Merge pull request #10 from tscheypidi/hardcore

adjusted package to mrcommons split
pik-piam · May 13, 2024 · 206aa05 · 206aa05
2 parents 3d8beb7 + 877cb5b
commit 206aa05
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diff --git a/.buildlibrary b/.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'

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: '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:

diff --git a/DESCRIPTION b/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 = "beier@pik-potsdam.de", role = c("aut","cre")),
              person("Jens", "Heinke", email = "heinke@pik-potsdam.de", role = "aut"),
              person("Kristine", "Karstens", email = "karstens@pik-potsdam.de", 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,

diff --git a/NAMESPACE b/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)

diff --git a/R/calcAreaPotIrrig.R b/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)

diff --git a/R/calcAvlWater.R b/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)

diff --git a/R/calcCropAreaPotIrrig.R b/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) {

diff --git a/R/calcCropAreaShare.R b/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")

diff --git a/R/calcCropareaAdjusted.R b/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") {
 

diff --git a/R/calcEnvmtlFlowRequirementsShare.R b/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

diff --git a/R/calcFullIrrigationRequirement.R b/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,

diff --git a/R/calcGrowingPeriod.R b/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) {

diff --git a/R/calcIrrigWatRequirements.R b/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