Merge pull request #49 from johanneskoch94/master

Drop SSP2EU and pop_ prefixes

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '30770038'
+ValidationKey: '30831500'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package .* was built under R version'

.github/workflows/check.yaml

@@ -44,6 +44,13 @@ jobs:
           [ -f requirements.txt ] && python -m pip install --upgrade pip wheel || true
           [ -f requirements.txt ] && pip install -r requirements.txt || true
 
+      - name: Run pre-commit checks
+        shell: bash
+        run: |
+          python -m pip install pre-commit
+          python -m pip freeze --local
+          pre-commit run --show-diff-on-failure --color=always --all-files
+
       - name: Verify validation key
         shell: Rscript {0}
         run: lucode2:::validkey(stopIfInvalid = TRUE)

.pre-commit-config.yaml

@@ -25,4 +25,4 @@ repos:
     -   id: readme-rmd-rendered
     -   id: use-tidy-description
 ci:
-    autoupdate_schedule: quarterly
+    autoupdate_schedule: weekly

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: 'mrmagpie: madrat based MAgPIE Input Data Library'
-version: 1.53.1
-date-released: '2025-01-10'
+version: 1.53.2
+date-released: '2025-02-06'
 abstract: Provides functions for MAgPIE country and cellular input data generation.
 authors:
 - family-names: Karstens

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: mrmagpie
 Title: madrat based MAgPIE Input Data Library
-Version: 1.53.1
-Date: 2025-01-10
+Version: 1.53.2
+Date: 2025-02-06
 Authors@R: c(
     person("Kristine", "Karstens", , "[email protected]", role = c("aut", "cre")),
     person("Jan Philipp", "Dietrich", , "[email protected]", role = "aut"),

R/calcGridPop.R

@@ -53,13 +53,12 @@ calcGridPop <- function(source = "ISIMIP", subtype = "all", # nolint
 
       if (subtype == "past") {
         # Add scenario dimension and fill with same value
-        x <- add_columns(x, dim = 3.1, addnm = c("pop_SSP1", "pop_SSP2", "pop_SSP3", "pop_SSP4", "pop_SSP5"))
+        x <- add_columns(x, dim = 3.1, addnm = c("SSP1", "SSP2", "SSP3", "SSP4", "SSP5"))
         x[, , 2:6] <- x[, , 1]
         x <- (x[, , -1])
       }
     } else if (src == "Gao") {
       x <- readSource("GridPopGao", subtype = subtype, convert = FALSE)
-      getNames(x, dim = 1) <- paste0("pop_", getNames(x, dim = 1))
 
       if (!urban && subtype == "future") {
         x <- collapseNames(dimSums(x, dim = 3.2))
@@ -90,8 +89,7 @@ calcGridPop <- function(source = "ISIMIP", subtype = "all", # nolint
                 "Use Gao source instead for cellular urban/rural population")
 
         # urban population at country-level
-        urbanPop <- calcOutput("Urban", aggregate = FALSE)
-        getNames(urbanPop) <- gsub("urb_", "", getNames(urbanPop))
+        urbanPop <- calcOutput("Urban", scenario = c("SSPs", "SDPs"), naming = "scenario", aggregate = FALSE)
         # disaggregate to cell level
         coordMapping <- toolGetMappingCoord2Country()
         urbanPop <- toolAggregate(urbanPop,
@@ -111,7 +109,7 @@ calcGridPop <- function(source = "ISIMIP", subtype = "all", # nolint
     # harmonize future SSPs to divergence year by making them SSP2
     selectY <- 1:which(getYears(future, as.integer = TRUE) == harmonize_until)
     harmY   <- getYears(future, as.integer = TRUE)[selectY]
-    future[, harmY, ] <- future[, harmY, "pop_SSP2"]
+    future[, harmY, ] <- future[, harmY, "SSP2"]
 
     # take future years in case of overlap
     pYears <- setdiff(getYears(past), getYears(future))
@@ -126,24 +124,18 @@ calcGridPop <- function(source = "ISIMIP", subtype = "all", # nolint
   }
 
   # Add SDP, SDP_EI, SDP_RC and SDP_MC scenarios as copy of SSP1
-  if ("pop_SSP1" %in% getNames(x, dim = 1) && !("pop_SDP" %in% getNames(x, dim = 1))) {
-    combinedSDP <- x[, , "pop_SSP1"]
+  if ("SSP1" %in% getNames(x, dim = 1) && !("SDP" %in% getNames(x, dim = 1))) {
+    combinedSDP <- x[, , "SSP1"]
     for  (i in c("SDP", "SDP_EI", "SDP_RC", "SDP_MC")) {
-      getNames(combinedSDP) <- gsub("SSP1", i, getNames(x[, , "pop_SSP1"]))
+      getNames(combinedSDP) <- gsub("SSP1", i, getNames(x[, , "SSP1"]))
       x <- mbind(x, combinedSDP)
     }
   }
-  # Add SSP2EU as copy of SSP2
-  if ("pop_SSP2" %in% getNames(x, dim = 1) && !("pop_SSP2EU" %in% getNames(x, dim = 1))) {
-    combinedEU <- x[, , "pop_SSP2"]
-    getNames(combinedEU) <- gsub("SSP2", "SSP2EU", getNames(x[, , "pop_SSP2"]))
-    x <- mbind(x, combinedEU)
-  }
 
   if (scale) {
     ## Scale to match country-level data
     # Country-level population data (in million)
-    pop <- calcOutput("Population", aggregate = FALSE)
+    pop <- calcOutput("Population", scenario = c("SSPs", "SDPs"), naming = "scenario", aggregate = FALSE)
     # aggregate to country-level and scale to match WDI country-level pop
     if (cells == "lpjcell") {
       agg <- collapseNames(dimSums(x, dim = c("x", "y")))
@@ -172,7 +164,7 @@ calcGridPop <- function(source = "ISIMIP", subtype = "all", # nolint
     # even division of population across cells
     missing <- magclass::where(scF[commonCountries, , ] == 0)$true$regions
     for (i in missing) {
-      x[i, , ] <- pop[i, , "pop_SSP2"] / length(getCells(x[i, , ]))
+      x[i, , ] <- pop[i, , "SSP2"] / length(getCells(x[i, , ]))
     }
   }
   # unit conversion to million people
@@ -183,9 +175,6 @@ calcGridPop <- function(source = "ISIMIP", subtype = "all", # nolint
     x <- x[, intersect(years, getYears(x)), ]
   }
 
-  if (subtype == "all") {
-    getNames(x) <- gsub("pop_", "", getNames(x))
-  }
   # Checks
   if (any(is.na(x))) {
     stop("Function calcGridPop returned NAs.")

R/readGridPopIsimip.R

@@ -68,8 +68,8 @@ readGridPopIsimip <- function(subtype) {
     sspNaming <- NULL
     for (file in files) {
       sspNaming <- append(sspNaming,
-                          paste0("pop_", toupper(unlist(regmatches(file,
-                                                                   gregexpr("ssp[0-9]", file))))))
+                          paste0(toupper(unlist(regmatches(file,
+                                                           gregexpr("ssp[0-9]", file))))))
       x[[file]] <- read(file)
     }
     x           <- mbind(x)

README.md

@@ -1,6 +1,6 @@
 # madrat based MAgPIE Input Data Library
 
-R package **mrmagpie**, version **1.53.1**
+R package **mrmagpie**, version **1.53.2**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/mrmagpie)](https://cran.r-project.org/package=mrmagpie) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4319612.svg)](https://doi.org/10.5281/zenodo.4319612) [![R build status](https://github.com/pik-piam/mrmagpie/workflows/check/badge.svg)](https://github.com/pik-piam/mrmagpie/actions) [![codecov](https://codecov.io/gh/pik-piam/mrmagpie/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/mrmagpie) [![r-universe](https://pik-piam.r-universe.dev/badges/mrmagpie)](https://pik-piam.r-universe.dev/builds)
 
@@ -39,7 +39,7 @@ In case of questions / problems please contact Kristine Karstens <karstens@pik-p
 
 To cite package **mrmagpie** in publications use:
 
-Karstens K, Dietrich J, Chen D, Windisch M, Alves M, Beier F, Köberle A, v. Jeetze P, Mishra A, Humpenoeder F, Sauer P (2025). "mrmagpie: madrat based MAgPIE Input Data Library." doi:10.5281/zenodo.4319612 <https://doi.org/10.5281/zenodo.4319612>, Version: 1.53.1, <https://github.com/pik-piam/mrmagpie>.
+Karstens K, Dietrich J, Chen D, Windisch M, Alves M, Beier F, Köberle A, v. Jeetze P, Mishra A, Humpenoeder F, Sauer P (2025). "mrmagpie: madrat based MAgPIE Input Data Library." doi:10.5281/zenodo.4319612 <https://doi.org/10.5281/zenodo.4319612>, Version: 1.53.2, <https://github.com/pik-piam/mrmagpie>.
 
 A BibTeX entry for LaTeX users is
 
@@ -48,9 +48,9 @@ A BibTeX entry for LaTeX users is
   title = {mrmagpie: madrat based MAgPIE Input Data Library},
   author = {Kristine Karstens and Jan Philipp Dietrich and David Chen and Michael Windisch and Marcos Alves and Felicitas Beier and Alexandre Köberle and Patrick {v. Jeetze} and Abhijeet Mishra and Florian Humpenoeder and Pascal Sauer},
   doi = {10.5281/zenodo.4319612},
-  date = {2025-01-10},
+  date = {2025-02-06},
   year = {2025},
   url = {https://github.com/pik-piam/mrmagpie},
-  note = {Version: 1.53.1},
+  note = {Version: 1.53.2},
 }
 ```