caviddhen · caviddhen · Aug 12, 2025 · Jul 11, 2025 · Jul 16, 2025 · Jul 16, 2025
diff --git a/.buildlibrary b/.buildlibrary
@@ -1,4 +1,4 @@
-ValidationKey: '528165690'
+ValidationKey: '530787363'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package .* was built under R version'

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
@@ -4,11 +4,13 @@ on:
   push:
     branches: [main, master]
   pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
     branches: [main, master]
 
 jobs:
   check:
     runs-on: ubuntu-latest
+    if: github.event.pull_request.draft == false
 
     steps:
       - uses: actions/checkout@v4

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: 'mrvalidation: madrat data preparation for validation purposes'
-version: 2.61.30
-date-released: '2025-05-05'
+version: 2.61.33
+date-released: '2025-08-11'
 abstract: Package contains routines to prepare data for validation exercises.
 authors:
 - family-names: Bodirsky

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: mrvalidation
 Title: madrat data preparation for validation purposes
-Version: 2.61.30
-Date: 2025-05-05
+Version: 2.61.33
+Date: 2025-08-11
 Authors@R: c(
     person("Benjamin Leon", "Bodirsky", , "[email protected]", role = c("aut", "cre")),
     person("Stephen", "Wirth", role = "aut"),

diff --git a/NAMESPACE b/NAMESPACE
@@ -109,7 +109,6 @@ importFrom(tidyr,drop_na)
 importFrom(tidyr,expand_grid)
 importFrom(tidyr,nest)
 importFrom(tidyr,pivot_longer)
-importFrom(tidyr,pivot_wider)
 importFrom(tidyr,unnest)
 importFrom(tools,file_path_sans_ext)
 importFrom(utils,download.file)

diff --git a/R/calcNitrogenSurplusByCrop.R b/R/calcNitrogenSurplusByCrop.R
@@ -7,7 +7,7 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Benjamin Leon Bodirsky
 #' @seealso
-#' \code{\link{calcNitrogenBudgetCropland}}
+#' \code{\link[mrcommons]{calcNitrogenBudgetCropland}}
 #' @examples
 #' 
 #' \dontrun{ 

diff --git a/R/calcValidDemand.R b/R/calcValidDemand.R
@@ -9,7 +9,7 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Benjamin Leon Bodirsky, Isabelle Weindl
 #' @seealso
-#' \code{\link{calcFoodSupplyPast}},
+#' \code{\link[mrcommons]{calcFoodSupplyPast}},
 #' \code{\link{calcValidLivestockShare}}
 #' @examples
 #'

diff --git a/R/calcValidFeed.R b/R/calcValidFeed.R
@@ -8,8 +8,8 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Benjamin Leon Bodirsky
 #' @seealso
-#' \code{\link{calcFoodSupplyPast}},
-#' \code{\link{calcValidLivestockShare}}
+#' \code{\link[mrcommons]{calcFoodSupplyPast}},
+#' \code{\link[mrvalidation]{calcValidLivestockShare}}
 #' @examples
 #' \dontrun{
 #' calcOutput("ValidFeed")

diff --git a/R/calcValidFeedConversion.R b/R/calcValidFeedConversion.R
@@ -9,7 +9,7 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Benjamin Leon Bodirsky, github Copilot
 #' @seealso
-#' \code{\link{calcFoodSupplyPast}},
+#' \code{\link[mrcommons]{calcFoodSupplyPast}},
 #' \code{\link{calcValidLivestockShare}}
 #' @examples
 #' \dontrun{

diff --git a/R/calcValidGrassLSUha.R b/R/calcValidGrassLSUha.R
@@ -4,7 +4,7 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Marcos Alves
 #' @seealso
-#' \code{\link{calcFAOmassbalance}},
+#' \code{\link[mrcommons]{calcFAOmassbalance}},
 #' @examples
 #' \dontrun{
 #' calcOutput("ValidGrassLSUha")

diff --git a/R/calcValidGrassSoilCarbon.R b/R/calcValidGrassSoilCarbon.R
diff --git a/R/calcValidKcal.R b/R/calcValidKcal.R
@@ -10,7 +10,7 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Benjamin Leon Bodirsky, Kristine Karstens
 #' @seealso
-#' \code{\link{calcFoodSupplyPast}},
+#' \code{\link[mrcommons]{calcFoodSupplyPast}},
 #' \code{\link{calcValidLivestockShare}}
 #' @examples
 #' \dontrun{

diff --git a/R/calcValidLivestockDemStructure.R b/R/calcValidLivestockDemStructure.R
@@ -6,7 +6,7 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Isabelle Weindl
 #' @seealso
-#' \code{\link{calcFoodSupplyPast}},
+#' \code{\link[mrcommons]{calcFoodSupplyPast}},
 #' \code{\link{calcValidLivestockShare}}
 #' @examples
 #'

diff --git a/R/calcValidLivestockShare.R b/R/calcValidLivestockShare.R
@@ -6,7 +6,7 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Benjamin Leon Bodirsky
 #' @seealso
-#' \code{\link{calcFoodSupplyPast}},
+#' \code{\link[mrcommons]{calcFoodSupplyPast}},
 #' \code{\link{calcValidKcal}}
 #' @examples
 #'

diff --git a/R/calcValidManure.R b/R/calcValidManure.R
@@ -6,8 +6,8 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Benjamin Leon Bodirsky
 #' @seealso
-#' \code{\link{calcExcretion}},
-#' \code{\link{calcExcretionIPCC}}
+#' \code{\link[mrcommons]{calcExcretion}},
+#' \code{\link[mrcommons]{calcExcretionIPCC}}
 #' @examples
 #'
 #' \dontrun{

diff --git a/R/calcValidNitrogenBudgetCropland.R b/R/calcValidNitrogenBudgetCropland.R
@@ -11,7 +11,7 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Benjamin Leon Bodirsky
 #' @seealso
-#' \code{\link{calcNitrogenBudgetCropland}}
+#' \code{\link[mrcommons]{calcNitrogenBudgetCropland}}
 #' @examples
 #' \dontrun{
 #' calcOutput("ValidNitrogenBudgetCropland")

diff --git a/R/calcValidNitrogenBudgetPasture.R b/R/calcValidNitrogenBudgetPasture.R
@@ -10,7 +10,7 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Benjamin Leon Bodirsky
 #' @seealso
-#' \code{\link{calcNitrogenBudgetCropland}}
+#' \code{\link[mrcommons]{calcNitrogenBudgetCropland}}
 #' @examples
 #' 
 #' \dontrun{ 

diff --git a/R/calcValidPriceAgriculture.R b/R/calcValidPriceAgriculture.R
@@ -8,7 +8,7 @@
 #' @return List with a magpie object with commodity prices on global and country level.
 #' @author Mishko Stevanovic
 #' @seealso
-#' \code{\link{readIMPACT3.2.2World_Price}}
+#' \code{\link[mrcommons]{readIMPACT3.2.2World_Price}}
 #' @examples
 #' 
 #' \dontrun{ 

diff --git a/R/calcValidProcessing.R b/R/calcValidProcessing.R
@@ -9,7 +9,7 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author David Chen, Benjamin Leon Bodirsky
 #' @seealso
-#' \code{\link{calcFoodSupplyPast}},
+#' \code{\link[mrcommons]{calcFoodSupplyPast}},
 #' \code{\link{calcValidLivestockShare}}
 #' @examples
 #' \dontrun{

diff --git a/R/calcValidProduction.R b/R/calcValidProduction.R
@@ -8,7 +8,7 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Benjamin Leon Bodirsky
 #' @seealso
-#' \code{\link{calcFAOmassbalance}},
+#' \code{\link[mrcommons]{calcFAOmassbalance}},
 #' \code{\link{calcValidDemand}}
 #' @examples
 #' \dontrun{

diff --git a/R/calcValidSOCDensity.R b/R/calcValidSOCDensity.R
@@ -6,7 +6,7 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Kristine Karstens
 #' @seealso
-#' \code{\link{calcSOM}}
+#' \code{\link[mrcommons]{calcSOM}}
 #' \code{\link{calcValidSOCStocks}}
 #' @examples
 #' \dontrun{

diff --git a/R/calcValidSOCStocks.R b/R/calcValidSOCStocks.R
@@ -7,7 +7,7 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Benjamin Leon Bodirsky, Kristine Karstens
 #' @seealso
-#' \code{\link{calcFoodSupplyPast}},
+#' \code{\link[mrcommons]{calcFoodSupplyPast}},
 #' \code{\link{calcValidLivestockShare}}
 #' @examples
 #' \dontrun{

diff --git a/R/calcValidSSPResults.R b/R/calcValidSSPResults.R
@@ -5,7 +5,7 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Kristine Karstens
 #' @seealso
-#' \code{\link{convertSSPResults}}
+#' \code{\link[mrcommons]{convertSSPResults}}
 #' @examples
 #' 
 #' \dontrun{ 

diff --git a/R/calcValidSelfsuff.R b/R/calcValidSelfsuff.R
@@ -18,8 +18,7 @@
 calcValidSelfsuff <- function(datasource = "FAO", detail = TRUE) {
 
   if (datasource == "FAO") {
-    kTrade <- findset("k_trade")
-    mb2 <- collapseNames(calcOutput("FAOmassbalance", aggregate = FALSE)[, , kTrade][, , "dm"])
+    mb2 <- collapseNames(calcOutput("FAOmassbalance", aggregate = FALSE)[, , "dm"])
 
     # self sufficiency
     tmp1 <- round(collapseNames(mb2[, , c("production")]), 8)

diff --git a/R/calcValidTrade.R b/R/calcValidTrade.R
@@ -11,7 +11,7 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Benjamin Leon Bodirsky, Xiaoxi Wang, David M Chen
 #' @seealso
-#' \code{\link{calcFAOmassbalance}},
+#' \code{\link[mrcommons]{calcFAOmassbalance}},
 #' \code{\link{calcValidDemand}}
 #' @examples
 #' \dontrun{

diff --git a/R/calcValidVegfruitShare.R b/R/calcValidVegfruitShare.R
@@ -6,7 +6,7 @@
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author Benjamin Leon Bodirsky
 #' @seealso
-#' \code{\link{calcFoodSupplyPast}},
+#' \code{\link[mrcommons]{calcFoodSupplyPast}},
 #' \code{\link{calcValidKcal}}
 #' @examples
 #'

diff --git a/R/calcValidYield.R b/R/calcValidYield.R
@@ -18,8 +18,8 @@
 #'         Max.&Min. values alongwith description.
 #' @author Abhijeet Mishra, Isabelle Weindl, Florian Humpenoeder
 #' @seealso
-#' \code{\link{calcFAOmassbalance}},
-#' \code{\link{calcCroparea}}
+#' \code{\link[mrcommons]{calcFAOmassbalance}},
+#' \code{\link[mrlandcore]{calcCroparea}}
 #'
 #' @examples
 #' \dontrun{

diff --git a/R/convertGMIA.R b/R/convertGMIA.R
@@ -10,7 +10,7 @@
 #' @return Global Map on Irrigation data as MAgPIE object on country level Missing values are added as NA
 #'
 #' @author Stephen Wirth
-#' @seealso \code{\link{readSource}}
+#' @seealso \code{\link[madrat]{readSource}}
 #' @examples
 #' \dontrun{
 #' a <- readSource("GlobalIrrigationMap", "all_data_national")

diff --git a/R/convertGasser.R b/R/convertGasser.R
@@ -8,7 +8,7 @@
 #' @param x MAgPIE object containing Gasser emissions data
 #' @return Historical LUC emission data
 #' @author Abhijeet Mishra
-#' @seealso \code{\link{readSource}}
+#' @seealso \code{\link[madrat]{readSource}}
 #' 
 #' @importFrom madrat toolCountryFill
 

diff --git a/R/convertHID.R b/R/convertHID.R
@@ -9,7 +9,7 @@
 #' @param subtype : No subtype needed
 #' @return Irrigated Area data as MAgPIE object on country level Missing values are added as NA
 #' @author Stephen Wirth
-#' @seealso \code{\link{readSource}}
+#' @seealso \code{\link[madrat]{readSource}}
 #' @importFrom madrat getISOlist
 #' @examples
 #' 

diff --git a/R/convertIMPACTIrrigInvCosts.R b/R/convertIMPACTIrrigInvCosts.R
@@ -10,7 +10,7 @@
 #'
 #' @author Felicitas Beier
 #'
-#' @seealso \code{\link{readSource}}
+#' @seealso \code{\link[madrat]{readSource}}
 #' @examples
 #' \dontrun{
 #' a <- readSource("IMPACTIrrigInvCosts", convert = TRUE)

diff --git a/R/convertPardeyAgRD.R b/R/convertPardeyAgRD.R
@@ -5,7 +5,7 @@
 #' @param x MAgPIE object containing PardeyRD data
 #' @return magpie object containing expenditure in Ag R&D, 2009 USD PPP
 #' @author David Chen
-#' @seealso \code{\link{readSource}}
+#' @seealso \code{\link[madrat]{readSource}}
 #' @examples
 #'
 #' \dontrun{

diff --git a/R/convertWaterUsage.R b/R/convertWaterUsage.R
@@ -6,7 +6,7 @@
 #' @param subtype : No subtype needed
 #' @return Data on water use as MAgPIE object on country level Missing values are added as NA
 #' @author Stephen Wirth
-#' @seealso \code{\link{readSource}}
+#' @seealso \code{\link[madrat]{readSource}}
 #' @examples
 #' \dontrun{
 #' a <- readSource("WaterUsage", "aquastat_2008_12")

diff --git a/R/correctGMIA.R b/R/correctGMIA.R
@@ -9,7 +9,7 @@
 #' @param subtype : subtypes are the same as in readGMIA
 #' @return Global Map on Irrigation data as MAgPIE object at a 0.5 Degree resolution.
 #' @author Stephen Wirth
-#' @seealso \code{\link{readSource}}
+#' @seealso \code{\link[madrat]{readSource}}
 #' @examples
 #' \dontrun{
 #' a <- readSource("IrrigatedArea")

diff --git a/R/correctHID.R b/R/correctHID.R
@@ -9,7 +9,7 @@
 #' @param subtype : subtypes are the same as in readGMIA
 #' @return Global Map on Irrigation data as MAgPIE object at a 0.5 Degree resolution.
 #' @author Stephen Wirth
-#' @seealso \code{\link{readSource}}
+#' @seealso \code{\link[madrat]{readSource}}
 #' @examples
 #' \dontrun{
 #' a <- readSource("IrrigatedArea")

diff --git a/R/fullVALIDATION.R b/R/fullVALIDATION.R
@@ -6,7 +6,7 @@
 #' \code{\link[base]{numeric_version}} when called via \code{\link[madrat]{retrieveData}}.
 #' @author Jan Philipp Dietrich, Benjamin Leon Bodirsky
 #' @seealso
-#' \code{\link{readSource}},\code{\link{getCalculations}},\code{\link{calcOutput}}
+#' \code{\link[madrat]{readSource}},\code{\link[madrat]{getCalculations}},\code{\link[madrat]{calcOutput}}
 #' @examples
 #' \dontrun{
 #' retrieveData("Validation")
@@ -211,10 +211,6 @@ fullVALIDATION <- function(rev = 0.1) {
   # Carbon Stocks
   calcOutput("ValidCarbon", datasource = "LPJmL4_for_MAgPIE_44ac93de:GSWP3-W5E5:historical", aggregate = "REG+GLO",
              file = valfile, append = TRUE, try = TRUE)
-  # calcOutput("ValidGrassSoilCarbon", datasource = "ISIMIP3b:IPSL-CM6A-LR:ssp126:1965-2100", model = "c7491e",
-  #           lpjml = "lpjml5p2_pasture", aggregate = FALSE, file = valfile, append = TRUE, try = TRUE)
-  # Temporaraly swiched off for debugging
-
 
   # Growing Stocks
   calcOutput("ValidGS", datasource = "FAO", aggregate = "REG+GLO", indicator = "relative",