readLPJmL

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '2358938'
+ValidationKey: '2399520'
 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: 'mrlandcore: One-line description of this awesome package'
-version: 1.1.8
-date-released: '2024-09-25'
+version: 1.2.0
+date-released: '2024-09-30'
 abstract: One-paragraph description of this awesome package.
 authors:
 - family-names: Beier

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: mrlandcore
 Title: One-line description of this awesome package
-Version: 1.1.8
-Date: 2024-09-25
+Version: 1.2.0
+Date: 2024-09-30
 Authors@R: c(
     person("Felicitas", "Beier", , "beier@pik-potsdam.de", role = c("aut", "cre")),
     person("Kristine", "Karstens", role = "aut"),

R/readLPJmL.R

@@ -0,0 +1,102 @@
+#' @title readLPJmL
+#'
+#' @description Read in LPJmL outputs
+#'
+#' @param subtype Switch between different inputs
+#'                (eg. "LPJmL5.2_Pasture:IPSL_CM6A_LR:ssp126_co2_limN_00:soilc_past_hist")
+#'
+#' @return List of magpie objects with results on cellular level, weight, unit and description.
+#'
+#' @author Felicitas Beier, Sebastian Ostberg, Michael Crawford
+#'
+#' @seealso
+#' [readLPJ()]
+#' @examples
+#' \dontrun{
+#' readSource("LPJmL", convert = FALSE)
+#' }
+
+# nolint start
+### This function should be adjusted during the LPJmL - MAgPIE - Hackathon ###
+# Testing locations:
+# /p/projects/rd3mod/inputdata/sources/LPJmL
+# example subtype: lpjml5.9.5.mag1.MRI.ESM2.0.ssp370.crop.sdate
+
+# Testing data:
+# subtype <- "lpjml5.9.5.mag1.MRI.ESM2.0.ssp370.crop.sdate"
+# setwd("/p/projects/rd3mod/inputdata/sources/LPJmL/lpjml5.9.5.mag1.MRI.ESM2.0.ssp370.pnv.mrunoff")
+# setwd("/p/projects/rd3mod/inputdata/sources/LPJmL/lpjml5.9.5.mag1.MRI.ESM2.0.ssp370.crop.sdate")
+# nolint end
+
+readLPJmL <- function(subtype = "lpjml5.9.5.mag1.MRI.ESM2.0.ssp370.crop.sdate") {
+
+  # filenames for dataset and grid
+  files <- list.files(path = subtype, pattern = "\\.bin\\.json$", full.names = TRUE)
+  gridname <- lpjmlkit::find_varfile(subtype, variable = "grid")
+  dataname <- grep("grid", files, invert = TRUE, value = TRUE)
+  if (length(dataname) != 1) {
+    stop("More than one data file is present in the LPJmL source directory.")
+  }
+
+  # read in LPJmL dataset
+  x <- lpjmlkit::read_io(dataname)
+
+  # generate a mapping from LPJmL lon-lat to MAgPIE coord
+  # extract grid information
+  x$add_grid(gridname, silent = TRUE)
+  grid <- x$grid$data
+
+  # transform to format of magpie object while maintaining cell order
+  lon <- gsub("\\.", "p", grid[, "lon"])
+  lat <- gsub("\\.", "p", grid[, "lat"])
+  coordsLPJmL <- paste(lon, lat, sep = ".")
+
+  # sort mapping according to provided grid to ensure consistency
+  mapping <- mstools::toolGetMappingCoord2Country(pretty = FALSE, extended = FALSE)
+  matches <- match(x = coordsLPJmL, table = mapping$coords)
+  if (any(is.na(matches))) {
+    stop("Discrepancy between spatial extent of LPJmL coords and MAgPIE coords")
+  }
+  mapping <- mapping[matches, ]
+
+  # transform time dimension
+  x$transform(to = "year_month_day")
+  if ("month" %in% names(dimnames(x))) {
+    x <- aperm(x$data, c("cell", "year", "month", "band"))
+  } else {
+    x <- x$data
+  }
+  x <- drop(x)
+
+  # transform x into a MAgPIE object
+  x <- magclass::as.magpie(x, spatial = 1)
+
+  meta <- lpjmlkit::read_meta(dataname)
+  bandNames <- sub("^(rainfed|irrigated)\\s+", "", meta$band_names)
+
+  # MIKE: Move mapping to mrlandcore
+  lpj2mag <- madrat::toolGetMapping("MAgPIE_LPJmL.csv", type = "sectoral", where = "mappingfolder")
+  hasCrops <- any(bandNames %in% lpj2mag$LPJmL5)
+  if (hasCrops) {
+
+    # differentiate between rainfed and irrigated crops in the case of crop data
+    irrigation <- sub(" .*", "", getNames(x)) # select first word (of, e.g. "rainfed temperature cereals")
+    crop <- sub("^[^ ]+\\s+", "", getNames(x)) # select everything after first word
+    x <- magclass::add_dimension(x, dim = 3.1, add = "irrigation", nm = "dummy")
+    getNames(x, dim = "irrigation") <- irrigation
+    getNames(x, dim = "band") <- crop
+
+    # transform LPJmL5 to LPJmL-internal names
+    x <- madrat::toolAggregate(x, rel = lpj2mag, from = "LPJmL5", to = "LPJmL", dim = 3.2, partrel = TRUE)
+    magclass::getSets(x)["d3.2"] <- "crop"
+
+  }
+
+  # use coordinate mapping to assign MAgPIE coords and iso
+  x <- magclass::add_dimension(x, dim = 1.1, add = "lon", nm = "dummy")
+  x <- magclass::add_dimension(x, dim = 1.2, add = "lat", nm = "dummy")
+  magclass::getItems(x, dim = 1, raw = TRUE) <- paste(mapping$coords, mapping$iso, sep = ".")
+  magclass::getSets(x)[c("d1.1", "d1.2", "d1.3")] <- c("x", "y", "iso")
+
+  return(x)
+}

README.md

@@ -1,6 +1,6 @@
 # One-line description of this awesome package
 
-R package **mrlandcore**, version **1.1.8**
+R package **mrlandcore**, version **1.2.0**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/mrlandcore)](https://cran.r-project.org/package=mrlandcore)  [![R build status](https://github.com/pik-piam/mrlandcore/workflows/check/badge.svg)](https://github.com/pik-piam/mrlandcore/actions) [![codecov](https://codecov.io/gh/pik-piam/mrlandcore/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/mrlandcore) [![r-universe](https://pik-piam.r-universe.dev/badges/mrlandcore)](https://pik-piam.r-universe.dev/builds)
 
@@ -38,7 +38,7 @@ In case of questions / problems please contact Felicitas Beier <beier@pik-potsda
 
 To cite package **mrlandcore** in publications use:
 
-Beier F, Karstens K, Alves M, Philipp Dietrich J, Leon Bodirsky B, Hoetten D, Humpenoeder F, Heinke J, v. Jeetze P, Mishra A, Beier F, Wirth S, Chen D, Kreidenweis U (2024). _mrlandcore: One-line description of this awesome package_. R package version 1.1.8, <https://github.com/pik-piam/mrlandcore>.
+Beier F, Karstens K, Alves M, Philipp Dietrich J, Leon Bodirsky B, Hoetten D, Humpenoeder F, Heinke J, v. Jeetze P, Mishra A, Beier F, Wirth S, Chen D, Kreidenweis U (2024). _mrlandcore: One-line description of this awesome package_. R package version 1.2.0, <https://github.com/pik-piam/mrlandcore>.
 
 A BibTeX entry for LaTeX users is
 
@@ -47,7 +47,7 @@ A BibTeX entry for LaTeX users is
   title = {mrlandcore: One-line description of this awesome package},
   author = {Felicitas Beier and Kristine Karstens and Marcos Alves and Jan {Philipp Dietrich} and Benjamin {Leon Bodirsky} and David Hoetten and Florian Humpenoeder and Jens Heinke and Patrick {v. Jeetze} and Abhijeet Mishra and Felcitas Beier and Stephen Wirth and David Chen and Ulrich Kreidenweis},
   year = {2024},
-  note = {R package version 1.1.8},
+  note = {R package version 1.2.0},
   url = {https://github.com/pik-piam/mrlandcore},
 }
 ```