add new subtype specific output option for CarbonInputMultiplier

.buildlibrary

@@ -1,7 +1,8 @@
-ValidationKey: '4207815'
+ValidationKey: '4360620'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'
 AcceptedNotes: unable to verify current time
 AutocreateReadme: yes
 allowLinterWarnings: yes
+enforceVersionUpdate: no

.github/workflows/check.yaml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -23,7 +23,6 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
-            gamstransfer=?ignore
             any::lucode2
             any::covr
             any::madrat
@@ -36,7 +35,7 @@ jobs:
           # gms, goxygen, GDPuc) will usually have an outdated binary version
           # available; by using extra-packages we get the newest version
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3.9
 
@@ -49,6 +48,11 @@ jobs:
         shell: Rscript {0}
         run: lucode2:::validkey(stopIfInvalid = TRUE)
 
+      - name: Verify that lucode2::buildLibrary was successful
+        if: github.event_name == 'pull_request'
+        shell: Rscript {0}
+        run: lucode2:::isVersionUpdated()
+
       - name: Checks
         shell: Rscript {0}
         run: |

.pre-commit-config.yaml

@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: v0.3.2.9025
+    rev: v0.4.0
     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: 2.1.3
-date-released: '2024-02-02'
+version: 2.2.0
+date-released: '2024-04-08'
 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: 2.1.3
-Date: 2024-02-02
+Version: 2.2.0
+Date: 2024-04-08
 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.

R/calcCarbonInputMultiplier.R

@@ -3,6 +3,8 @@
 #'              using the steady-state method (Tier 2) of the 2019 Refinement to the 2006 IPP Guidelines
 #'              for National Greenhouse Gas Inventories
 #'
+#' @param inputType switch between 'kcr' (default), or 'kli', 'generic'
+#'
 #' @return magpie object on choosen resolution
 #' @author Kristine Karstens
 #'
@@ -13,7 +15,7 @@
 #'
 #' @importFrom magpiesets findset
 
-calcCarbonInputMultiplier <- function() {
+calcCarbonInputMultiplier <- function(inputType = "kcr") {
 
   soilParam      <- readSource("IPCCSoil", convert = FALSE)
 
@@ -23,31 +25,44 @@ calcCarbonInputMultiplier <- function() {
   f2struc2act <- setNames(soilParam[, , tillage2param], names(tillage2param))
   f4act2slo   <- calcOutput("TransferActive2Slow", aggregate = FALSE)
 
-  inputProp <- NULL
-  # get lignin to c and nitrogen to c values for all residues classes
-  inputProp   <- mbind(inputProp,
-                       calcOutput("ParamResidues", input = "IPCC+woody", aggregate = FALSE))
-  # get lignin to c and nitrogen to c values for all manure classes
-  inputProp   <- mbind(inputProp,
-                       calcOutput("ParamManure", input = "IPCC", aggregate = FALSE))
-  # get lignin to c and nitrogen to c values for generic input classes
-  param     <- readSource("IPCC", subtype = "residues_table5p5b", convert = FALSE)
-  generic   <- "Generic value for crops not indicated below"
-  c2dm      <- 0.45
-  inputProp <- mbind(inputProp,
-                     setNames(param[, , generic] / c2dm,
-                              paste0("generic.", gsub("_dm", "", getNames(param, dim = 2)))))
+  # get lignin to c and nitrogen to c values for input classes
+  if (inputType == "kcr") {
+    # get lignin to c and nitrogen to c values for crop type residue classes
+    inputProp   <- calcOutput("ParamResidues", input = "IPCC+woody", aggregate = FALSE)
+  } else if (inputType == "kli") {
+    # get lignin to c and nitrogen to c values for all manure classes
+    inputProp   <- calcOutput("ParamManure", input = "IPCC", aggregate = FALSE)
+  } else if (inputType == "generic") {
+    # get lignin to c and nitrogen to c values for generic input classes
+    param     <- readSource("IPCC", subtype = "residues_table5p5b", convert = FALSE)
+    generic   <- "Generic value for crops not indicated below"
+    c2dm      <- 0.45
+    inputProp <- setNames(param[, , generic] / c2dm,
+                          paste0("generic.", gsub("_dm", "", getNames(param, dim = 2))))
+  } else {
+    stop("inputType setting unknown.")
+  }
 
   # calculate carbon input multipliers for crop-related inputs
   out <- toolCarbonInputMultiplier(inputProp   = inputProp,
                                    soilParam   = soilParam,
                                    f4act2slo   = f4act2slo,
                                    f2struc2act = f2struc2act)
 
-  weight <- collapseNames(calcOutput("ResBiomass", cellular = TRUE, aggregate = FALSE)[, "y1995", "c"])
-  weight <- mbind(dimSums(weight, dim = 3.1),
-                  setNames(dimSums(weight, dim = 3), "generic"),
-                  collapseNames(calcOutput("CarbonManure", aggregate = FALSE)[, "y1995", "c"]))
+  # get weights
+  if (inputType %in% c("kcr", "generic")) {
+
+    weight <- collapseNames(calcOutput("ResBiomass", cellular = TRUE, aggregate = FALSE)[, "y1995", "c"])
+    weight <- ifelse(inputType == "kcr",
+                     dimSums(weight, dim = 3.1),                             # for kcr
+                     setNames(dimSums(weight, dim = 3), "generic"))          # for 'generic'
+  } else if (inputType == "kli") {
+
+    weight <- collapseNames(calcOutput("CarbonManure", aggregate = FALSE)[, "y1995", "c"])
+  } else {
+    stop("inputType setting unknown.")
+  }
+
   weight <- weight + 10^-10 # important for empty categories such as betr, begr
 
   getSets(out,    fulldim = FALSE)[1] <- "x.y.iso"
@@ -56,7 +71,7 @@ calcCarbonInputMultiplier <- function() {
   return(list(x            = out,
               weight       = weight,
               unit         = "tC per ha",
-              description  = "Carbon input multiplier in tonnes carbon per hectare/ tonnes carbon per hectare
+              description  = "Carbon input multiplier in tonnes carbon per hectare / tonnes carbon per hectare
                               to all carbon subpools for different tillage and input (manure and residue) types",
               isocountries = FALSE))
 }

R/calcSoilCarbon.R

@@ -40,6 +40,7 @@ calcSoilCarbon <- function(output      = "actualstate",
                                landuse)[, , output]
 
   getSets(out, fulldim = FALSE)[1] <- "x.y.iso"
+  out <- collapseDim(out)
 
   return(list(x            = out,
               weight       = NULL,

README.md

@@ -1,6 +1,6 @@
 # MadRat Soil Organic Carbon Budget Library
 
-R package **mrsoil**, version **2.1.3**
+R package **mrsoil**, version **2.2.0**
 
 [![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 2.1.3, <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 2.2.0, <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 2.1.3},
+  note = {R package version 2.2.0},
   doi = {10.5281/zenodo.4317933},
   url = {https://github.com/pik-piam/mrsoil},
 }