added critical nitrogen boundary exceedance to getReportGridNitrogenP…

…ollution

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '5787530'
+ValidationKey: '41932800'
 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: 2.9.0
-date-released: '2024-08-22'
+version: 2.10.0
+date-released: '2024-09-02'
 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: 2.9.0
-Date: 2024-08-22
+Version: 2.10.0
+Date: 2024-09-02
 Authors@R: c(
     person("Benjamin Leon", "Bodirsky", , "[email protected]", role = c("aut", "cre")),
     person("Florian", "Humpenoeder", , "[email protected]", role = "aut"),

NAMESPACE

@@ -98,6 +98,7 @@ export(getReportFSECStevenLord)
 export(getReportFableScenathon)
 export(getReportGridEmissions)
 export(getReportGridINMS)
+export(getReportGridNitrogenPollution)
 export(getReportINMS)
 export(getReportIso)
 export(getReportMAgPIE2GAINS)

R/getReportGridNitrogenPollution.R

@@ -0,0 +1,123 @@
+#' @title getReportGridNitrogenPollution
+#' @description Reports nutrient surplus indicators as well as exceedance of the critical nitrogen surplus at the
+#' grid level
+#' @author Michael Crawford
+#'
+#' @export
+#'
+#' @param reportOutputDir a folder name for the output to be written to. If NULL the report is not saved to
+#' disk, and only returned to the calling function.
+#' @param magpieOutputDir a magpie output directory which contains a mapping file (clustermap*.rds) for the
+#' disaggregation of grid output
+#' @param scenario the name of the scenario used. If NULL the report is not saved to disk, and only returned to the
+#' calling function.
+#'
+#' @return A list of MAgPIE objects containing the reports
+#'
+#' @importFrom madrat toolConditionalReplace
+#'
+#' @examples
+#'
+#'   \dontrun{
+#'     x <- getReportGridNitrogenPollution(gdx, magpieOutputDir)
+#'   }
+#'
+
+getReportGridNitrogenPollution <- function(magpieOutputDir, reportOutputDir = NULL, scenario = NULL) {
+
+    # -----------------------------------------------------------------------------------------------------------------
+    # Helper functions
+
+    .formatReport <- function(x, name) {
+        getSets(x)[c("d1.1", "d1.2", "d1.3")] <- c("x", "y", "iso")
+        getSets(x, fulldim = FALSE)[3] <- "variable"
+        getNames(x) <- name
+
+        return(x)
+    }
+
+    .saveReport <- function(x, file, comment = NULL) {
+        if (!is.null(reportOutputDir) && !is.null(scenario)) {
+            write.magpie(x,
+                         file_name = file.path(reportOutputDir, paste0(scenario, "-", file, ".nc")),
+                         comment = comment)
+        }
+    }
+
+    # -----------------------------------------------------------------------------------------------------------------
+    # Nutrient surplus from different land-use types
+
+    gdxPath <- file.path(magpieOutputDir, "fulldata.gdx")
+
+    # Cropland
+    croplandBudget  <- reportNitrogenBudgetCropland(gdxPath, grid = TRUE, dir = magpieOutputDir, include_emissions = TRUE)
+    croplandSurplus <- croplandBudget[, , "Nutrient Surplus"]
+    croplandSurplus <- .formatReport(croplandSurplus, "Nutrient surplus from cropland")
+
+    # Pasture
+    pastureBudget  <- reportNitrogenBudgetPasture(gdxPath, grid = TRUE, dir = magpieOutputDir, include_emissions = TRUE)
+    pastureSurplus <- pastureBudget[, , "Nutrient Surplus"]
+    pastureSurplus <- .formatReport(pastureSurplus, "Nutrient surplus from pasture")
+
+    # Manure excretion
+    manureBudget  <- reportGridManureExcretion(gdxPath, dir = magpieOutputDir)
+    manureSurplus <- manureBudget[, , "Manure|Manure In Confinements|+|Losses"]
+    manureSurplus <- .formatReport(manureSurplus, "Nutrient surplus from manure losses in confinements")
+
+    # Non-agricultural land
+    nonAgLandBudget <- reportNitrogenBudgetNonagland(gdxPath, grid = TRUE, dir = magpieOutputDir)
+    nonAgLandSurplus <- nonAgLandBudget[, , "Nutrient Surplus"]
+    nonAgLandSurplus <- .formatReport(nonAgLandSurplus, "Nutrient surplus from non-agricultural land")
+
+    # Calculate total nutrient surplus
+    total <- mbind(croplandSurplus, pastureSurplus, manureSurplus, nonAgLandSurplus)
+    total <- dimSums(total, dim = 3)
+    total <- .formatReport(total, "Nutrient surplus from land and manure management")
+
+    # Save raw surpluses to output folder
+    surpluses <- mbind(croplandSurplus, pastureSurplus, manureSurplus, nonAgLandSurplus, total)
+    .saveReport(surpluses, file = "gridNitrogenSurplus", comment = "Mt N/yr")
+
+    # Total land
+    gridLand  <- reportGridLand(gdxPath, dir = magpieOutputDir)
+    totalLand <- dimSums(gridLand, dim = 3)
+
+    # Calculate intensity of nutrient surplus
+    nutrientSurplus_perTotalArea <- (total / totalLand) * 1e3 # Mt X / Mha to kg X / ha
+
+    # Five cells have 0 "totalLand", which leads to INFs
+    nutrientSurplus_perTotalArea <- toolConditionalReplace(x = nutrientSurplus_perTotalArea,
+                                                           conditions = "!is.finite()",
+                                                           replaceby = 0)
+
+    # Save nutrient surplus intensity to output folder
+    nutrientSurplus_perTotalArea <- .formatReport(nutrientSurplus_perTotalArea, "Nutrient surplus intensity, incl natural vegetation")
+    .saveReport(nutrientSurplus_perTotalArea, file = "gridNutrientSurplus_intensity", comment = "kg N / ha")
+
+    # -----------------------------------
+    # Exceedance of critical nitrogen surplus (based on Schulte-Uebbing et al. 2022)
+
+    nutrientSurplus_exceedance <- NULL
+    criticalNitrogenSurplusPath <- file.path(magpieOutputDir, "criticalNitrogenSurplus.mz")
+    if (file.exists(criticalNitrogenSurplusPath)) {
+        criticalNitrogenSurplus <- read.magpie(criticalNitrogenSurplusPath)
+
+        # Calculate exceedance of the critical nitrogen surplus
+        nutrientSurplus_exceedance <- -1 * (criticalNitrogenSurplus - nutrientSurplus_perTotalArea)
+
+        # Save nutrient surplus exceedance to output folder
+        .saveReport(nutrientSurplus_exceedance, "Exceedance of Critical Nitrogen Surplus", comment = "kg N / ha")
+    }
+
+    # -----------------------------------------------------------------------------------------------------------------
+    # Return
+
+    return(list("nutrientSurplus_cropland"   = croplandSurplus,
+                "nutrientSurplus_pasture"    = pastureSurplus,
+                "nutrientSurplus_manure"     = manureSurplus,
+                "nutrientSurplus_nonAgLand"  = nonAgLandSurplus,
+                "nutrientSurplus_total"      = total,
+                "nutrientSurplus_intensity"  = nutrientSurplus_perTotalArea,
+                "nutrientSurplus_exceedance" = nutrientSurplus_exceedance))
+
+}

README.md

@@ -1,6 +1,6 @@
 # MAgPIE outputs R package for MAgPIE version 4.x
 
-R package **magpie4**, version **2.9.0**
+R package **magpie4**, version **2.10.0**
 
 [![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 (2024). _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 2.9.0, <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 (2024). _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 2.10.0, <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 = {2024},
-  note = {R package version 2.9.0},
+  note = {R package version 2.10.0},
   url = {https://github.com/pik-piam/magpie4},
   doi = {10.5281/zenodo.1158582},
 }