Adjusted the where value in toolGetMapping() (#14)

* Adjusted the where value in toolGetMapping()

* fix where FAOitems_online.rda

* linter

* empty line

---------

Co-authored-by: Baseer Ahmad Baheer <[email protected]>
Co-authored-by: Pascal Führlich <[email protected]>

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '49392085'
+ValidationKey: '49429336'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

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: 2.51.5
-date-released: '2023-10-09'
+version: 2.51.6
+date-released: '2023-10-16'
 abstract: Package contains routines to prepare data for validation exercises.
 authors:
 - family-names: Bodirsky

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: mrvalidation
 Title: madrat data preparation for validation purposes
-Version: 2.51.5
-Date: 2023-10-09
+Version: 2.51.6
+Date: 2023-10-16
 Authors@R: c(
  person("Benjamin Leon", "Bodirsky", , "[email protected]", role = c("aut", "cre")),
  person("Stephen", "Wirth", role = "aut"),

R/calcValidCarbon.R

@@ -40,7 +40,7 @@ calcValidCarbon <- function(datasource = "LPJmL4_for_MAgPIE_44ac93de:GSWP3-W5E5:
  area <- dimSums(calcOutput("LUH2v2", landuse_types = "LUH2v2", irrigation = FALSE, cellular = TRUE, years = "y1995", aggregate = FALSE), dim = 3)
  stock <- toolCoord2Isocell(stock) * setYears(area, NULL)
 
- mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell")
+ mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell", where = "mappingfolder")
  stock <- toolAggregate(stock, rel = mapping, from = "celliso", to = "iso", dim = 1)
  stock <- toolCountryFill(stock, fill = 0)
 

R/calcValidGrassLSUha.R

@@ -29,7 +29,7 @@ calcValidGrassLSUha<-function(datasource = "MAgPIEown"){
  grassl_shares[, , "range"] <- 1 - grassl_shares[, , "pastr"]
  grassl_shares[is.nan(grassl_shares) | is.infinite(grassl_shares)] <- 0
 
- mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell")
+ mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell", where = "mappingfolder")
 
  livestock <- setNames(toolCell2isoCell(readSource("GLW3")), "liv_numb")
  livst_split <- livestock * grassl_shares

R/calcValidGrassSoilCarbon.R

@@ -24,7 +24,7 @@ calcValidGrassSoilCarbon <- function(datasource = "ISIMIP3b:IPSL-CM6A-LR:ssp126:
  soilc_range_past_tha <- calcOutput("RangeSoilCarbonHist", subtype = datasource, model = model, lpjml = lpjml, aggregate = F)
  past <- getYears(soilc_range_past_tha)
 
- map_reg <- toolGetMapping(type = "regional", name = "clustermapping.csv")
+ map_reg <- toolGetMapping(type = "regional", name = "clustermapping.csv", where = "mappingfolder")
 
  soilc_range_past_mt <- setNames(land_ini_LUH2v2[, past, "range"] * soilc_range_past_tha, "range")
  soilc_pastr_past_mt <- setNames(land_ini_LUH2v2[, past, "pastr"] * soilc_pastr_past_tha[, past, "pastr"], "pastr")

R/calcValidLSUdensity.R

@@ -15,7 +15,7 @@ prod <- calcOutput("GrasslandBiomass", aggregate = F)[, past, "range"]
 prod <- toolCountryFill(prod, fill = 0)
 
 # regional mapping
-cell2reg <- toolGetMapping("CountryToCellMapping.csv", type = "cell")
+cell2reg <- toolGetMapping("CountryToCellMapping.csv", type = "cell", where = "mappingfolder")
 
  # pasture areas
 area <- calcOutput("LUH2v2",

R/calcValidLand.R

@@ -125,7 +125,7 @@ calcValidLand <- function(datasource = "MAgPIEown") {
  # Renaming reporting categories from SSPResults to MAgPie validation names
  # (not all SSP-categories have MAgPIE-equivalents)
 
- mapping <- toolGetMapping(type = "sectoral", name = "mappingSSPResultsToMAgPIEValid.csv")
+ mapping <- toolGetMapping(type = "sectoral", name = "mappingSSPResultsToMAgPIEValid.csv", where = "mappingfolder")
  mappingFrom <- as.vector(mapping[, "SSPResults"])
  mappingTo <- as.vector(mapping[, "MAgPIEValid"])
  names(mappingTo) <- mappingFrom

R/calcValidManure.R

@@ -77,13 +77,13 @@ calcValidManure<-function(datasource="Bodirsky"){
  )
 
  confinement<-collapseNames(confinement[,,selection][,,"Manure_treated_(N_content)_(kg)"])
- mapping<-toolGetMapping(type = "sectoral",name = "IPCCitems_fao_online.csv")
+ mapping<-toolGetMapping(type = "sectoral",name = "IPCCitems_fao_online.csv", where = "mappingfolder")
  confinement<-toolAggregate(confinement,rel=mapping,from="fao",to="magpie",dim = 3.1)
 
  pasture<-collapseNames(pasture[,,getNames(pasture,dim=1)[getNames(pasture,dim=1)%in%selection]][,,"Manure_left_on_pasture_(N_content)_(kg)"])
 
  #pasture<-collapseNames(pasture[,,selection][,,"Manure_(N_content)_(Manure_management)_(Kg)"])
- mapping<-toolGetMapping(type = "sectoral",name = "IPCCitems_fao_online.csv")
+ mapping<-toolGetMapping(type = "sectoral",name = "IPCCitems_fao_online.csv", where = "mappingfolder")
  pasture<-toolAggregate(pasture,rel=mapping,from="fao",to="magpie",dim = 3.1,partrel = T)
 
  out<-pasture+confinement

R/calcValidNitrogenBudgetCropland.R

@@ -95,7 +95,7 @@ calcValidNitrogenBudgetCropland <- function(datasource = "Bodirsky") {
  "961|Cattle, non-dairy"
  )
  tmp2 <- collapseNames(manure[, , selection][, , "Manure_applied_to_soils_(N_content)_(kg)"])
- mapping <- toolGetMapping(type = "sectoral", name = "IPCCitems_fao_online.csv")
+ mapping <- toolGetMapping(type = "sectoral", name = "IPCCitems_fao_online.csv", where = "mappingfolder")
  tmp2 <- toolAggregate(tmp2, rel = mapping, from = "fao", to = "magpie", dim = 3.1)
  tmp2 <- tmp2 / 1e12
  manure <- setNames(dimSums(tmp2, dim = 3.1), "manure_conf")

R/calcValidSDG12.R

@@ -16,7 +16,7 @@ calcValidSDG12 <- function(datasource = "FAO") {
  indicatorname <- "SDG|SDG12|Food loss"
  unit <- "Mt"
  foodLoss <- readSource("FAO_online", subtype = "CBCrop")
- aggregation <- toolGetMapping("FAOitems_online.rda", type = "sectoral")
+ aggregation <- toolGetMapping("FAOitems_online.rda", type = "sectoral", where = "mrvalidation")
  # standarized items _ magpie object
  aAgg <- toolAggregate(foodLoss, rel = aggregation, from = "FAOaggregatedItem_fromWebsite",
  to = "k", dim = 3.1, partrel = TRUE)
@@ -49,7 +49,7 @@ calcValidSDG12 <- function(datasource = "FAO") {
  indicatorname <- "SDG|SDG12|Food waste"
  unit <- "kcal/cap/day"
  # Reads food supply including household waste
- avFood <- calcOutput(type = "FoodSupplyPast", aggregate = FALSE)[,,"kcal"]
+ avFood <- calcOutput(type = "FoodSupplyPast", aggregate = FALSE)[, , "kcal"]
  avFood <- dimSums(avFood, dim = 3)
  # Calculate expected intake. Source is Lutz2014. Average for male,female,ages.ssp1 (historical trend)
  intake <- calcOutput("Intake", aggregate = FALSE)
@@ -67,7 +67,9 @@ calcValidSDG12 <- function(datasource = "FAO") {
  unitsX <- c(unitsX, unit)
  popul <- popul[, comYears, ]
 
- } else stop("No data exist for the given datasource!")
+ } else {
+ stop("No data exist for the given datasource!")
+ }
 
  return(list(x = x,
  weight = popul,

R/calcValidSOCDensity.R

@@ -26,7 +26,7 @@ calcValidSOCDensity <- function(datasource = "GSOC") {
  cellular = TRUE, selectyears = "past_all", aggregate = FALSE)
  area <- setYears(dimSums(area[, 2010, ], dim = 3), NULL)
 
- mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell")
+ mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell", where = "mappingfolder")
  soilc <- toolAggregate(soilc, weight = area, rel = mapping, from = "celliso", to = "iso", dim = 1)
  soilc <- toolCountryFill(soilc, fill = 0)
  out <- setNames(soilc, "Resources|Soil Carbon|Actual|Density|SOC in top 30 cm (tC/ha)")
@@ -48,7 +48,7 @@ calcValidSOCDensity <- function(datasource = "GSOC") {
  cellular = TRUE, selectyears = "past_all", aggregate = FALSE)
  area <- setYears(dimSums(area[, 2010, ], dim = 3), NULL)
 
- mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell")
+ mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell", where = "mappingfolder")
  soilc <- toolAggregate(soilc, weight = area, rel = mapping, from = "celliso", to = "iso", dim = 1)
  soilc <- toolCountryFill(soilc, fill = 0)
  out <- setNames(soilc, "Resources|Soil Carbon|Actual|Density|SOC in top 30 cm (tC/ha)")
@@ -70,7 +70,7 @@ calcValidSOCDensity <- function(datasource = "GSOC") {
  cellular = TRUE, selectyears = "past_all", aggregate = FALSE)
  area <- setYears(dimSums(area[, 2010, ], dim = 3), NULL)
 
- mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell")
+ mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell", where = "mappingfolder")
  soilc <- toolAggregate(soilc, weight = area, rel = mapping, from = "celliso", to = "iso", dim = 1)
  soilc <- toolCountryFill(soilc, fill = 0)
  out <- setNames(soilc, "Resources|Soil Carbon|Actual|Density|SOC in top 30 cm (tC/ha)")

R/calcValidSOCStocks.R

@@ -22,7 +22,7 @@ calcValidSOCStocks <- function(datasource = "LPJ_IPCC2006", baseyear = 1995) {
 
  if (datasource == "LPJ_IPCC2006") {
 
- mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell")
+ mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell", where = "mappingfolder")
  somStock <- calcOutput("SOM", subtype = "stock", aggregate = FALSE)
  somStock <- toolAggregate(somStock, rel = mapping,
  from = ifelse(nregions(somStock) > 1, "celliso", "cell"), to = "iso", dim = 1)
@@ -75,7 +75,7 @@ calcValidSOCStocks <- function(datasource = "LPJ_IPCC2006", baseyear = 1995) {
  area <- setYears(dimSums(area[, 2010, ], dim = 3), NULL)
  stock <- soilc * area
 
- mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell")
+ mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell", where = "mappingfolder")
  stock <- toolAggregate(stock, rel = mapping, from = "celliso", to = "iso", dim = 1)
  stock <- toolCountryFill(stock, fill = 0)
  out <- setNames(stock, "Resources|Soil Carbon|Actual|Stock|SOC in top 30 cm (Mt C)")
@@ -91,7 +91,7 @@ calcValidSOCStocks <- function(datasource = "LPJ_IPCC2006", baseyear = 1995) {
  area <- setYears(dimSums(area[, 2010, ], dim = 3), NULL)
  stock <- soilc * area
 
- mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell")
+ mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell", where = "mappingfolder")
  stock <- toolAggregate(stock, rel = mapping, from = "celliso", to = "iso", dim = 1)
  stock <- toolCountryFill(stock, fill = 0)
  out <- setNames(stock, "Resources|Soil Carbon|Actual|Stock|SOC in top 30 cm (Mt C)")
@@ -108,7 +108,7 @@ calcValidSOCStocks <- function(datasource = "LPJ_IPCC2006", baseyear = 1995) {
  area <- setYears(dimSums(area[, 2010, ], dim = 3), NULL)
  stock <- soilc * area
 
- mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell")
+ mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell", where = "mappingfolder")
  stock <- toolAggregate(stock, rel = mapping, from = "celliso", to = "iso", dim = 1)
  stock <- toolCountryFill(stock, fill = 0)
  out <- setNames(stock, "Resources|Soil Carbon|Actual|Stock|SOC in top 30 cm (Mt C)")
@@ -126,7 +126,7 @@ calcValidSOCStocks <- function(datasource = "LPJ_IPCC2006", baseyear = 1995) {
  area <- setYears(dimSums(area[, 2010, ], dim = 3), NULL)
  stock <- soilc * area
 
- mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell")
+ mapping <- toolGetMapping(name = "CountryToCellMapping.csv", type = "cell", where = "mappingfolder")
  stock <- toolAggregate(stock, rel = mapping, from = "celliso", to = "iso", dim = 1)
  stock <- toolCountryFill(stock, fill = 0)
  out <- setNames(stock, "Resources|Soil Carbon|Actual|Stock|SOC in top 30 cm (Mt C)")

R/calcValidTau.R

@@ -76,9 +76,9 @@ calcValidTau <- function(datasource = "FAO2012") {
  unit = "-",
  description = description,
  note = c("data uses initialization values for 1995 based on ",
- "Dietrich J.P., Schmitz C., M\uFCller C., Fader M., Lotze-Campen H., Popp A.,",
- "Measuring agricultural land-use intensity - A global analysis using a model-assisted approach",
- "Ecological Modelling, Volume 232, 10 May 2012, 109-118, DOI 10.1016/j.ecolmodel.2012.03.002.",
- "preprint available \u40 http://edoc.gfz-potsdam.de/pik/display.epl?mode=doc&id=5281")))
+  "Dietrich J.P., Schmitz C., M\uFCller C., Fader M., Lotze-Campen H., Popp A.,",
+  "Measuring agricultural land-use intensity - A global analysis using a model-assisted approach",
+  "Ecological Modelling, Volume 232, 10 May 2012, 109-118, DOI 10.1016/j.ecolmodel.2012.03.002.",
+  "preprint available \u40 http://edoc.gfz-potsdam.de/pik/display.epl?mode=doc&id=5281")))
 
 }

R/calcValidTauPastr.R

@@ -11,25 +11,22 @@
 calcValidTauPastr <- function() {
  past <- findset("past")
  # Production
- prod <- calcOutput("GrasslandBiomass", aggregate = F)[, past, "pastr"]
+ prod <- calcOutput("GrasslandBiomass", aggregate = FALSE)[, past, "pastr"]
  prod <- toolCountryFill(prod, fill = 0)
 
  # regional mapping
- cell2reg <- toolGetMapping("CountryToCellMapping.csv", type = "cell")
+ cell2reg <- toolGetMapping("CountryToCellMapping.csv", type = "cell", where = "mappingfolder")
 
  # pasture areas
- area <- calcOutput("LUH2v2",
- landuse_types = "LUH2v2",
- cellular = F, aggregate = F
- )[, past, "pastr"]
+ area <- calcOutput("LUH2v2", landuse_types = "LUH2v2", cellular = FALSE, aggregate = FALSE)[, past, "pastr"]
  area <- toolCountryFill(area, fill = 0)
 
  # Adding 'otherland' as an extra source of grass biomass comparable
  # to managed pastures in India, Pakistan and Bangladesh.
  otherland <-
  calcOutput("LUH2v2",
  landuse_types = "LUH2v2",
- cellular = F, aggregate = F
+ cellular = FALSE, aggregate = FALSE
  )[, past, c("secdn", "primn")]
  area["IND", , "pastr"] <-
  area["IND", , "pastr"] +
@@ -47,21 +44,20 @@ calcValidTauPastr <- function() {
 
  # reference yields
  yref <- calcOutput("GrasslandsYields",
- lpjml = "lpjml5p2_pasture",
- climatetype = "MRI-ESM2-0:ssp245",
- subtype = "/co2/Nreturn0p5",
- lsu_levels = c(seq(0, 2.2, 0.2), 2.5), past_mngmt = "mdef",
- aggregate = F
- )[, past, "pastr.rainfed"]
+ lpjml = "lpjml5p2_pasture",
+ climatetype = "MRI-ESM2-0:ssp245",
+ subtype = "/co2/Nreturn0p5", # nolint: absolute_path_linter.
+ lsu_levels = c(seq(0, 2.2, 0.2), 2.5), past_mngmt = "mdef",
+ aggregate = FALSE)[, past, "pastr.rainfed"]
 
- yref_weights <- calcOutput("LUH2v2",
- landuse_types = "LUH2v2", cellular = T,
- aggregate = F
+ yrefWeights <- calcOutput("LUH2v2",
+ landuse_types = "LUH2v2", cellular = TRUE,
+ aggregate = FALSE
  )[, past, "pastr"]
  yref <- toolAggregate(yref,
- rel = cell2reg, from = "celliso", 
- to = "iso", 
- weight = yref_weights
+ rel = cell2reg, from = "celliso",
+ to = "iso",
+ weight = yrefWeights
  )
  yref <- toolCountryFill(yref, fill = 0)
 
@@ -71,21 +67,21 @@ calcValidTauPastr <- function() {
  t <- collapseNames(t)
 
  # replacing unrealistic high tau values by regional averages
- reg_map <- toolGetMapping("regionmappingH12.csv", type = "regional")
- t_reg <- toolAggregate(t,
- rel = reg_map, weight = area,
+ regMap <- toolGetMapping("regionmappingH12.csv", type = "regional", where = "madrat")
+ tReg <- toolAggregate(t,
+ rel = regMap, weight = area,
  from = "CountryCode", to = "RegionCode"
  )
- regions <- reg_map$RegionCode
- names(regions) <- reg_map[, "CountryCode"]
+ regions <- regMap$RegionCode
+ names(regions) <- regMap[, "CountryCode"]
 
  largeTC <- where(t >= 10)$true$individual # tau threshold
  colnames(largeTC)[1] <- "country"
  largeTC <- as.data.frame(largeTC)
 
  for (i in as.vector(largeTC[, "country"])) {
  for (j in as.vector(largeTC[largeTC$country == i, "year"])) {
- t[i, j, ] <- t_reg[regions[i], j, ]
+ t[i, j, ] <- tReg[regions[i], j, ]
  }
  }
 
@@ -100,4 +96,4 @@ calcValidTauPastr <- function() {
  description =
  "Historic Trends in managed pastures Land Use Intensity Tau based on FAO yield trends" # nolint
  ))
-}
+}