reworked gridded output of protectedArea.R

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '233229291'
+ValidationKey: '233260784'
 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: 1.191.1
-date-released: '2023-08-12'
+version: 1.191.2
+date-released: '2023-08-13'
 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: 1.191.1
-Date: 2023-08-12
+Version: 1.191.2
+Date: 2023-08-13
 Authors@R: c(
     person("Benjamin Leon", "Bodirsky", , "[email protected]", role = c("aut", "cre")),
     person("Florian", "Humpenoeder", , "[email protected]", role = "aut"),

R/protectedArea.R

@@ -4,6 +4,7 @@
 #' @export
 #'
 #' @param gdx GDX file
+#' @param cfg config file
 #' @param file a file name the output should be written to using write.magpie
 #' @param level Level of regional aggregation; "cell", "grid", "iso, "reg" (regional), "glo" (global), "regglo" (regional and global) or any secdforest aggregation level defined in superAggregate
 #' @param sum sum over land pools (default = FALSE)
@@ -20,14 +21,116 @@
 #' x <- protectedArea(gdx)
 #' }
 #'
-protectedArea <- function(gdx, file = NULL, level = "cell", sum = FALSE, dir = "."){
+protectedArea <- function(gdx, cfg = NULL, file = NULL, level = "cell", sum = FALSE, dir = "."){
 
   # read in protected areas
   if (level %in% c("grid","iso")) {
     mapfile <- system.file("extdata", "mapping_grid_iso.rds", package="magpie4")
     map_grid_iso <- readRDS(mapfile)
-    a <- setCells(read.magpie(file.path(dir, "cell.conservation_land_0.5.mz")), map_grid_iso$grid)
-    if(level == "iso") a <- gdxAggregate(gdx, a , to = "iso", dir = dir)
+    cmap <- Sys.glob(file.path(dir, "clustermap_*.rds"))
+
+    wdpa_hr_file <- c(
+      file.path(dir, "wdpa_baseline_0.5.mz"),
+      "input/wdpa_baseline_0.5.mz",
+      "modules/22_land_conservation/input/wdpa_baseline_0.5.mz",
+      "../input/wdpa_baseline_0.5.mz",
+      "../modules/22_land_conservation/input/wdpa_baseline_0.5.mz",
+      "../../input/wdpa_baseline_0.5.mz",
+      "../../modules/22_land_conservation/input/wdpa_baseline_0.5.mz.mz"
+    )
+    wdpa_hr_file <- suppressWarnings(wdpa_hr_file[min(which(file.exists(wdpa_hr_file)))])
+
+    consv_prio_hr_file <- c(
+      file.path(dir, "consv_prio_areas_0.5.mz"),
+      "input/consv_prio_areas_0.5.mz",
+      "modules/22_land_conservation/input/consv_prio_areas_0.5.mz",
+      "../input/consv_prio_areas_0.5.mz",
+      "../modules/22_land_conservation/input/consv_prio_areas_0.5.mz",
+      "../../input/consv_prio_areas_0.5.mz",
+      "../../modules/22_land_conservation/input/consv_prio_areas_0.5.mz"
+    )
+    consv_prio_hr_file <- suppressWarnings(consv_prio_hr_file[min(which(file.exists(consv_prio_hr_file)))])
+
+    if (!is.na(wdpa_hr_file)) {
+
+      land_consv_lr <- readGDX(gdx, "pm_land_conservation", react = "silent")
+      wdpa_hr <- read.magpie(wdpa_hr_file)
+
+      # create full time series
+      land_consv_hr <- new.magpie(map_grid_iso$grid, getYears(land_consv_lr), getNames(wdpa_hr))
+      land_consv_hr[, getYears(land_consv_hr), ] <- wdpa_hr[, nyears(wdpa_hr), ]
+      land_consv_hr[, getYears(wdpa_hr), ] <- wdpa_hr
+
+      if (!is.null(cfg)) {
+        if (!all(c(cfg$gms$c22_protect_scenario, cfg$gms$c22_protect_scenario_noselect) %in% "none")) {
+          if (!is.na(consv_prio_hr_file)) {
+            consv_prio_all <- read.magpie(consv_prio_hr_file)
+            consv_prio_hr <- new.magpie(
+              cells_and_regions = map_grid_iso$grid,
+              names = getNames(consv_prio_all, dim = 2), fill = 0
+            )
+            iso <- readGDX(gdx, "iso")
+            consv_iso <- readGDX(gdx, "policy_countries22")
+            consv_iso <- consv_iso[consv_iso %in% getItems(consv_prio_all, dim = 1.1)]
+            consv_select <- cfg$gms$c22_protect_scenario
+            consv_noselect <- cfg$gms$c22_protect_scenario_noselect
+
+            if (consv_noselect != "none") {
+              consv_prio_hr <- collapseDim(consv_prio_all[, , consv_noselect], dim = 3.1)
+            }
+            if (consv_select != "none") {
+              consv_prio_hr[consv_iso, , ] <- collapseDim(consv_prio_all[consv_iso, , consv_select], dim = 3.1)
+            } else if (consv_select == "none") {
+              consv_prio_hr[consv_iso, , ] <- 0
+            }
+            # future conservation only pertains to natveg
+            consv_prio_hr[, , c("crop", "past", "forestry", "urban")] <- 0
+
+            consv_fader <- readGDX(gdx, "p22_conservation_fader", format = "first_found")
+            consv_prio_hr <- consv_prio_hr * consv_fader[, getYears(land_consv_hr), ]
+
+            # add conservation priority areas
+            land_consv_hr <- (land_consv_hr + consv_prio_hr)
+          } else {
+            warning(paste(
+              "Future land conservation used in MAgPIE run but high resolution",
+              "conservation priority data for disaggregation not found."
+            ))
+          }
+        }
+      }
+
+      # Due to internal constraints and compensation (e.g. NDC forest conservation)
+      # the actual land conservation can sometimes be smaller than the land
+      # conservation in the input data (this can especially happen also if
+      # land restoration is switched off). Therefore a scaling is applied here separately
+      # for grassland and natural vegetation
+      if (!is.null(land_consv_lr)) {
+        natveg <- c("primforest", "secdforest", "other")
+        consv_sum_lr <- mbind(
+          dimSums(land_consv_lr[, , "past"], 3.2),
+          setNames(dimSums(land_consv_lr[, , natveg], dim = 3), "natveg")
+        )
+        consv_sum_hr_agg <- mbind(
+          toolAggregate(land_consv_hr[, , "past"], cmap, from = "cell", to = "cluster"),
+          toolAggregate(setNames(dimSums(land_consv_hr[, , natveg], dim = 3), "natveg"),
+            cmap,
+            from = "cell", to = "cluster"
+          )
+        )
+        consv_scaling <- consv_sum_lr / consv_sum_hr_agg
+        consv_scaling[is.na(consv_scaling) | is.infinite(consv_scaling)] <- 1
+        consv_scaling <- toolAggregate(consv_scaling, cmap, from = "cluster", to = "cell")
+        land_consv_hr[, , "past"] <- consv_scaling[, , "past"] * land_consv_hr[, , "past"]
+        land_consv_hr[, , natveg] <- consv_scaling[, , "natveg"] * land_consv_hr[, , natveg]
+      }
+      a <- land_consv_hr
+    } else {
+      stop("Cannot find gridded land conservation input data in output folder.")
+    }
+    if(level == "iso") {
+      a <- gdxAggregate(gdx, a , to = "iso", dir = dir)
+    }
   } else {
     a <- readGDX(gdx, "pm_land_conservation", react = "silent")
     # sum protection and restoration area
@@ -61,6 +164,5 @@ protectedArea <- function(gdx, file = NULL, level = "cell", sum = FALSE, dir = "
   # sum
   if (sum) a <- dimSums(a, dim = 3.1)
 
-
   out(a, file)
 }

README.md

@@ -1,6 +1,6 @@
 # MAgPIE outputs R package for MAgPIE version 4.x
 
-R package **magpie4**, version **1.191.1**
+R package **magpie4**, version **1.191.2**
 
 [![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 1.191.1, <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 (URL: https://doi.org/10.5281/zenodo.1158582), R package version 1.191.2, <URL: 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 1.191.1},
+  note = {R package version 1.191.2},
   doi = {10.5281/zenodo.1158582},
   url = {https://github.com/pik-piam/magpie4},
 }