bugfix soil carbon layer data

pik-piam · Jan 10, 2025 · 2f1473a · 2f1473a
1 parent 206160e
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diff --git a/.buildlibrary b/.buildlibrary
@@ -1,4 +1,4 @@
-ValidationKey: '30673440'
+ValidationKey: '30770038'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package .* was built under R version'
@@ -9,3 +9,4 @@ AcceptedNotes:
 allowLinterWarnings: no
 enforceVersionUpdate: no
 skipCoverage: no
+AutocreateCITATION: yes
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -3,7 +3,7 @@
 exclude: '^tests/testthat/_snaps/.*$'
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: 2c9f875913ee60ca25ce70243dc24d5b6415598c  # frozen: v4.6.0
+    rev: cef0300fd0fc4d2a87a85fa2093c6b283ea36f4b  # frozen: v5.0.0
     hooks:
     -   id: check-case-conflict
     -   id: check-json
@@ -15,7 +15,7 @@ repos:
     -   id: mixed-line-ending
 
 -   repo: https://github.com/lorenzwalthert/precommit
-    rev: bae853d82da476eee0e0a57960ee6b741a3b3fb7  # frozen: v0.4.3
+    rev: 3b70240796cdccbe1474b0176560281aaded97e6  # frozen: v0.4.3.9003
     hooks:
     -   id: parsable-R
     -   id: deps-in-desc

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: 1.53.0
-date-released: '2024-11-21'
+version: 1.53.1
+date-released: '2025-01-10'
 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: 1.53.0
-Date: 2024-11-21
+Version: 1.53.1
+Date: 2025-01-10
 Authors@R: c(
     person("Kristine", "Karstens", , "[email protected]", role = c("aut", "cre")),
     person("Jan Philipp", "Dietrich", , "[email protected]", role = "aut"),

diff --git a/R/calcTopsoilCarbon.R b/R/calcTopsoilCarbon.R
@@ -27,8 +27,13 @@ calcTopsoilCarbon <- function(cells = "lpjcell",
     stage <- "harmonized2020"
   }
 
-  soilcLayerNatveg <- calcOutput("LPJmL_new", version = lpjml["natveg"], climatetype = climatetype,
+  soilcLayerShare  <- calcOutput("LPJmL_new", version = lpjml["natveg"], climatetype = climatetype,
                                  subtype = "soilc_layer", stage = stage, aggregate = FALSE)
+  soilcLayerShare  <- soilcLayerShare / dimSums(soilcLayerShare, dim = 3) # calculating a share per layer
+  soilcLayerShare  <- toolConditionalReplace(soilcLayerShare, conditions = c("is.na()"), replaceby = 0)
+  soilcLayerNatveg <- calcOutput("LPJmL_new", version = lpjml["natveg"], climatetype = climatetype,
+                                 subtype = "soilc", stage = stage, aggregate = FALSE) * soilcLayerShare
+
   topsoilc           <- soilcLayerNatveg[, , 1] + 1 / 3 * soilcLayerNatveg[, , 2]
   getNames(topsoilc) <- "topsoilc"
 

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # madrat based MAgPIE Input Data Library
 
-R package **mrmagpie**, version **1.53.0**
+R package **mrmagpie**, version **1.53.1**
 
 [![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)
 
@@ -39,17 +39,18 @@ 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 <https://doi.org/10.5281/zenodo.4319612>, R package version 1.53.0, <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 (2025). "mrmagpie: madrat based MAgPIE Input Data Library." doi:10.5281/zenodo.4319612 <https://doi.org/10.5281/zenodo.4319612>, Version: 1.53.1, <https://github.com/pik-piam/mrmagpie>.
 
 A BibTeX entry for LaTeX users is
 
  ```latex
-@Manual{,
+@Misc{,
   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 1.53.0},
   doi = {10.5281/zenodo.4319612},
+  date = {2025-01-10},
+  year = {2025},
   url = {https://github.com/pik-piam/mrmagpie},
+  note = {Version: 1.53.1},
 }
 ```