update emisCO2

Author: flohump

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '4431010'
+ValidationKey: '4450880'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

CITATION.cff

@@ -2,7 +2,7 @@ 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: 2.2.3
+version: 2.2.4
 date-released: '2024-05-27'
 abstract: Common output routines for extracting results from the MAgPIE framework
   (versions 4.x).

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: magpie4
 Title: MAgPIE outputs R package for MAgPIE version 4.x
-Version: 2.2.3
+Version: 2.2.4
 Date: 2024-05-27
 Authors@R: c(
     person("Benjamin Leon", "Bodirsky", , "[email protected]", role = c("aut", "cre")),

R/emisCO2.R

@@ -75,26 +75,6 @@ emisCO2 <- function(gdx, file = NULL, level = "cell", unit = "gas",
     return(x)
   }
 
-  .reorder <- function(x) {
-    a <- getSets(x)
-    if(a[names(a)=="d3.1"]=="ac") {
-      a2 <- a
-      a2[names(a2)=="d3.1"] <- a[names(a)=="d3.2"]
-      a2[names(a2)=="d3.2"] <- a[names(a)=="d3.1"]
-      y <- new.magpie(getCells(x),getYears(x),getNames(x,dim=a2[names(a2)=="d3.1"]),fill=0)
-      names(dimnames(y))[3] <- a2[names(a2)=="d3.1"]
-      y <- add_dimension(y,3.2,a2[names(a2)=="d3.2"],getNames(x,dim=a2[names(a2)=="d3.2"]))
-      if(length(a2[names(a2)=="d3.3"])>0) {
-        y <- add_dimension(y,3.3,a2[names(a2)=="d3.3"],getNames(x,dim=a2[names(a2)=="d3.3"]))
-      }
-      names(dimnames(y))[1] <- names(dimnames(x))[1]
-      names(dimnames(y))[2] <- names(dimnames(x))[2]
-      y[,,] <- x
-      return(y)
-    }
-    return(x)
-  }
-
   ###
   # compose list of total area per land type, compartment
   composeAreas <- function() {
@@ -112,7 +92,6 @@ emisCO2 <- function(gdx, file = NULL, level = "cell", unit = "gas",
 
     other <- readGDX(gdx, "ov_land_other", select = list(type = "level"), react = "silent")
     if(!is.null(other)) {
-      other <- .reorder(other)
       getSets(other)["d3.1"] <- "land"
     } else {
       other <- readGDX(gdx, "ov35_other", select = list(type = "level"))
@@ -170,9 +149,9 @@ emisCO2 <- function(gdx, file = NULL, level = "cell", unit = "gas",
     other <- readGDX(gdx, "ov_land_other", select = list(type = "level"), react = "silent")
     if(!is.null(other)) {
       other <- readGDX(gdx, "p35_carbon_density_other", react = "silent")
-      other <- .reorder(other)
       getSets(other)["d3.1"] <- "land"
       other <- other[, years, ]
+      #other[,,"youngsecdf"][,,"ac0"] <- other[,,"othernat"][,,"ac0"]
     } else {
       other <- readGDX(gdx, "pm_carbon_density_ac")[, years, ]
       other <- add_dimension(other, dim = 3.1, add = "land", nm = "other")
@@ -385,10 +364,10 @@ emisCO2 <- function(gdx, file = NULL, level = "cell", unit = "gas",
     densityMtC   <- densities$other[, , agPools]
     p35_maturesecdf <- readGDX(gdx,"p35_maturesecdf", react = "silent")
     if(!is.null(p35_maturesecdf)) {
-      areaBefore <- .reorder(readGDX(gdx, "p35_land_other"))
-      areaAfter <- .reorder(readGDX(gdx, "ov_land_other", select = list(type = "level")))
+      areaBefore <- readGDX(gdx, "p35_land_other")
+      areaAfter <- readGDX(gdx, "ov_land_other", select = list(type = "level"))
       reductionMha <- .changeAC(areaBefore, areaAfter, mode = "reduction")
-      harvestMha   <- .reorder(readGDX(gdx, "ov35_hvarea_other", select = list(type = "level"), react = "silent"))
+      harvestMha   <- readGDX(gdx, "ov35_hvarea_other", select = list(type = "level"), react = "silent")
     } else {
       densityMtC   <- densities$other[, , agPools]
       reductionMha <- readGDX(gdx, "ov35_other_reduction", select = list(type = "level"), react = "silent")
@@ -702,14 +681,8 @@ emisCO2 <- function(gdx, file = NULL, level = "cell", unit = "gas",
     # --- Ensure that area - subcomponent residual is nearly zero
     # Crop and past are not accounted for in grossEmissions
     residual <- output[, , c("crop", "past"), invert = TRUE][, , "residual"]
-    # saveRDS(residual,"residual.rds")
-    # round(dimSums(residual,dim=1),6)[,,c("youngsecdf")][,,"litc"]
-    # round(dimSums(residual,dim=1),6)[,,c("youngsecdf")][,,"vegc"]
-    p35_forest_recovery_area <- readGDX(gdx,"p35_forest_recovery_area", react = "silent")
-    if (is.null(p35_forest_recovery_area)) {
-      if (any(residual > 1e-06, na.rm = TRUE)) {
-        stop("Inappropriately high residuals in land use sub-components in magpie4::emisCO2")
-      }
+    if (any(residual > 1e-06, na.rm = TRUE)) {
+      stop("Inappropriately high residuals in land use sub-components in magpie4::emisCO2")
     }
 
     # --- Ensure that total net emissions are additive of cc, lu, and interaction (now included in cc)

README.md

@@ -1,6 +1,6 @@
 # MAgPIE outputs R package for MAgPIE version 4.x
 
-R package **magpie4**, version **2.2.3**
+R package **magpie4**, version **2.2.4**
 
 [![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 2.2.3, <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 2.2.4, <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 2.2.3},
+  note = {R package version 2.2.4},
   url = {https://github.com/pik-piam/magpie4},
   doi = {10.5281/zenodo.1158582},
 }