updated reportTrade and reportEmmissions to allow for reporting of va…

…riables required for AgMIP

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '2377813140'
+ValidationKey: '2377832920'
 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: 1.202.13
+version: 1.202.14
 date-released: '2024-02-27'
 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: 1.202.13
+Version: 1.202.14
 Date: 2024-02-27
 Authors@R: c(
     person("Benjamin Leon", "Bodirsky", , "[email protected]", role = c("aut", "cre")),

R/getReportAgMIP.R

@@ -93,7 +93,6 @@ getReportAgMIP <- function(gdx, file = NULL, scenario = NULL, filter = c(1, 2, 7
                     "reportEmissions(gdx)",
                     #                    "reportEmisAerosols(gdx)", #nolint
                     #                    "reportEmissionsBeforeTechnicalMitigation(gdx)", #nolint
-                    #                    "reportEmisPhosphorus(gdx)", #nolint
                     #                    "reportCosts(gdx)", #nolint
                     #                    "reportCostsPresolve(gdx)", #nolint
                     #                    "reportPriceFoodIndex(gdx)", #nolint
@@ -102,6 +101,7 @@ getReportAgMIP <- function(gdx, file = NULL, scenario = NULL, filter = c(1, 2, 7
                     #                    "reportPriceLand(gdx)", #nolint
                     #                    "reportPriceWater(gdx)", #nolint
                     "reportValueTrade(gdx, detail = TRUE)",
+                    "reportFactorCostShares(gdx, type = 'requirements')",
                     #                    "reportValueConsumption(gdx)", #nolint
                     #                   "reportProcessing(gdx, indicator='primary_to_process')", #nolint
                     #                    "reportProcessing(gdx, indicator='secondary_from_primary')", #nolint
@@ -126,6 +126,10 @@ getReportAgMIP <- function(gdx, file = NULL, scenario = NULL, filter = c(1, 2, 7
   x <- .filtermagpie(mbind(output), gdx, filter = filter)
   names(dimnames(x)) <- c("i", "year", "data")
 
+  # Add non-traded goods with value of zero to trade reporting
+  nontraded <- findset("k_notrade")
+
+
   ### conversion to AgMIP regions in 3 steps
   # Downscaling from MAgPIE regions to country level
   # Aggregation from country level to AgMIP regions

R/reportEmissions.R

@@ -8,7 +8,6 @@
 #' @return GHG emissions as MAgPIE object (Unit: Mt CO2/yr, Mt N2O/yr, and Mt CH4/yr, for cumulative emissions Gt CO2)
 #' @author Florian Humpenoeder, Benjamin Leon Bodirsky, Michael Crawford
 #' @examples
-#'
 #' \dontrun{
 #' x <- reportEmissions(gdx)
 #' }
@@ -31,7 +30,6 @@
 #' @md
 #'
 reportEmissions <- function(gdx, storageWood = TRUE) {
-
   # -----------------------------------------------------------------------------------------------------------------
   # Calculate CO2 emissions from a MAgPIE .gdx file
 
@@ -46,8 +44,8 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
   .calcCO2 <- function(.lowpass = 3, .cumulative = FALSE, .raw = FALSE, .landCarbonSink = "grassi") {
 
     co2 <- emisCO2(gdx,
-                     level = "regglo", unit = "gas", sum_land = FALSE, sum_cpool = FALSE,
-                     lowpass = .lowpass, cumulative = .cumulative)
+                   level = "regglo", unit = "gas", sum_land = FALSE, sum_cpool = FALSE,
+                   lowpass = .lowpass, cumulative = .cumulative)
 
     if (.landCarbonSink == "grassi") {
       # To ensure consistency with national forest inventories, we replace our estimates of indirect emissions
@@ -157,7 +155,7 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
     if (is.null(peatland)) {
       peatland <- new.magpie(getCells(co2), getYears(co2), "peatland", fill = 0)
     } else {
-      peatland <- setNames(dimSums(peatland[,,c("co2","doc")], dim = 3), "peatland")
+      peatland <- setNames(dimSums(peatland[, , c("co2", "doc")], dim = 3), "peatland")
     }
 
     if (!is.null(peatland)) {
@@ -333,11 +331,10 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
   # Calculated indirect emissions from land-use change from a .gdx file
 
   .calcLandCarbonSink <- function(.lowpass = 3, .cumulative = FALSE) {
-
     # Estimate of land-carbon sink from LPJmL
     co2 <- emisCO2(gdx,
-                     level = "regglo", unit = "gas", sum_land = FALSE, sum_cpool = FALSE,
-                     lowpass = .lowpass, cumulative = .cumulative)
+                   level = "regglo", unit = "gas", sum_land = FALSE, sum_cpool = FALSE,
+                   lowpass = .lowpass, cumulative = .cumulative)
 
     # Estimate of land-carbon sink from LPJmL
     LPJmlLCS <- co2[, , "cc", drop = TRUE]
@@ -467,15 +464,15 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
     peatland_n2o <- c("peatland")
 
     nEmissions <- Emissions(gdx, level = "regglo", type = .type, unit = "gas", subcategories = TRUE, inorg_fert_split = TRUE)
-    #use PeatlandEmissions for reporting to exclude emissions from intact peatlands
-    if (.type %in% c("n2o_n","n2o_n_direct")) {
-      if ("peatland" %in% getItems(nEmissions, dim = 3.1)) nEmissions <- nEmissions[,,"peatland",invert=TRUE]
+    # use PeatlandEmissions for reporting to exclude emissions from intact peatlands
+    if (.type %in% c("n2o_n", "n2o_n_direct")) {
+      if ("peatland" %in% getItems(nEmissions, dim = 3.1)) nEmissions <- nEmissions[, , "peatland", invert = TRUE]
       peatlandN2O <- PeatlandEmissions(gdx, unit = "gas", level = "regglo", intact = FALSE)
       if (is.null(peatlandN2O)) {
         nEmissions <- add_columns(nEmissions, addnm = "peatland", dim = "emis_source", fill = 0)
       } else {
         nEmissions <- add_columns(nEmissions, addnm = "peatland", dim = "emis_source", fill = 0)
-        nEmissions[,,"peatland"] <- collapseNames(peatlandN2O[, , "n2o"])
+        nEmissions[, , "peatland"] <- collapseNames(peatlandN2O[, , "n2o"])
       }
     }
 
@@ -528,8 +525,8 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
 
   # combine all CH4 emissions in one object
   ch4 <- collapseNames(Emissions(gdx, level = "regglo", type = "ch4", unit = "gas", subcategories = TRUE), collapsedim = 2)
-  #use PeatlandEmissions for reporting to exclude emissions from intact peatlands
-  if ("peatland" %in% getNames(ch4, dim = 1)) ch4 <- ch4[,,"peatland",invert=TRUE]
+  # use PeatlandEmissions for reporting to exclude emissions from intact peatlands
+  if ("peatland" %in% getNames(ch4, dim = 1)) ch4 <- ch4[, , "peatland", invert = TRUE]
   peatlandCH4 <- PeatlandEmissions(gdx, unit = "gas", level = "regglo", intact = FALSE)
   if (is.null(peatlandCH4)) {
     ch4 <- add_columns(ch4, addnm = "peatland", dim = "emis_source", fill = 0)
@@ -564,6 +561,18 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
     emissions <- Emissions(gdx, level = "regglo", type = "n2o_n", unit = .unit, subcategories = TRUE)
     emissions <- collapseNames(emissions, collapsedim = 2)
 
+    # disaggregate N2O emissions to croparea by crop using Nitrogen withdrawals as weight
+    withdrawalN  <- collapseNames(NitrogenBudgetWithdrawals(gdx, kcr = "kcr", net = TRUE, level = "regglo"))
+    emisCroparea <- dimSums(emissions[, , c("SOM", "inorg_fert", "man_crop", "awms", "resid", "rice")], dim = 3)
+    mapping <- data.frame(kall = getItems(withdrawalN, dim = 3),
+                          d3 = rep("NULL", length(getItems(withdrawalN, dim = 3))))
+    emisCropareabycrop <- toolAggregate(x = emisCroparea, rel = mapping,
+                                        weight = withdrawalN,
+                                        from = "d3", to = "kall", dim = 3)
+    emisCropareabycrop <- reporthelper(emisCropareabycrop, dim = 3.1,
+                                       level_zero_name = "Emissions|N2O_GWP100AR6|Land|Agriculture|Croparea",
+                                       detail = TRUE, sort = FALSE, partly = FALSE, version = NULL)
+
     .createReport <- function(.emission, .name = NULL) {
       t <- dimSums(emissions[, , .emission], dim = 3)
       n <- paste0("Emissions|N2O_", .unit, "|Land", .name, " (Mt CO2e/yr)")
@@ -586,7 +595,8 @@ reportEmissions <- function(gdx, storageWood = TRUE) {
       .createReport(c("resid_burn"),                                                  "|+|Biomass Burning"),
       .createReport(c("resid_burn"),                                                  "|Biomass Burning|+|Burning of Crop Residues"),
       .createReport(c("peatland"),                                                    "|+|Peatland"),
-      .createReport(c("peatland"),                                                    "|Peatland|+|Managed")
+      .createReport(c("peatland"),                                                    "|Peatland|+|Managed"),
+      emisCropareabycrop
     )
     # nolint end
 

R/reportTrade.R

@@ -17,45 +17,58 @@
 
 reportTrade <- function(gdx, detail = FALSE) {
 
+  nontraded <- findset("k_notrade")
+
   x <- NULL
 
   # net-exports
   out <- trade(gdx,level = "regglo",type = "net-exports")
+  # add non-traded goods with value of 0
+  out <- add_columns(out, addnm = nontraded, dim = 3)
+  out[, , nontraded] <- 0
 
-  out <- reporthelper(x=out,dim = 3.1,level_zero_name = "Trade|Net-Trade", detail = detail,partly=TRUE)
-  getNames(out) <- paste(getNames(out),"(Mt DM/yr)",sep=" ")
+  out <- reporthelper(x = out, dim = 3.1, level_zero_name = "Trade|Net-Trade",
+                      detail = detail, partly = TRUE)
+  getNames(out) <- paste(getNames(out), "(Mt DM/yr)", sep = " ")
   x <- mbind(x,out)
-  x <- summationhelper(x,excludeLevels=1)
+  x <- summationhelper(x, excludeLevels = 1)
 
   # # gross exports
    out <- trade(gdx,level = "regglo",type = "exports")
-   out<-reporthelper(x=out,dim = 3.1,level_zero_name = "Trade|Exports",detail = detail, partly = TRUE)
+   # add non-traded goods with value of 0
+   out <- add_columns(out, addnm = nontraded, dim = 3)
+   out[, , nontraded] <- 0
+
+   out <- reporthelper(x = out, dim = 3.1,
+                       level_zero_name = "Trade|Exports", detail = detail, partly = TRUE)
    getNames(out) <- paste(getNames(out),"(Mt DM/yr)",sep=" ")
-   out <- summationhelper(out,excludeLevels=1)
-   x <- mbind(x,out)
+   out <- summationhelper(out, excludeLevels = 1)
+   x   <- mbind(x,out)
   #
   # # gross imports
-   out<-trade(gdx,level = "regglo",type = "imports")
-   out<-reporthelper(x=out,dim = 3.1,level_zero_name = "Trade|Imports",detail = detail, partly = TRUE)
-   getNames(out) <- paste(getNames(out),"(Mt DM/yr)",sep=" ")
-   out <- summationhelper(out,excludeLevels=1)
-   x <- mbind(x,out)
+   out <- trade(gdx,level = "regglo",type = "imports")
+   # add non-traded goods with value of 0
+   out <- add_columns(out, addnm = nontraded, dim = 3)
+   out[, , nontraded] <- 0
+
+   out <- reporthelper(x = out, dim = 3.1,level_zero_name = "Trade|Imports", detail = detail, partly = TRUE)
+   getNames(out) <- paste(getNames(out), "(Mt DM/yr)", sep=" ")
+   out <- summationhelper(out, excludeLevels = 1)
+   x <- mbind(x, out)
 
   # self_sufficiency
-  self_suff<-suppressMessages(trade(gdx,level = "regglo",relative=TRUE,weight=TRUE))
-  weight<-self_suff$weight
-  self_suff<-self_suff$x
-  out<-(
-    reporthelper(x=self_suff*weight,dim = 3.1,level_zero_name = "Trade|Self-sufficiency",detail = detail)
-    / reporthelper(x=weight,dim = 3.1,level_zero_name = "Trade|Self-sufficiency",detail = detail)
-  )
-
-  #correct after report helping here
-#x/0 --> 100
-#0/0 --> 1
-
-  getNames(out) <- paste(getNames(out),"(1)",sep=" ")
-  x <- mbind(x,out)
+  self_suff <- suppressMessages(trade(gdx, level = "regglo", relative = TRUE, weight = TRUE))
+  weight    <- self_suff$weight
+  self_suff <- self_suff$x
+  out <- (reporthelper(x = self_suff * weight, dim = 3.1,
+                       level_zero_name = "Trade|Self-sufficiency",
+                       detail = detail) / reporthelper(x = weight,
+                                                       dim = 3.1,
+                                                       level_zero_name = "Trade|Self-sufficiency",
+                                                       detail = detail))
+
+  getNames(out) <- paste(getNames(out), "(1)", sep = " ")
+  x <- mbind(x, out)
 
   return(x)
 }

README.md

@@ -1,6 +1,6 @@
 # MAgPIE outputs R package for MAgPIE version 4.x
 
-R package **magpie4**, version **1.202.13**
+R package **magpie4**, version **1.202.14**
 
 [![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 (URL: https://doi.org/10.5281/zenodo.1158582), R package version 1.202.13, <URL: 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 1.202.14, <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 1.202.13},
+  note = {R package version 1.202.14},
   doi = {10.5281/zenodo.1158582},
   url = {https://github.com/pik-piam/magpie4},
 }