add new SOC function to fullCELLULAR, fix raster import to new roxyge…

…n version
pik-piam · Jan 16, 2024 · 1f7e028 · 1f7e028
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diff --git a/.buildlibrary b/.buildlibrary
@@ -1,4 +1,4 @@
-ValidationKey: '27545872'
+ValidationKey: '27633200'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

diff --git a/CITATION.cff b/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: 'mrmagpie: madrat based MAgPIE Input Data Library'
-version: 1.39.6
-date-released: '2024-01-10'
+version: 1.40.0
+date-released: '2024-01-16'
 abstract: Provides functions for MAgPIE country and cellular input data generation.
 authors:
 - family-names: Karstens

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: mrmagpie
 Title: madrat based MAgPIE Input Data Library
-Version: 1.39.6
-Date: 2024-01-10
+Version: 1.40.0
+Date: 2024-01-16
 Authors@R: c(
     person("Kristine", "Karstens", , "[email protected]", role = c("aut", "cre")),
     person("Jan Philipp", "Dietrich", , "[email protected]", role = "aut"),
@@ -58,4 +58,4 @@ VignetteBuilder:
     knitr
 Encoding: UTF-8
 LazyData: no
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.0
diff --git a/R/calcCollectEnvironmentData_new.R b/R/calcCollectEnvironmentData_new.R
@@ -17,7 +17,7 @@
 #' @import mstools
 #' @importFrom raster rasterFromXYZ
 #' @importFrom raster area
-#' @importFrom raster "crs<-"
+#' @importFrom raster crs<-
 #' @importFrom magpiesets findset
 #'
 
@@ -63,7 +63,7 @@ calcCollectEnvironmentData_new <- function(subtype = "ISIMIP3b:IPSL-CM6A-LR:ssp1
                     subtype = paste(x$version, x$scenario, sep = ":"),
                     co2Evolution = "rising")[, (syear - sar / 2):fyear, ]
   co2 <- toolHoldConstant(co2,  seq((max(getYears(co2, as.integer = TRUE)) + 1), 2150, 5))
-  soil <- calcOutput("SoilCharacteristics", aggregate = FALSE)[, getYears(co2), ]          ### To Do (Alex K., Marcos, Kristine, Feli): adjust to 67k 
+  soil <- calcOutput("SoilCharacteristics", aggregate = FALSE)[, getYears(co2), ]          ### To Do (Alex K., Marcos, Kristine, Feli): adjust to 67k
 
   constants <- mbind(co2, soil)
   constants <- constants[, getYears(variables), ]

diff --git a/R/calcCollectSoilCarbonLSU.R b/R/calcCollectSoilCarbonLSU.R
@@ -17,7 +17,7 @@
 #' @import magclass
 #' @importFrom raster rasterFromXYZ
 #' @importFrom raster area
-#' @importFrom raster "crs<-"
+#' @importFrom raster crs<-
 #' @importFrom tidyr pivot_longer
 #' @importFrom dplyr mutate select
 #'

diff --git a/R/calcCollectSoilCarbonPastr.R b/R/calcCollectSoilCarbonPastr.R
@@ -17,7 +17,7 @@
 #' @import magclass
 #' @importFrom raster rasterFromXYZ
 #' @importFrom raster area
-#' @importFrom raster "crs<-"
+#' @importFrom raster crs<-
 #' @importFrom tidyr pivot_longer
 #' @importFrom dplyr mutate select
 #'

diff --git a/R/calcScaleEnvironmentData_new.R b/R/calcScaleEnvironmentData_new.R
@@ -17,7 +17,7 @@
 #' @import mstools
 #' @importFrom raster rasterFromXYZ
 #' @importFrom raster area
-#' @importFrom raster "crs<-"
+#' @importFrom raster crs<-
 #' @importFrom magpiesets findset
 #' @importFrom stats sd
 #'

diff --git a/R/calcScaledPastSoilCarbon.R b/R/calcScaledPastSoilCarbon.R
@@ -18,7 +18,7 @@
 #' @import magclass
 #' @importFrom raster rasterFromXYZ
 #' @importFrom raster area
-#' @importFrom raster "crs<-"
+#' @importFrom raster crs<-
 #' @importFrom tidyr pivot_longer
 #' @importFrom dplyr mutate select
 #'

diff --git a/R/calcSoilCharacteristics.R b/R/calcSoilCharacteristics.R
@@ -13,7 +13,7 @@
 #' @importFrom raster rasterFromXYZ
 #' @importFrom raster area
 #' @importFrom dplyr left_join
-#' @importFrom raster "crs<-"
+#' @importFrom raster crs<-
 #'
 
 calcSoilCharacteristics <- function() {

diff --git a/R/fullCELLULARMAGPIE.R b/R/fullCELLULARMAGPIE.R
@@ -422,6 +422,22 @@ fullCELLULARMAGPIE <- function(rev = 0.1, dev = "",
   calcOutput("SOCLossShare", aggregate = "cluster", rate = "loss", round = 6, cells = cells,
              file = paste0("cshare_released_", ctype, ".mz"))
 
+  if (dev == "+newSOC") {
+
+    calcOutput("CarbonInputMultiplier", aggregate = "region",
+               round = 6, file = "f59_cinput_multiplier.cs3")
+    calcOutput("CarbonLitter", aggregate = "region", years = lpjYears,
+               lpjmlNatveg = lpjml[["natveg"]], climatetype = climatetype,
+               mode = "magpieInput", fixFpc = TRUE,
+               round = 6, file = "f59_litter_recycling.cs3")
+    calcOutput("DecayFuture", aggregate = "region", years = lpjYears,
+               lpjmlNatveg = lpjml[["natveg"]], climatetype = climatetype,
+               round = 6, file = "f59_topsoilc_decay.cs3")
+    calcOutput("SoilCarbon", aggregate = "region", years = "y1995",
+               lpjmlNatveg = lpjml[["natveg"]], climatetype = climatetype,
+               round = 6, file = "f59_topsoilc_actualstate.cs3")
+  }
+
   ##### AGGREGATION ######
 
   # create info file

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # madrat based MAgPIE Input Data Library
 
-R package **mrmagpie**, version **1.39.6**
+R package **mrmagpie**, version **1.40.0**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/mrmagpie)](https://cran.r-project.org/package=mrmagpie) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4319612.svg)](https://doi.org/10.5281/zenodo.4319612) [![R build status](https://github.com/pik-piam/mrmagpie/workflows/check/badge.svg)](https://github.com/pik-piam/mrmagpie/actions) [![codecov](https://codecov.io/gh/pik-piam/mrmagpie/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/mrmagpie) [![r-universe](https://pik-piam.r-universe.dev/badges/mrmagpie)](https://pik-piam.r-universe.dev/builds)
 
@@ -39,7 +39,7 @@ In case of questions / problems please contact Kristine Karstens <karstens@pik-p
 
 To cite package **mrmagpie** in publications use:
 
-Karstens K, Dietrich J, Chen D, Windisch M, Alves M, Beier F, Köberle A, v. Jeetze P, Mishra A, Humpenoeder F, Sauer P (2024). _mrmagpie: madrat based MAgPIE Input Data Library_. doi: 10.5281/zenodo.4319612 (URL: https://doi.org/10.5281/zenodo.4319612), R package version 1.39.6, <URL: https://github.com/pik-piam/mrmagpie>.
+Karstens K, Dietrich J, Chen D, Windisch M, Alves M, Beier F, Köberle A, v. Jeetze P, Mishra A, Humpenoeder F, Sauer P (2024). _mrmagpie: madrat based MAgPIE Input Data Library_. doi:10.5281/zenodo.4319612 <https://doi.org/10.5281/zenodo.4319612>, R package version 1.40.0, <https://github.com/pik-piam/mrmagpie>.
 
 A BibTeX entry for LaTeX users is
 
@@ -48,7 +48,7 @@ A BibTeX entry for LaTeX users is
   title = {mrmagpie: madrat based MAgPIE Input Data Library},
   author = {Kristine Karstens and Jan Philipp Dietrich and David Chen and Michael Windisch and Marcos Alves and Felicitas Beier and Alexandre Köberle and Patrick {v. Jeetze} and Abhijeet Mishra and Florian Humpenoeder and Pascal Sauer},
   year = {2024},
-  note = {R package version 1.39.6},
+  note = {R package version 1.40.0},
   doi = {10.5281/zenodo.4319612},
   url = {https://github.com/pik-piam/mrmagpie},
 }