From 2f1473a71b6cc7effaa1e9582527009e93dae078 Mon Sep 17 00:00:00 2001 From: Kristine Karstens Date: Fri, 10 Jan 2025 13:35:44 +0100 Subject: [PATCH] bugfix soil carbon layer data --- .buildlibrary | 3 ++- .pre-commit-config.yaml | 4 ++-- CITATION.cff | 4 ++-- DESCRIPTION | 4 ++-- R/calcTopsoilCarbon.R | 7 ++++++- README.md | 11 ++++++----- 6 files changed, 20 insertions(+), 13 deletions(-) diff --git a/.buildlibrary b/.buildlibrary index f08a9ce1..8b62436e 100644 --- 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 index 7ccf77e0..7dcd45b7 100644 --- 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 index 249f1156..ab75fcf3 100644 --- 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 index 2195061a..d823eeba 100644 --- 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", , "karstens@pik-potsdam.de", role = c("aut", "cre")), person("Jan Philipp", "Dietrich", , "dietrich@pik-potsdam.de", role = "aut"), diff --git a/R/calcTopsoilCarbon.R b/R/calcTopsoilCarbon.R index fd9efae9..29370be9 100644 --- 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 index da667c72..29b49c03 100644 --- 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 , R package version 1.53.0, . +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 , Version: 1.53.1, . 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}, } ```