteadyState[, t, ] -
-                                       setYears(soilCarbonNatural[, t - 1, ], t)) * decay[, t, ])
-    soilCarbonNatural[, , "crop"]  <- 0
+    n <- "natveg"
+    soilCarbonNatural[, t, n]  <- (setYears(soilCarbonNatural[, t - 1, n], t) +
+                                     (soilCarbonSteadyState[, t, n] -
+                                        setYears(soilCarbonNatural[, t - 1, n], t)) * decay[, t, n])
+    # Set crop values to the natveg values to create an output object
+    # that calculates a full carbon stock of a natveg world, when multiplying with landuse information
+    soilCarbonNatural[, , "crop"]  <- soilCarbonNatural[, , n]
 
     print(t)
   }

README.md

@@ -1,6 +1,6 @@
 # MadRat Soil Organic Carbon Budget Library
 
-R package **mrsoil**, version **2.2.1**
+R package **mrsoil**, version **2.3.0**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/mrsoil)](https://cran.r-project.org/package=mrsoil) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4317933.svg)](https://doi.org/10.5281/zenodo.4317933) [![R build status](https://github.com/pik-piam/mrsoil/workflows/check/badge.svg)](https://github.com/pik-piam/mrsoil/actions) [![codecov](https://codecov.io/gh/pik-piam/mrsoil/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/mrsoil) [![r-universe](https://pik-piam.r-universe.dev/badges/mrsoil)](https://pik-piam.r-universe.dev/builds)
 
@@ -38,7 +38,7 @@ In case of questions / problems please contact Kristine Karstens <karstens@pik-p
 
 To cite package **mrsoil** in publications use:
 
-Karstens K, Dietrich J (2024). _mrsoil: MadRat Soil Organic Carbon Budget Library_. doi:10.5281/zenodo.4317933 <https://doi.org/10.5281/zenodo.4317933>, R package version 2.2.1, <https://github.com/pik-piam/mrsoil>.
+Karstens K, Dietrich J (2024). _mrsoil: MadRat Soil Organic Carbon Budget Library_. doi:10.5281/zenodo.4317933 <https://doi.org/10.5281/zenodo.4317933>, R package version 2.3.0, <https://github.com/pik-piam/mrsoil>.
 
 A BibTeX entry for LaTeX users is
 
@@ -47,7 +47,7 @@ A BibTeX entry for LaTeX users is
   title = {mrsoil: MadRat Soil Organic Carbon Budget Library},
   author = {Kristine Karstens and Jan Philipp Dietrich},
   year = {2024},
-  note = {R package version 2.2.1},
+  note = {R package version 2.3.0},
   doi = {10.5281/zenodo.4317933},
   url = {https://github.com/pik-piam/mrsoil},
 }