added functions to calculate area on cropland covered by trees and sn…

…v target cropland

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '10409831'
+ValidationKey: '10470150'
 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: 'mrland: MadRaT land data package'
-version: 0.52.7
-date-released: '2024-01-31'
+version: 0.53.0
+date-released: '2024-02-02'
 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: 0.52.7
-Date: 2024-01-31
+Version: 0.53.0
+Date: 2024-02-02
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "[email protected]", role = c("aut", "cre")),
     person("Abhijeet", "Mishra", role = "aut"),
@@ -58,4 +58,4 @@ VignetteBuilder:
     knitr
 Encoding: UTF-8
 LazyData: no
-RoxygenNote: 7.3.0
+RoxygenNote: 7.3.1

R/calcCroplandTreecover.R

@@ -0,0 +1,55 @@
+#' @title calcCroplandTreecover
+#'
+#' @description Returns area on cropland covered by trees (Mha).
+
+#' @param maginput Whether data should be corrected to align with cropland
+#' initialised in MAgPIE.
+#' @param cells magpiecell (59199 cells) or lpjcell (67420 cells)
+#'
+#' @return List with a magpie object
+#' @author Patrick v. Jeetze
+#' @seealso
+#' \code{\link{readCopernicus}}
+#'
+#' @examples
+#' \dontrun{
+#' calcOutput("calcCroplandTreecover", aggregate = FALSE)
+#' }
+#'
+#' @importFrom mrcommons toolCoord2Isocell
+#'
+calcCroplandTreecover <- function(maginput = TRUE, cells = "magpiecell") {
+  treecover <- readSource("Copernicus", subtype = "CroplandTreecover", convert = "onlycorrect")
+
+  if (maginput) {
+    luh <- calcOutput("LUH2v2",
+      landuse_types = "magpie", aggregate = FALSE,
+      cellular = TRUE, cells = "lpjcell", irrigation = FALSE,
+      selectyears = "y2015"
+    )
+    getYears(luh) <- NULL
+    getCells(luh) <- getCells(treecover)
+
+    # cropland treecover area is corrected to make sure that it is not
+    # larger than cropland area reported by LUH
+    treecover <- pmax(treecover, luh[, , "crop"])
+  } else {
+    out <- treecover
+  }
+
+  if (cells == "magpiecell") {
+    out <- toolCoord2Isocell(out)
+  } else if (cells != "lpjcell") {
+    stop("Please specify cells argument")
+  }
+
+  return(list(
+    x = out,
+    weight = NULL,
+    unit = "Mha",
+    description = paste(
+      "Cropland area covered by trees"
+    ),
+    isocountries = FALSE
+  ))
+}

R/calcSNVTargetCropland.R

@@ -0,0 +1,57 @@
+#' @title calcSNVTargetCropland
+#'
+#' @description Returns cropland area (Mha) that requires relocation in response of increasing
+#' semi-natural vegetation in farmed landscapes.
+
+#' @param maginput Whether data should be corrected to align with cropland
+#' initialised in MAgPIE.
+#' @param cells magpiecell (59199 cells) or lpjcell (67420 cells)
+#'
+#' @return List with a magpie object
+#' @author Patrick v. Jeetze
+#' @seealso
+#' \code{\link{readCopernicus}}
+#'
+#' @examples
+#' \dontrun{
+#' calcOutput("calcSNVTargetCropland", aggregate = FALSE)
+#' }
+#'
+#' @importFrom mrcommons toolCoord2Isocell
+#'
+calcSNVTargetCropland <- function(maginput = TRUE, cells = "magpiecell") {
+  targetCropland <- readSource("Copernicus", subtype = "SNVTargetCropland", convert = "onlycorrect")
+
+  if (maginput) {
+    luh <- calcOutput("LUH2v2",
+      landuse_types = "magpie", aggregate = FALSE,
+      cellular = TRUE, cells = "lpjcell", irrigation = FALSE,
+      selectyears = "y2015"
+    )
+    getYears(luh) <- NULL
+    getCells(luh) <- getCells(targetCropland)
+
+    # SNV target cropland area is corrected to make sure that it is not
+    # larger than cropland area reported by LUH
+    targetCropland <- pmax(targetCropland, luh[, , "crop"])
+  } else {
+    out <- targetCropland
+  }
+
+  if (cells == "magpiecell") {
+    out <- toolCoord2Isocell(out)
+  } else if (cells != "lpjcell") {
+    stop("Please specify cells argument")
+  }
+
+  return(list(
+    x = out,
+    weight = NULL,
+    unit = "Mha",
+    description = paste(
+      "Cropland area (Mha) that requires relocation in",
+      "response of increasing semi-natural vegetation in farmed landscapes"
+    ),
+    isocountries = FALSE
+  ))
+}

R/correctCopernicus.R

@@ -0,0 +1,19 @@
+#' @title correctCopernicus
+#' @description correct Copernicus data.
+#' @return magpie object on cellular level
+#' @param x magpie object provided by the read function
+#' @author Patrick v. Jeetze
+#' @seealso
+#'   \code{\link{readCopernicus}}
+#' @examples
+#' \dontrun{
+#' readSource("Copernicus", convert = "onlycorrect")
+#' }
+#'
+#' @importFrom madrat toolConditionalReplace
+
+correctCopernicus <- function(x) {
+  x <- toolConditionalReplace(x, conditions = "is.na()", replaceby = 0)
+
+  return(x)
+}

R/readCopernicus.R

@@ -0,0 +1,61 @@
+#' @title readCopernicus
+#' @description Reads either information on the area on cropland covered by trees or
+#' information the cropland area that requires relocation in response of increasing
+#' semi-natural vegetation in farmed landscapes. The data was derived from high resolution
+#' land cover information (LC100) from the Copernicus Global Land Service.
+#' (https://zenodo.org/records/3939050)
+#'
+#' @param subtype For cropland area covered by trees choose \code{"CroplandTreecover"}.
+#' For cropland area requiring relocation in response to increasing SNV choose \code{"SNVTargetCropland"}.
+#'
+#' @return Returns magpie objects with cropland area covered by trees or cropland area
+#' requiring relocation in order to increase SNV in farmed landscapes.
+#'
+#' @author Patrick v. Jeetze
+#'
+#' @examples
+#' \dontrun{
+#' readSource("Copernicus", subtype = "CroplandTreecover", convert = "onlycorrect")
+#' }
+#'
+#' @importFrom terra rast terraOptions
+#' @importFrom withr local_tempdir defer
+#' @importFrom mrcommons toolGetMappingCoord2Country
+#'
+
+readCopernicus <- function(subtype = "CroplandTreecover") {
+  # Set up 'terra' options
+  terraOptions(tempdir = local_tempdir(tmpdir = getConfig("tmpfolder")), todisk = TRUE, memfrac = 0.5)
+  defer(terraOptions(tempdir = tempdir()))
+
+  # read data
+  if (subtype == "CroplandTreecover") {
+    r <- rast(paste0(
+      "./land_cover/copernicus_lc100_2019_crop_treecover_area_0.5.tif"
+    ))
+    name <- "CropTreecoverArea"
+  } else if (subtype == "SNVTargetCropland") {
+    r <- rast(paste0(
+      "./land_cover/copernicus_lc100_2019_SNV50_target_crop_area_0.5.tif"
+    ))
+    name <- "SNVTargetCropland"
+  } else {
+    stop("Please select an existing subtype")
+  }
+
+  # get spatial mapping
+  map <- toolGetMappingCoord2Country(pretty = TRUE)
+  # transform raster to magpie object
+  out <- mbind(
+    as.magpie(extract(r, map[c("lon", "lat")], ID = FALSE), spatial = 1)
+  )
+
+  # set dimension names
+  dimnames(out) <- list(
+    "x.y.iso" = paste(map$coords, map$iso, sep = "."),
+    "t" = NULL,
+    "data" = name
+  )
+
+  return(out)
+}

README.md

@@ -1,6 +1,6 @@
 # MadRaT land data package
 
-R package **mrland**, version **0.52.7**
+R package **mrland**, version **0.53.0**
 
 [![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 (2024). _mrland: MadRaT land data package_. doi:10.5281/zenodo.3822083 <https://doi.org/10.5281/zenodo.3822083>, R package version 0.52.7, <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 (2024). _mrland: MadRaT land data package_. doi:10.5281/zenodo.3822083 <https://doi.org/10.5281/zenodo.3822083>, R package version 0.53.0, <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},
   year = {2024},
-  note = {R package version 0.52.7},
+  note = {R package version 0.53.0},
   doi = {10.5281/zenodo.3822083},
   url = {https://github.com/pik-piam/mrland},
 }