adjusted package to mrcommons split

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '220716090'
+ValidationKey: '22437280'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

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: 'mrwater: madrat based MAgPIE water Input Data Library'
-version: 1.11.22
-date-released: '2024-05-02'
+version: 1.13.0
+date-released: '2024-05-13'
 abstract: Provides functions for MAgPIE cellular input data generation and stand-alone
  water calculations.
 authors:

DESCRIPTION

@@ -1,11 +1,11 @@
 Type: Package
 Package: mrwater
 Title: madrat based MAgPIE water Input Data Library
-Version: 1.11.22
+Version: 1.13.0
 URL: https://github.com/pik-piam/mrwater, 
 https: //doi.org/10.5281/zenodo.5801680
 License: LGPL-3 | file LICENSE
-Date: 2024-05-02
+Date: 2024-05-13
 Authors@R: c(person("Felicitas", "Beier", email = "[email protected]", role = c("aut","cre")),
  person("Jens", "Heinke", email = "[email protected]", role = "aut"),
  person("Kristine", "Karstens", email = "[email protected]", role = "aut"),
@@ -17,11 +17,12 @@ Depends:
  R (>= 2.10.0),
  madrat (>= 1.72),
  magclass (>= 6.0.0),
- mrcommons (>= 1.37.0),
- mrland (>= 0.51.0)
+ mrcommons (>= 1.41.0),
+ mrlandcore (>= 1.0.0),
+ mrland (>= 0.59.0)
 Imports:
  magpiesets,
- mstools,
+ mstools (>= 0.6.0),
  raster,
  stats,
  stringr,

NAMESPACE

@@ -27,6 +27,7 @@ import(madrat)
 import(magclass)
 import(mrcommons)
 import(mrland)
+import(mrlandcore)
 importFrom(madrat,calcOutput)
 importFrom(madrat,readSource)
 importFrom(madrat,toolAggregate)
@@ -60,13 +61,13 @@ importFrom(magclass,time_interpolate)
 importFrom(magclass,where)
 importFrom(magpiesets,addLocation)
 importFrom(magpiesets,findset)
-importFrom(mrcommons,toolCell2isoCell)
-importFrom(mrcommons,toolCoord2Isocell)
-importFrom(mrcommons,toolGetMappingCoord2Country)
-importFrom(mrcommons,toolHarmonize2Baseline)
-importFrom(mrcommons,toolLPJmLVersion)
-importFrom(mrcommons,toolSmooth)
+importFrom(mrlandcore,toolLPJmLVersion)
+importFrom(mstools,toolCell2isoCell)
+importFrom(mstools,toolCoord2Isocell)
+importFrom(mstools,toolGetMappingCoord2Country)
+importFrom(mstools,toolHarmonize2Baseline)
 importFrom(mstools,toolHoldConstant)
+importFrom(mstools,toolSmooth)
 importFrom(raster,brick)
 importFrom(stats,lm)
 importFrom(stats,quantile)

R/calcAreaPotIrrig.R

@@ -27,8 +27,7 @@
 #'
 #' @importFrom madrat calcOutput toolSplitSubtype
 #' @importFrom magclass collapseNames getCells getYears getNames dimSums time_interpolate
-#' @importFrom mrcommons toolGetMappingCoord2Country
-#' @importFrom mstools toolHoldConstant
+#' @importFrom mstools toolHoldConstant toolGetMappingCoord2Country
 
 calcAreaPotIrrig <- function(selectyears, comagyear, iniyear, landScen) {
 
@@ -66,7 +65,7 @@ calcAreaPotIrrig <- function(selectyears, comagyear, iniyear, landScen) {
  # urbanLand <- calcOutput("UrbanLandFuture", subtype = "LUH2v2",
  # timestep = "yearly", cells = "lpjcell",
  # aggregate = FALSE)[, selectyears, ]
- # getItems(urbanLand, dim = 3) <- gsub("SSP", "ssp", getItems(urbanLand, dim = 3))
+ # getItems(urbanLand, dim = 3) <- gsub("SSP", "ssp", getItems(urbanLand, dim = 3)) # nolint: comment_code_linter
 
  # Read in suitable land for irrigation based on Zabel [in mio. ha]
  # excluding land that is marginal under irrigated conditions (< suitability index of 0.33)

R/calcAvlWater.R

@@ -12,7 +12,8 @@
 #'
 #' @import magclass
 #' @import madrat
-#' @importFrom mrcommons toolHarmonize2Baseline toolLPJmLVersion
+#' @importFrom mstools toolHarmonize2Baseline
+#' @importFrom mrlandcore toolLPJmLVersion
 #'
 #' @return magpie object in cellular resolution
 #' @author Felicitas Beier, Kristine Karstens, Abhijeet Mishra
@@ -43,27 +44,27 @@ calcAvlWater <- function(lpjml = c(natveg = "LPJmL4_for_MAgPIE_44ac93de", crop =
  if (stage %in% c("raw", "smoothed")) {
  ### Monthly Discharge (unit (after calcLPJmL): mio. m^3/month)
  monthDischargeMAG <- calcOutput("LPJmL_new", subtype = "mdischarge",
-  stage = "raw",
-  version = lpjmlReadin["natveg"],
-  climatetype = climatetype,
-  aggregate = FALSE)
+ stage = "raw",
+ version = lpjmlReadin["natveg"],
+ climatetype = climatetype,
+ aggregate = FALSE)
 
  ### Monthly Runoff (unit (after calcLPJmL): mio. m^3/month)
  monthRunoffMAG <- calcOutput("LPJmL_new", subtype = "mrunoff",
-  stage = "raw",
-  version = lpjmlReadin["natveg"],
-  climatetype = climatetype,
-  aggregate = FALSE)
+ stage = "raw",
+ version = lpjmlReadin["natveg"],
+ climatetype = climatetype,
+ aggregate = FALSE)
 
  ## River basin water allocation algorithm:
  # Read in river structure
  rs <- readRDS(system.file("extdata/riverstructure_stn_coord.rds",
- package = "mrwater"))
+  package = "mrwater"))
  basinCode <- rs$endcell
 
  if (any(paste(getItems(monthRunoffMAG, dim = "x", full = TRUE),
- getItems(monthRunoffMAG, dim = "y", full = TRUE),
- sep = ".") != rs$coordinates)) {
+  getItems(monthRunoffMAG, dim = "y", full = TRUE),
+  sep = ".") != rs$coordinates)) {
  stop("Wrong cell ordering of basin in calcAvlWater.R")
  }
 
@@ -133,8 +134,8 @@ calcAvlWater <- function(lpjml = c(natveg = "LPJmL4_for_MAgPIE_44ac93de", crop =
 
  # Growing days per month
  growDAYS <- calcOutput("GrowingPeriod", cells = "lpjcell",
-  lpjml = lpjmlReadin, climatetype = climatetype,
-  stage = stage, yield_ratio = 0.1, aggregate = FALSE)
+ lpjml = lpjmlReadin, climatetype = climatetype,
+ stage = stage, yield_ratio = 0.1, aggregate = FALSE)
 
  # Adjust years
  yearsWAT <- getYears(dailyAvlWat)

R/calcCropAreaPotIrrig.R

@@ -31,7 +31,7 @@
 #'
 #' @importFrom madrat calcOutput toolSplitSubtype
 #' @importFrom magclass collapseNames getCells getYears getNames dimSums
-#' @importFrom mrcommons toolGetMappingCoord2Country
+#' @importFrom mstools toolGetMappingCoord2Country
 
 calcCropAreaPotIrrig <- function(selectyears, comagyear, iniyear,
  cropmix, landScen) {

R/calcCropAreaShare.R

@@ -19,13 +19,13 @@
 #'
 #' @importFrom madrat calcOutput toolGetMapping
 #' @importFrom magclass collapseNames getCells getSets getYears getNames new.magpie dimSums
-#' @importFrom mrcommons toolCell2isoCell toolGetMappingCoord2Country
+#' @importFrom mstools toolCell2isoCell toolGetMappingCoord2Country
 
 calcCropAreaShare <- function(iniyear, cropmix) {
 
  # read physical croparea
  croparea <- calcOutput("CropareaAdjusted", iniyear = iniyear,
-  aggregate = FALSE)
+ aggregate = FALSE)
 
  # total croparea (irrigated + rainfed)
  totCroparea <- dimSums(croparea, dim = "irrigation")

R/calcCropareaAdjusted.R

@@ -18,7 +18,7 @@
 #'
 #' @importFrom madrat calcOutput
 #' @importFrom magclass getCells getNames add_dimension new.magpie
-#' @importFrom mrcommons toolGetMappingCoord2Country
+#' @importFrom mstools toolGetMappingCoord2Country
 
 calcCropareaAdjusted <- function(iniyear, dataset = "LandInG", sectoral = "kcr") {
 

R/calcEnvmtlFlowRequirementsShare.R

@@ -10,7 +10,7 @@
 #'
 #' @importFrom magclass collapseNames new.magpie getYears setYears as.array as.magpie add_dimension mbind
 #' @importFrom madrat calcOutput
-#' @importFrom mrcommons toolLPJmLVersion
+#' @importFrom mrlandcore toolLPJmLVersion
 #' @importFrom stats quantile
 #'
 #' @return magpie object in cellular resolution representing share of discharge

R/calcFullIrrigationRequirement.R

@@ -14,8 +14,8 @@
 #' or drip, surface, sprinkler for full irrigation by selected system
 #' @param landScen Land availability scenario consisting of two parts separated by ":":
 #' 1. available land scenario (currCropland, currIrrig, potCropland)
-#' 2. protection scenario (WDPA, or one of the scenarios available in calcConservationPriorities,
-#' e.g., 30by20, BH, BH_IFL, PBL_HalfEarth,
+#' 2. protection scenario (WDPA, or one of the scenarios available in
+#' calcConservationPriorities, e.g., 30by20, BH, BH_IFL, PBL_HalfEarth,
 #' or NA for no protection).
 #' For case of no land protection select "NA" in second part of argument
 #' or do not specify second part of the argument
@@ -47,7 +47,7 @@
 #'
 #' @importFrom madrat calcOutput toolGetMapping
 #' @importFrom magclass collapseNames getItems new.magpie dimSums
-#' @importFrom mrcommons toolCell2isoCell toolGetMappingCoord2Country
+#' @importFrom mstools toolCell2isoCell toolGetMappingCoord2Country
 
 calcFullIrrigationRequirement <- function(lpjml, climatetype,
  selectyears, iniyear, comagyear,

R/calcGrowingPeriod.R

@@ -19,7 +19,8 @@
 #'
 #' @importFrom madrat toolGetMapping toolAggregate
 #' @importFrom magclass collapseNames getItems new.magpie getYears dimSums magpie_expand
-#' @importFrom mrcommons toolHarmonize2Baseline toolSmooth toolLPJmLVersion toolGetMappingCoord2Country
+#' @importFrom mstools toolHarmonize2Baseline toolSmooth toolGetMappingCoord2Country
+#' @importFrom mrlandcore toolLPJmLVersion
 #'
 #' @export
 
@@ -37,7 +38,7 @@ calcGrowingPeriod <- function(lpjml = c(natveg = "LPJmL4_for_MAgPIE_44ac93de",
  crop = unname(cfgCrop$readin_version))
 
  lpjmlBaseline <- c(natveg = unname(cfgNatveg$baseline_version),
-  crop = unname(cfgCrop$baseline_version))
+ crop = unname(cfgCrop$baseline_version))
 
  if (stage %in% c("raw", "smoothed")) {
 
@@ -62,8 +63,8 @@ calcGrowingPeriod <- function(lpjml = c(natveg = "LPJmL4_for_MAgPIE_44ac93de",
  ####################################################################################
 
  lpj2mag <- toolGetMapping("MAgPIE_LPJmL.csv",
-  type = "sectoral",
-  where = "mappingfolder")
+ type = "sectoral",
+ where = "mappingfolder")
 
  # Read yields first
  yields <- collapseNames(calcOutput("LPJmL_new", version = lpjmlReadin["crop"],
@@ -72,11 +73,11 @@ calcGrowingPeriod <- function(lpjml = c(natveg = "LPJmL4_for_MAgPIE_44ac93de",
 
  # Load Sowing dates from LPJmL (use just rainfed dates since they do not differ for irrigated and rainfed)
  sowd <- collapseNames(calcOutput("LPJmL_new", version = lpjmlReadin["crop"],
-  climatetype = climatetype, subtype = "sdate",
-  stage = "raw", aggregate = FALSE)[, , "rainfed"])
+ climatetype = climatetype, subtype = "sdate",
+ stage = "raw", aggregate = FALSE)[, , "rainfed"])
  hard <- collapseNames(calcOutput("LPJmL_new", version = lpjmlReadin["crop"],
-  climatetype = climatetype, subtype = "hdate",
-  stage = "raw", aggregate = FALSE)[, , "rainfed"])
+ climatetype = climatetype, subtype = "hdate",
+ stage = "raw", aggregate = FALSE)[, , "rainfed"])
 
  goodCrops <- lpj2mag$MAgPIE[which(lpj2mag$LPJmL %in% getItems(sowd, dim = 3))]
  badCrops <- lpj2mag$MAgPIE[which(!lpj2mag$LPJmL %in% getItems(sowd, dim = 3))]
@@ -93,7 +94,7 @@ calcGrowingPeriod <- function(lpjml = c(natveg = "LPJmL4_for_MAgPIE_44ac93de",
 
  if (length(badCrops) > 0) {
  vcat(2, "No information on the growing period found for those crops: ",
-  paste(unique(badCrops), collapse = ", "))
+ paste(unique(badCrops), collapse = ", "))
  }
 
  #####################################################################################
@@ -123,8 +124,8 @@ calcGrowingPeriod <- function(lpjml = c(natveg = "LPJmL4_for_MAgPIE_44ac93de",
  yields <- collapseNames(yields[, , goodCrops])
 
  cell2GLO <- array(c(getItems(yields, dim = 1),
- rep("GLO", length(getItems(yields, dim = 1)))),
-  dim = c(length(getItems(yields, dim = 1)), 2))
+  rep("GLO", length(getItems(yields, dim = 1)))),
+ dim = c(length(getItems(yields, dim = 1)), 2))
  gloYields <- toolAggregate(yields, cell2GLO, weight = setYears(area, NULL))
  yieldsRatio <- yields / gloYields
 
@@ -152,9 +153,8 @@ calcGrowingPeriod <- function(lpjml = c(natveg = "LPJmL4_for_MAgPIE_44ac93de",
 
  # define all crops sowed after 180 days and where sowing date is after harvest date as wintercrops
  rmWintercrops[cellsNrthnHem, , ] <- ifelse(sowd[cellsNrthnHem, , ] > 180 &
- hard[cellsNrthnHem, , ] < sowd[cellsNrthnHem, , ],
- NA,
- 1)
+ hard[cellsNrthnHem, , ] < sowd[cellsNrthnHem, , ],
+ NA, 1)
 
  ####################################################################################
 
@@ -240,9 +240,9 @@ calcGrowingPeriod <- function(lpjml = c(natveg = "LPJmL4_for_MAgPIE_44ac93de",
 
  # mag object for the growing days per month
  growdaysPERmonth <- new.magpie(cells_and_regions = getItems(meanSowd, dim = 1),
-  years = getItems(meanSowd, dim = 2),
-  names = month,
-  fill = 0)
+ years = getItems(meanSowd, dim = 2),
+ names = month,
+ fill = 0)
 
  # determine the harvest day, take care if it is greater than 365
  meanHard <- (meanSowd + meanGrper - 1) %% 365
@@ -319,8 +319,8 @@ calcGrowingPeriod <- function(lpjml = c(natveg = "LPJmL4_for_MAgPIE_44ac93de",
  } else {
 
  x <- calcOutput("GrowingPeriod", lpjml = lpjml, climatetype = climatetype,
-  stage = "smoothed", yield_ratio = yield_ratio,
-  cells = "lpjcell", aggregate = FALSE)
+ stage = "smoothed", yield_ratio = yield_ratio,
+ cells = "lpjcell", aggregate = FALSE)
  # Harmonize to baseline
  out <- toolHarmonize2Baseline(x = x, base = baseline, ref_year = cfgNatveg$ref_year_hist)
  }
@@ -329,8 +329,8 @@ calcGrowingPeriod <- function(lpjml = c(natveg = "LPJmL4_for_MAgPIE_44ac93de",
 
  # read in historical data for subtype
  baseline2020 <- calcOutput("GrowingPeriod", lpjml = lpjmlBaseline, climatetype = cfgNatveg$baseline_gcm,
-  stage = "harmonized", yield_ratio = yield_ratio,
-  cells = "lpjcell", aggregate = FALSE)
+ stage = "harmonized", yield_ratio = yield_ratio,
+ cells = "lpjcell", aggregate = FALSE)
 
 
  if (climatetype == cfgNatveg$baseline_gcm) {

R/calcIrrigWatRequirements.R

@@ -30,7 +30,7 @@
 #'
 #' @importFrom magclass getItems new.magpie add_dimension
 #' @importFrom madrat calcOutput toolAggregate toolGetMapping
-#' @importFrom mrcommons toolCell2isoCell
+#' @importFrom mstools toolCell2isoCell
 #' @importFrom stringr str_split
 #' @importFrom withr local_options