remove filtering rules from calcMulticroppingYieldIncrease and only e…

…xclude zeros for numerical reasons

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '12833461'
+ValidationKey: '12856050'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

.github/workflows/check.yaml

@@ -63,6 +63,6 @@ jobs:
         shell: Rscript {0}
         run: |
           nonDummyTests <- setdiff(list.files("./tests/testthat/"), c("test-dummy.R", "_snaps"))
-          if(length(nonDummyTests) > 0) covr::codecov(quiet = FALSE)
+          if(length(nonDummyTests) > 0 && !lucode2:::loadBuildLibraryConfig()[["skipCoverage"]]) covr::codecov(quiet = FALSE)
         env:
           NOT_CRAN: "true"

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: 'mrland: MadRaT land data package'
-version: 0.64.1
-date-released: '2024-10-25'
+version: 0.64.2
+date-released: '2024-10-29'
 abstract: The package provides land related data via the madrat framework.
 authors:
 - family-names: Dietrich

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: mrland
 Title: MadRaT land data package
-Version: 0.64.1
-Date: 2024-10-25
+Version: 0.64.2
+Date: 2024-10-29
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "[email protected]", role = c("aut", "cre")),
     person("Abhijeet", "Mishra", role = "aut"),

R/calcMulticroppingYieldIncrease.R

@@ -14,10 +14,6 @@
 #' @param fallowFactor  Factor determining yield reduction in off season due to
 #'                      fallow period between harvest of first (main) season and
 #'                      sowing of second (off) season
-#' @param minThreshold  Minimum threshold of grass GPP in crop growing period
-#'                      and crop yield to exclude low yielding cells
-#'                      Unit of the threshold is gC/m^2.
-#'                      Default: 100 gC/m^2
 #'
 #' @return magpie object in cellular resolution
 #' @author Felicitas Beier
@@ -32,22 +28,13 @@
 #'
 
 calcMulticroppingYieldIncrease <- function(selectyears, lpjml, climatetype,
-                                           fallowFactor = 0.75, minThreshold = 100) {
+                                           fallowFactor = 0.75) {
 
   # Function requires lpjml argument in standard format
   if (length(lpjml) == 1) {
     lpjml <- c(natveg = "NULL", crop = lpjml)
   }
 
-  ####################
-  ### Definitions  ###
-  ####################
-  # Transformation factor gC/m^2 -> tDM/ha
-  yieldTransform <- 0.01 / 0.45
-
-  # Minimum threshold in tDM/ha
-  minThreshold   <- minThreshold * yieldTransform
-
   ####################
   ### Read in data ###
   ####################
@@ -80,21 +67,13 @@ calcMulticroppingYieldIncrease <- function(selectyears, lpjml, climatetype,
   ### Calculations ###
   ####################
 
-  # Exclude cells with grass yields (in growing period of crop) below minimum threshold
-  # (Note: for numerical reasons)
-  rule1 <- grassGPPgrper > minThreshold
-
-  # Exclude low yielding cells (minimum crop yield in main season below minimum threshold)
-  # (Note: to account for non-matching growing periods)
-  rule2 <- cropYields > minThreshold
-
   ### Yield Increase Factor  ###
   # Calculate multiple cropping factor based on annual grass GPP and
   # grass GPP in growing period of crop
   grassGPPoffseason <- (grassGPPannual[, , cropIrrigList] - grassGPPgrper[, , cropIrrigList])
   grassGPPoffseason[grassGPPoffseason < 0] <- 0
 
-  increaseFACTOR <- ifelse(rule1 & rule2,
+  increaseFACTOR <- ifelse(grassGPPgrper > 0,
                            grassGPPoffseason / grassGPPgrper,
                            0) * fallowFactor
 
@@ -123,7 +102,7 @@ calcMulticroppingYieldIncrease <- function(selectyears, lpjml, climatetype,
   ##############
   ### Return ###
   ##############
-  unit        <- "unitless"
+  unit        <- "factor"
   description <- paste0("Factor of yield increase through multiple cropping ",
                         "to be applied on LPJmL crop yield")
 

README.md

@@ -1,6 +1,6 @@
 # MadRaT land data package
 
-R package **mrland**, version **0.64.1**
+R package **mrland**, version **0.64.2**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/mrland)](https://cran.r-project.org/package=mrland) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3822083.svg)](https://doi.org/10.5281/zenodo.3822083) [![R build status](https://github.com/pik-piam/mrland/workflows/check/badge.svg)](https://github.com/pik-piam/mrland/actions) [![codecov](https://codecov.io/gh/pik-piam/mrland/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/mrland) [![r-universe](https://pik-piam.r-universe.dev/badges/mrland)](https://pik-piam.r-universe.dev/builds)
 
@@ -39,7 +39,7 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **mrland** in publications use:
 
-Dietrich J, Mishra A, Weindl I, Bodirsky B, Wang X, Baumstark L, Kreidenweis U, Klein D, Steinmetz N, Chen D, Humpenoeder F, von Jeetze P, Wirth S, Beier F, Hoetten D, Sauer P, Tommey J (2024). _mrland: MadRaT land data package_. doi:10.5281/zenodo.3822083 <https://doi.org/10.5281/zenodo.3822083>, R package version 0.64.1, <https://github.com/pik-piam/mrland>.
+Dietrich J, Mishra A, Weindl I, Bodirsky B, Wang X, Baumstark L, Kreidenweis U, Klein D, Steinmetz N, Chen D, Humpenoeder F, von Jeetze P, Wirth S, Beier F, Hoetten D, Sauer P, Tommey J (2024). _mrland: MadRaT land data package_. doi:10.5281/zenodo.3822083 <https://doi.org/10.5281/zenodo.3822083>, R package version 0.64.2, <https://github.com/pik-piam/mrland>.
 
 A BibTeX entry for LaTeX users is
 
@@ -48,7 +48,7 @@ A BibTeX entry for LaTeX users is
   title = {mrland: MadRaT land data package},
   author = {Jan Philipp Dietrich and Abhijeet Mishra and Isabelle Weindl and Benjamin Leon Bodirsky and Xiaoxi Wang and Lavinia Baumstark and Ulrich Kreidenweis and David Klein and Nele Steinmetz and David Chen and Florian Humpenoeder and Patrick {von Jeetze} and Stephen Wirth and Felicitas Beier and David Hoetten and Pascal Sauer and Jake Tommey},
   year = {2024},
-  note = {R package version 0.64.1},
+  note = {R package version 0.64.2},
   url = {https://github.com/pik-piam/mrland},
   doi = {10.5281/zenodo.3822083},
 }