introduce new litter funtion!

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '3946000'
+ValidationKey: '4147920'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

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: 2.0.0
-date-released: '2024-01-08'
+version: 2.1.0
+date-released: '2024-01-30'
 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: 2.0.0
-Date: 2024-01-08
+Version: 2.1.0
+Date: 2024-01-30
 Authors@R: c(person("Kristine", "Karstens", email = "[email protected]", role = c("aut","cre")),
  person("Jan Philipp", "Dietrich", email = "[email protected]", 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.
@@ -23,7 +23,7 @@ URL: https://github.com/pik-piam/mrsoil, https://doi.org/10.5281/zenodo.4317933
 BugReports: https://github.com/pik-piam/mrsoil/issues
 Encoding: UTF-8
 LazyData: no
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Suggests: 
  knitr,
  rmarkdown,

R/calcCarbonInputMultiplier.R

@@ -38,7 +38,7 @@ calcCarbonInputMultiplier <- function() {
  setNames(param[, , generic] / c2dm,
  paste0("generic.", gsub("_dm", "", getNames(param, dim = 2)))))
 
- # calculate carbon input multipliers
+ # calculate carbon input multipliers for crop-related inputs
  out <- toolCarbonInputMultiplier(inputProp = inputProp,
  soilParam = soilParam,
  f4act2slo = f4act2slo,
@@ -48,6 +48,7 @@ calcCarbonInputMultiplier <- function() {
  weight <- mbind(dimSums(weight, dim = 3.1),
  setNames(dimSums(weight, dim = 3), "generic"),
  collapseNames(calcOutput("CarbonManure", aggregate = FALSE)[, "y1995", "c"]))
+ weight <- weight + 10^-10 # important for empty categories such as betr, begr
 
  getSets(out, fulldim = FALSE)[1] <- "x.y.iso"
  getSets(weight, fulldim = FALSE)[1] <- "x.y.iso"
@@ -56,6 +57,6 @@ calcCarbonInputMultiplier <- function() {
  weight = weight,
  unit = "tC per ha",
  description = "Carbon input multiplier in tonnes carbon per hectare/ tonnes carbon per hectare
- to all carbon subpools for different tillage and input types",
+ to all carbon subpools for different tillage and input (manure and residue) types",
  isocountries = FALSE))
 }

R/calcLitterSoilinput.R

@@ -0,0 +1,50 @@
+#' @title calcLitterSoilinput
+#' @description Calculates Carbon Input from litter to the soil pools of the three pool model (Tier 2 IPCC)
+#'
+#' @param lpjmlNatveg Switch between LPJmL natveg versionstop
+#' @param climatetype Switch between different climate scenarios
+#' @param fixFpc if TRUE using fixed (old) fpc data
+#'
+#' @return List of magpie object with results on cellular level, weight on cellular level, unit and description.
+#' @author Kristine Karstens
+#' @examples
+#' \dontrun{
+#' calcOutput("calcLitterSoilinput", aggregate = FALSE)
+#' }
+
+calcLitterSoilinput <- function(lpjmlNatveg = "LPJmL4_for_MAgPIE_44ac93de",
+ climatetype = "GSWP3-W5E5:historical",
+ fixFpc = FALSE) {
+
+ # Load soil parameter collection
+ soilParam <- readSource("IPCCSoil", convert = FALSE)
+ # Load fractional transfer coefficients for active to slow (sand fraction depending)
+ f4act2slo <- calcOutput("TransferActive2Slow", aggregate = FALSE)
+ # Stabilization efficiencies for structural decay products entering the active pool
+ # for natural vegetation is no tillage
+ f2struc2act <- collapseDim(soilParam[, , "f2_nt"])
+
+ litter <- calcOutput("CarbonLitter", lpjmlNatveg = lpjmlNatveg, climatetype = climatetype,
+ mode = "magpieInput", fixFpc = fixFpc, aggregate = FALSE)
+
+ alpha <- dimSums(toolCarbonInputMultiplier(inputProp = litter[, , c("LC", "NC")],
+ soilParam = soilParam,
+ f4act2slo = f4act2slo,
+ f2struc2act = f2struc2act) *
+ collapseDim(litter[, , "c"]), dim = 3.2)
+
+ alpha <- toolConditionalReplace(alpha, conditions = c("is.na()", "<0", "is.infinite()"), replaceby = 0)
+
+ weight <- calcOutput("LanduseInitialisation", aggregate = FALSE, cellular = TRUE, years = "y1995")
+ weight <- collapseDim(dimSums(weight[, , "crop", invert = TRUE], dim = 3))
+
+ getSets(out, fulldim = FALSE)[1] <- "x.y.iso"
+ getSets(weight, fulldim = FALSE)[1] <- "x.y.iso"
+
+ return(list(x = out,
+ weight = weight,
+ unit = "tC per ha",
+ description = paste0("Litter C input to the soil pools of the 3-pool-model for natural vegetation"),
+ min = 0,
+ isocountries = FALSE))
+}

README.md

@@ -1,6 +1,6 @@
 # MadRat Soil Organic Carbon Budget Library
 
-R package **mrsoil**, version **2.0.0**
+R package **mrsoil**, version **2.1.0**
 
 [![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 2.0.0, <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 2.1.0, <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 2.0.0},
+ note = {R package version 2.1.0},
  doi = {10.5281/zenodo.4317933},
  url = {https://github.com/pik-piam/mrsoil},
 }