bugfix init switches

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '222888140'
+ValidationKey: '222907174'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "mrsoil: MadRat Soil Organic Carbon Budget Library",
-  "version": "1.17.10",
+  "version": "1.17.11",
   "description": "<p>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.<\/p>",
   "creators": [
     {

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: mrsoil
 Type: Package
 Title: MadRat Soil Organic Carbon Budget Library
-Version: 1.17.10
+Version: 1.17.11
 Date: 2022-02-11
 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"))

R/calcSoilCarbon.R

@@ -27,20 +27,33 @@ calcSoilCarbon <- function(output="full", cfg=NULL, cfg_default=NULL){
 
   if(cfg$soilinit>1900){
 
-    #change: add natural
     years <- getYears(Landuse, as.integer=TRUE)
     years <- years[years >= cfg$soilinit]
-    SoilCarbonInit        <- mbind(setNames(setYears(SoilCarbonSteadyState[,years[1],"natveg"],years[1]-1),
-                                            paste0("crop.",getNames(SoilCarbonSteadyState[,,"natveg"], dim=2))),
-                                   setYears(SoilCarbonSteadyState[,years[1],"natveg"],years[1]-1))
+
+    names                 <- as.vector(outer(c("actualstate", "naturalstate"),
+                                             getItems(Decay, dim = 3),
+                                             paste, sep = "."))
+
+    SoilCarbonInit        <- new.magpie(getItems(Decay, dim = 1), years[1]-1, names)
+    SoilCarbonInit[, , "actualstate.crop"]    <- SoilCarbonSteadyState[,years[1],"natveg"]
+    SoilCarbonInit[, , "actualstate.natveg"]  <- SoilCarbonSteadyState[,years[1],"natveg"]
+    SoilCarbonInit[, , "naturalstate.crop"]   <- SoilCarbonSteadyState[,years[1],"natveg"]
+    SoilCarbonInit[, , "naturalstate.natveg"] <- SoilCarbonSteadyState[,years[1],"natveg"]
+
     SoilCarbonSteadyState <- SoilCarbonSteadyState[,years,]
     Decay                 <- Decay[,years,]
     Landuse               <- Landuse[,c(years[1]-1,years),]
 
   } else if(cfg$soilinit<1){
 
-    #change: add natural
-    SoilCarbonInit        <- setYears(SoilCarbonSteadyState[,"y1901",],"y1900")
+    names                 <- as.vector(outer(c("actualstate", "naturalstate"),
+                                             getItems(Decay, dim = 3),
+                                             paste, sep = "."))
+
+    SoilCarbonInit        <- new.magpie(getItems(Decay, dim = 1), "y1900", names)
+
+    SoilCarbonInit[, , "actualstate"]    <- SoilCarbonSteadyState[, "y1901", ]
+    SoilCarbonInit[, , "naturalstate"]   <- SoilCarbonSteadyState[, "y1901", ]
 
   } else {
 

README.md

@@ -1,6 +1,6 @@
 # MadRat Soil Organic Carbon Budget Library
 
-R package **mrsoil**, version **1.17.10**
+R package **mrsoil**, version **1.17.11**
 
 [![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/ui#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 (2022). _mrsoil: MadRat Soil Organic Carbon Budget Library_. doi: 10.5281/zenodo.4317933 (URL: https://doi.org/10.5281/zenodo.4317933), R package version 1.17.10, <URL: https://github.com/pik-piam/mrsoil>.
+Karstens K, Dietrich J (2022). _mrsoil: MadRat Soil Organic Carbon Budget Library_. doi: 10.5281/zenodo.4317933 (URL: https://doi.org/10.5281/zenodo.4317933), R package version 1.17.11, <URL: 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 = {2022},
-  note = {R package version 1.17.10},
+  note = {R package version 1.17.11},
   doi = {10.5281/zenodo.4317933},
   url = {https://github.com/pik-piam/mrsoil},
 }