reworked land use reporting for SEALS

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '232244785'
+ValidationKey: '232366270'
 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: 'magpie4: MAgPIE outputs R package for MAgPIE version 4.x'
-version: 1.188.5
-date-released: '2023-07-03'
+version: 1.189.0
+date-released: '2023-07-05'
 abstract: Common output routines for extracting results from the MAgPIE framework
   (versions 4.x).
 authors:

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: magpie4
 Title: MAgPIE outputs R package for MAgPIE version 4.x
-Version: 1.188.5
-Date: 2023-07-03
+Version: 1.189.0
+Date: 2023-07-05
 Authors@R: c(
     person("Benjamin Leon", "Bodirsky", , "[email protected]", role = c("aut", "cre")),
     person("Florian", "Humpenoeder", , "[email protected]", role = "aut"),
@@ -54,6 +54,7 @@ Imports:
 Suggests:
     covr,
     luplot,
+    ncdf4,
     rworldmap,
     terra,
     testthat

NAMESPACE

@@ -26,7 +26,6 @@ export(Kcal)
 export(LivestockDemStructure)
 export(LivestockShare)
 export(ManureExcretion)
-export(MapLandUseForDownscaling)
 export(NetForestChange)
 export(NitrogenBudget)
 export(NitrogenBudgetNonagland)
@@ -178,6 +177,7 @@ export(reportLaborProductivity)
 export(reportLandFootprint)
 export(reportLandUse)
 export(reportLandUseChange)
+export(reportLandUseForSEALS)
 export(reportLivestockDemStructure)
 export(reportLivestockShare)
 export(reportLocalDemandShare)

R/PrimSecdOtherLand.R

@@ -14,7 +14,6 @@
 #' @param unit "Mha" or "share". Defines the unit of the gridded output, see also \code{level}.
 #' @return \code{x} including land area for primary and secondary non-forested vegetation in MAgPIE (other land) as MAgPIE object; either as unit of area (Mha) or as fraction of total land per grid cell (share).
 #' @author Patrick v. Jeetze, Kristine Karstens
-#' @seealso \code{\link{MapLandUseForDownscaling}}
 #' @examples
 #' \dontrun{
 #' x <- "./cell.land_0.5.nc"

R/reportLandUseForSEALS.R

@@ -0,0 +1,76 @@
+#' @title reportLandUseForSEALS
+#' @description Restructures NetCDF of magpie land use output and writes it to a specific NetCDF
+#' that can be read by the Spatial Economic Allocation Landscape Simulator (SEALS) model
+#' for generating high resolution land use maps.
+#'
+#' @export
+#'
+#' @param magCellLand Disaggregated land use (grid-cell land area share) in NetCDF format from a MAgPIE run.
+#' @param outFile a file name the output should be written to using \code{ncdf4::nc_create} and \code{ncdf4::ncvar_put}
+#' @param dir output directory which contains cellular magpie output
+#' @param scenName Optional scenario name
+#' @param selectyears Numeric vector of years to provide data for.
+#'
+#' @return Proportions of different land use classes per grid sell in a NetCDF format.
+#'
+#' @author Patrick v. Jeetze
+#' @examples
+#' \dontrun{
+#' x <- reportLandUseForSEALS(magCellLand = "cell.land_0.5_share.nc",
+#'                            outFile = "cell.land_0.5_SEALS.nc",
+#'                            selectyears = c(2015, 2050))
+#' }
+#'
+reportLandUseForSEALS <- function(magCellLand = "cell.land_0.5_share.nc", outFile = "cell.land_0.5_SEALS.nc",
+                                  scenName = NULL, dir = ".", selectyears = c(2015, 2050)) {
+  if (!is.null(scenName)) {
+    outFile <- sub(".nc", paste0("_", scenName, ".nc"), outFile)
+  }
+
+  ### Open the MAgPIE output NetCDF
+  magLand <- ncdf4::nc_open(file.path(dir, magCellLand))
+
+  ### Extract dimensions
+  lon <- ncdf4::ncdim_def("lon", "degrees_east", ncdf4::ncvar_get(magLand, "lon"))
+  # Make sure that order of latitudinal coordinates is in the right order
+  # Check whether latitudinal coordinates are ascending or descending
+  latAscends <- all(diff(ncdf4::ncvar_get(magLand, "lat")) > 0)
+  if (latAscends) {
+    lat <- ncdf4::ncdim_def("lat", "degrees_north", rev(ncdf4::ncvar_get(magLand, "lat")))
+  } else {
+    lat <- ncdf4::ncdim_def("lat", "degrees_north", ncdf4::ncvar_get(magLand, "lat"))
+  }
+  time <- ncdf4::ncdim_def("time", "years", selectyears, unlim = TRUE)
+
+  # Get variable names
+  vnames <- names(magLand$var)
+
+  # Create a new netCDF file with all variable names
+  sealsLand <- ncdf4::nc_create(file.path(dir, outFile),
+    vars = list(
+      ncdf4::ncvar_def("crop", "grid-cell land area fraction", dim = list(lon, lat, time), missval = -9999),
+      ncdf4::ncvar_def("past", "grid-cell land area fraction", dim = list(lon, lat, time), missval = -9999),
+      ncdf4::ncvar_def("primforest", "grid-cell land area fraction", dim = list(lon, lat, time), missval = -9999),
+      ncdf4::ncvar_def("secdforest", "grid-cell land area fraction", dim = list(lon, lat, time), missval = -9999),
+      ncdf4::ncvar_def("forestry", "grid-cell land area fraction", dim = list(lon, lat, time), missval = -9999),
+      ncdf4::ncvar_def("urban", "grid-cell land area fraction", dim = list(lon, lat, time), missval = -9999),
+      ncdf4::ncvar_def("other", "grid-cell land area fraction", dim = list(lon, lat, time), missval = -9999)
+    )
+  )
+
+  # Write values to NetCDF
+  for (vname in vnames) {
+    if (latAscends) {
+      yrIndx <- which(ncdf4::ncvar_get(magLand, "time") %in% selectyears)
+      ncdf4::ncvar_put(sealsLand, vname, ncdf4::ncvar_get(magLand, vname)[, lat$len:1, yrIndx])
+    } else {
+      ncdf4::ncvar_put(sealsLand, vname, ncdf4::ncvar_get(magLand, vname)[, , yrIndx])
+    }
+  }
+
+  # Close connection
+  ncdf4::nc_close(sealsLand)
+
+  # Report completion
+  message(paste0("Finished writing '", outFile, "' into\n'", dir, "'"))
+}

README.md

@@ -1,6 +1,6 @@
 # MAgPIE outputs R package for MAgPIE version 4.x
 
-R package **magpie4**, version **1.188.5**
+R package **magpie4**, version **1.189.0**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/magpie4)](https://cran.r-project.org/package=magpie4) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1158582.svg)](https://doi.org/10.5281/zenodo.1158582) [![R build status](https://github.com/pik-piam/magpie4/workflows/check/badge.svg)](https://github.com/pik-piam/magpie4/actions) [![codecov](https://codecov.io/gh/pik-piam/magpie4/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/magpie4) [![r-universe](https://pik-piam.r-universe.dev/badges/magpie4)](https://pik-piam.r-universe.dev/builds)
 
@@ -39,7 +39,7 @@ In case of questions / problems please contact Benjamin Leon Bodirsky <bodirsky@
 
 To cite package **magpie4** in publications use:
 
-Bodirsky B, Humpenoeder F, Dietrich J, Stevanovic M, Weindl I, Karstens K, Wang X, Mishra A, Beier F, Breier J, Yalew A, Chen D, Biewald A, Wirth S, von Jeetze P, Leip D, Crawford M, Alves M (2023). _magpie4: MAgPIE outputs R package for MAgPIE version 4.x_. doi:10.5281/zenodo.1158582 <https://doi.org/10.5281/zenodo.1158582>, R package version 1.188.5, <https://github.com/pik-piam/magpie4>.
+Bodirsky B, Humpenoeder F, Dietrich J, Stevanovic M, Weindl I, Karstens K, Wang X, Mishra A, Beier F, Breier J, Yalew A, Chen D, Biewald A, Wirth S, von Jeetze P, Leip D, Crawford M, Alves M (2023). _magpie4: MAgPIE outputs R package for MAgPIE version 4.x_. doi:10.5281/zenodo.1158582 <https://doi.org/10.5281/zenodo.1158582>, R package version 1.189.0, <https://github.com/pik-piam/magpie4>.
 
 A BibTeX entry for LaTeX users is
 
@@ -48,7 +48,7 @@ A BibTeX entry for LaTeX users is
   title = {magpie4: MAgPIE outputs R package for MAgPIE version 4.x},
   author = {Benjamin Leon Bodirsky and Florian Humpenoeder and Jan Philipp Dietrich and Miodrag Stevanovic and Isabelle Weindl and Kristine Karstens and Xiaoxi Wang and Abhijeet Mishra and Felicitas Beier and Jannes Breier and Amsalu Woldie Yalew and David Chen and Anne Biewald and Stephen Wirth and Patrick {von Jeetze} and Debbora Leip and Michael Crawford and Marcos Alves},
   year = {2023},
-  note = {R package version 1.188.5},
+  note = {R package version 1.189.0},
   doi = {10.5281/zenodo.1158582},
   url = {https://github.com/pik-piam/magpie4},
 }