Merge pull request #73 from caviddhen/master

Update to 2017 GDP Base Year
pik-piam · Sep 23, 2024 · c444ba3 · c444ba3
2 parents 3059901 + 48fc4df
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diff --git a/.buildlibrary b/.buildlibrary
@@ -1,4 +1,4 @@
-ValidationKey: '42496614'
+ValidationKey: '42576570'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

diff --git a/CITATION.cff b/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: 2.12.6
+version: 2.13.0
 date-released: '2024-09-23'
 abstract: Common output routines for extracting results from the MAgPIE framework
   (versions 4.x).

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: magpie4
 Title: MAgPIE outputs R package for MAgPIE version 4.x
-Version: 2.12.6
+Version: 2.13.0
 Date: 2024-09-23
 Authors@R: c(
     person("Benjamin Leon", "Bodirsky", , "[email protected]", role = c("aut", "cre")),

diff --git a/NAMESPACE b/NAMESPACE
@@ -198,7 +198,6 @@ export(reportNitrogenBudgetPasture)
 export(reportNitrogenEfficiencies)
 export(reportNitrogenPollution)
 export(reportOutputPerWorker)
-export(reportOverallCosts)
 export(reportPBbiosphere)
 export(reportPBland)
 export(reportPBnitrogen)

diff --git a/R/AgGDP.R b/R/AgGDP.R
@@ -6,7 +6,7 @@
 #' @param gdx GDX file
 #' @param file a file name the output should be written to using write.magpie
 #' @param level Level of regional aggregation; "reg" (regional), "glo" (global), "regglo" (regional and global) or any other aggregation level defined in superAggregate
-#' @return A MAgPIE object containing values related with overall value of production [million US$05]
+#' @return A MAgPIE object containing values related with overall value of production [million US$17]
 #' @author Edna Molina Bacca
 #' @importFrom luscale superAggregate
 #' @examples

diff --git a/R/CostCapital.R b/R/CostCapital.R
@@ -7,7 +7,7 @@
 #' @param type either capital stocks ("stocks") or overall capital investment "investment"
 #' @param file a file name the output should be written to using write.magpie
 #' @param level Level of regional aggregation; "reg" (regional), "glo" (global), "regglo" (regional and global) or any other aggregation level defined in superAggregate
-#' @return A MAgPIE object containing values related with overall value of production [million US$05]
+#' @return A MAgPIE object containing values related with overall value of production [million US$17]
 #' @author Edna Molina Bacca
 #' @importFrom luscale superAggregate
 #' @examples

diff --git a/R/CostInputFactorsCrop.R b/R/CostInputFactorsCrop.R
@@ -9,7 +9,7 @@
 #' the sticky realization.
 #' @param file a file name the output should be written to using write.magpie
 #' @param level Level of regional aggregation
-#' @return A MAgPIE object containing values related with overall value of production [million US$05]
+#' @return A MAgPIE object containing values related with overall value of production [million US$17]
 #' @author Edna Molina Bacca
 #' @importFrom luscale superAggregate
 #' @importFrom magpiesets findset

diff --git a/R/CostOverall.R b/R/CostOverall.R
@@ -6,7 +6,7 @@
 #' @param gdx GDX file
 #' @param file a file name the output should be written to using write.magpie
 #' @param level Level of regional aggregation; "reg" (regional), "glo" (global), "regglo" (regional and global) or any other aggregation level defined in superAggregate
-#' @return A MAgPIE object containing values related with overall value of production [million US$05]
+#' @return A MAgPIE object containing values related with overall value of production [million US$17]
 #' @author Edna Molina Bacca
 #' @importFrom luscale superAggregate
 #' @examples

diff --git a/R/CostTC.R b/R/CostTC.R
@@ -6,7 +6,7 @@
 #' @param gdx GDX file
 #' @param file a file name the output should be written to using write.magpie
 #' @param level Level of regional aggregation; "reg" (regional), "glo" (global), "regglo" (regional and global) or any other aggregation level defined in superAggregate
-#' @return A MAgPIE object containing values related with overall value of production [million US$05]
+#' @return A MAgPIE object containing values related with overall value of production [million US$17]
 #' @author David Chen
 #' @importFrom luscale superAggregate
 #' @examples

diff --git a/R/CostTransport.R b/R/CostTransport.R
@@ -7,7 +7,7 @@
 #' @param file a file name the output should be written to using write.magpie
 #' @param level Level of regional aggregation; "reg" (regional), "glo" (global), "regglo" (regional and global) or any other aggregation level defined in superAggregate
 #' @param sum total costs (TRUE) or detailed costs (FALSE)
-#' @return A MAgPIE object containing the transport costs [million US$05]
+#' @return A MAgPIE object containing the transport costs [million US$17]
 #' @author David Chen
 #' @importFrom magclass dimSums
 #' @importFrom luscale superAggregate

diff --git a/R/CostsAEI.R b/R/CostsAEI.R
@@ -6,7 +6,7 @@
 #' @param gdx GDX file
 #' @param file a file name the output should be written to using write.magpie
 #' @param level Level of regional aggregation ("reg", "glo", "regglo")
-#' @return MAgPIE object containing costs for AEI [million US$05]
+#' @return MAgPIE object containing costs for AEI [million US$17]
 #'
 #' @author Felicitas Beier
 #'

diff --git a/R/CostsFertilizer.R b/R/CostsFertilizer.R
@@ -7,7 +7,7 @@
 #' @param file a file name the output should be written to using write.magpie
 #' @param level Level of regional aggregation ("reg", "glo", "regglo")
 #' @param disagg whether costs should be disaggregated into the different crop types
-#' @return MAgPIE object containing fertilizer costs [million US$05]
+#' @return MAgPIE object containing fertilizer costs [million US$17]
 #' @author Debbora Leip
 #' @importFrom magclass dimSums
 #' @importFrom luscale superAggregate

diff --git a/R/CostsWithoutIncentives.R b/R/CostsWithoutIncentives.R
@@ -1,11 +1,12 @@
 #' @title CostsWithoutIncentives
-#' @description calculates agricultural costs without taxes and incentives (i.e. GHG taxes and BII incentives)
+#' @description calculates agricultural costs without taxes, incentives and technical penalty costs (i.e. GHG taxes and BII incentives)
 #'
 #' @export
 #'
 #' @param gdx GDX file
 #' @param file a file name the output should be written to using write.magpie
 #' @param level aggregation level, reg, glo or regglo
+#' @return A MAgPIE object containing the costs without taxes, incentives and technical penalty costs [million US$17]
 #' @author David M Chen
 
 #' @examples
@@ -76,7 +77,7 @@ CostsWithoutIncentives <- function(gdx, file = NULL, level = "regglo") {
 
   # peatland costs without slack are in v58_peatland_cost in realization "on"
   peatlandCosts <- readGDX(gdx, "ov58_peatland_cost", select = list(type = "level"), react = "silent")
-  # v58_peatland_cost does not exist in realization "v2" because there is no slack variable
+  # v58_peatland_cost does not exist in realization "v2"
   if(is.null(peatlandCosts)) peatlandCosts <- readGDX(gdx, "ov_peatland_cost", select = list(type = "level"), react = "silent")
   totCosts <- add_columns(totCosts, addnm = "Peatland", dim = 3.1, fill = 0)
 

diff --git a/R/PriceGHG.R b/R/PriceGHG.R
@@ -7,7 +7,7 @@
 #' @param file a file name the output should be written to using write.magpie
 #' @param level Level of regional aggregation; "reg" (regional), "glo" (global), "regglo" (regional and global) or any other aggregation level defined in superAggregate
 #' @param aggr aggregation used for global value; "max" (maxium value accross regions) or "weight" (weighted by population)
-#' @return GHG emission prices as MAgPIE object (US$2005/tCO2, US$2005/tN2O, US$2005/tCH4)
+#' @return GHG emission prices as MAgPIE object (US$2017/tCO2, US$2017/tN2O, US$2017/tCH4)
 #' @author Florian Humpenoeder, Amsalu W. Yalew
 #' @importFrom luscale superAggregate
 #' @seealso \code{\link{reportPriceGHG}}

diff --git a/R/costs.R b/R/costs.R
@@ -9,7 +9,7 @@
 #'  any other aggregation level defined in superAggregate
 #' @param sum total costs (TRUE) or detailed costs (FALSE)
 #' @param type either "annuity" (as it enters the objetive function) or "investment" (investment)
-#' @return A MAgPIE object containing the goal function costs including investments [million US$05]
+#' @return A MAgPIE object containing the goal function costs including investments [million US$17]
 #' @author Jan Philipp Dietrich, Markus Bonsch, Misko Stevanovic, Florian Humpenoeder,
 #' Edna J. Molina Bacca, Michael Crawford
 #' @importFrom magclass mbind dimSums collapseNames

diff --git a/R/costsMACCS.R b/R/costsMACCS.R
@@ -6,7 +6,7 @@
 #' @param gdx GDX file
 #' @param file a file name the output should be written to using write.magpie
 #' @param level Level of regional aggregation ("reg", "glo", "regglo")
-#' @return MAgPIE object containing mitigation costs [million US$05]
+#' @return MAgPIE object containing mitigation costs [million US$17]
 #' @author Debbora Leip
 #' @importFrom magclass dimSums
 #' @importFrom luscale superAggregate

diff --git a/R/costsPresolve.R b/R/costsPresolve.R
@@ -6,7 +6,7 @@
 #' @param gdx GDX file
 #' @param file a file name the output should be written to using write.magpie
 #' @param level Level of regional aggregation; "reg" (regional), "glo" (global), "regglo" (regional and global) or any other aggregation level defined in superAggregate
-#' @return A MAgPIE object containing the goal function costs in presolve mode [million US$05]
+#' @return A MAgPIE object containing the goal function costs in presolve mode [million US$17]
 #' @details Presolve is without bioenergy demand. Hence costs from a MAgPIE run with bioenergy demand minus costs from presolve reflect costs that can be attributed to bioenergy production
 #' @author Florian Humpenoeder
 #' @examples

diff --git a/R/costsProductionCrops.R b/R/costsProductionCrops.R
@@ -9,7 +9,7 @@
 #' @param type Type of reporting, either "annuity" or total "investments"
 #' @param dir directory with mapping for disaggregation to higher resolutions
 #' @return A MAgPIE object containing values related with costs for crops production
-#' per ton produced [million US$05/tDM]
+#' per ton produced [million US$17/tDM]
 #' @author Edna Molina Bacca
 #' @importFrom magclass mbind dimSums collapseNames
 #' @importFrom magpiesets findset

diff --git a/R/costsWholesale.R b/R/costsWholesale.R
@@ -5,7 +5,7 @@
 #' @param file a file name the output should be written to using write.magpie
 #' @param level Level of regional aggregation; "reg" (regional), "glo" (global),
 #' "regglo" (regional and global) or any other aggregation level defined in superAggregate
-#' @return A MAgPIE object containing values related with costs wholesale trade [million US$05/tDM]
+#' @return A MAgPIE object containing values related with costs wholesale trade [million US$17/tDM]
 #' @author David M Chen
 #' @importFrom luscale superAggregate
 #' @examples

diff --git a/R/factorCosts.R b/R/factorCosts.R
@@ -12,7 +12,7 @@
 #' "kli", "kres", "fish", or "pasture")
 #' @param file a file name the output should be written to using write.magpie
 #' @param level Level of regional aggregation ("reg", "glo", "regglo")
-#' @return MAgPIE object containing factor costs [million US$05]
+#' @return MAgPIE object containing factor costs [million US$17]
 #' @author Debbora Leip
 #' @importFrom magclass add_dimension getNames mbind
 #' @importFrom luscale superAggregate

diff --git a/R/getReportFSECCosts.R b/R/getReportFSECCosts.R
@@ -25,31 +25,31 @@ getReportFSECCosts <- function(gdx, reportOutputDir = NULL, scenario = NULL) {
   costs <- reportCostsAccounting(gdx = gdx)
 
   # Costs relevant to the FSEC context
-  costs <- costs[, , c("Costs Accounting|+|Land Conversion (million US$05/yr)",
-                      "Costs Accounting|+|Transport (million US$05/yr)",
-                      "Costs Accounting|+|N Fertilizer (million US$05/yr)",
-                      "Costs Accounting|+|P Fertilizer (million US$05/yr)",
-                      "Costs Accounting|+|MACCS (million US$05/yr)",
-                      "Costs Accounting|+|AEI (million US$05/yr)",
-                      "Costs Accounting|+|Trade (million US$05/yr)",
-                      "Costs Accounting|+|Timber production (million US$05/yr)",
-                      "Costs Accounting|+|Processing (million US$05/yr)",
-                      "Costs Accounting|+|Reward for producing bioenergy (million US$05/yr)",
-                      "Costs Accounting|+|Substitution processing (million US$05/yr)",
-                      "Costs Accounting|+|Punishment cost for additionally transported monogastric livst_egg (million US$05/yr)",
-                      "Costs Accounting|+|Land transition matrix (million US$05/yr)",
-                      "Costs Accounting|+|Timber harvest natveg (million US$05/yr)",
-                      "Costs Accounting|+|Input Factors (million US$05/yr)",
-                      "Costs Accounting|+|Peatland (million US$05/yr)",
-                      "Costs Accounting|+|Forestry (million US$05/yr)",
-                      "Costs Accounting|+|TC (million US$05/yr)")]
+  costs <- costs[, , c("Costs Accounting|+|Land Conversion (million US$2017/yr)",
+                      "Costs Accounting|+|Transport (million US$2017/yr)",
+                      "Costs Accounting|+|N Fertilizer (million US$2017/yr)",
+                      "Costs Accounting|+|P Fertilizer (million US$2017/yr)",
+                      "Costs Accounting|+|MACCS (million US$2017/yr)",
+                      "Costs Accounting|+|AEI (million US$2017/yr)",
+                      "Costs Accounting|+|Trade (million US$2017/yr)",
+                      "Costs Accounting|+|Timber production (million US$2017/yr)",
+                      "Costs Accounting|+|Processing (million US$2017/yr)",
+                      "Costs Accounting|+|Reward for producing bioenergy (million US$2017/yr)",
+                      "Costs Accounting|+|Substitution processing (million US$2017/yr)",
+                      "Costs Accounting|+|Punishment cost for additionally transported monogastric livst_egg (million US$2017/yr)",
+                      "Costs Accounting|+|Land transition matrix (million US$2017/yr)",
+                      "Costs Accounting|+|Timber harvest natveg (million US$2017/yr)",
+                      "Costs Accounting|+|Input Factors (million US$2017/yr)",
+                      "Costs Accounting|+|Peatland (million US$2017/yr)",
+                      "Costs Accounting|+|Forestry (million US$2017/yr)",
+                      "Costs Accounting|+|TC (million US$2017/yr)")]
 
   costs <- dimSums(costs, dim = 3)
 
   costs <- as.data.frame(costs) %>%
     dplyr::select(.data$Region, .data$Year, .data$Value) %>%
     dplyr::mutate(Value = round(.data$Value, digits = 2)) %>%
-    dplyr::rename(`Costs (million US$05/yr)` = .data$Value)
+    dplyr::rename(`Costs (million US$2017/yr)` = .data$Value)
 
   if (!is.null(reportOutputDir) & !is.null(scenario)) {
     write.csv(costs,

diff --git a/R/getReportFSECSimonDietz.R b/R/getReportFSECSimonDietz.R
@@ -165,7 +165,7 @@ getReportFSECSimonDietz <- function(magpieOutputDir, reportOutputDir = NULL, sce
 
     # aggregate GDP over countries from poverty model
     povertyGDP <- as.data.frame(GDP[presentCountries, c(2020, 2050), ]) %>%
-        mutate(Unit = "constant 2005 Int$PPP") %>%
+        mutate(Unit = "constant 2017 Int$PPP") %>%
         select(.data$Region, .data$Year, .data$Unit, .data$Value)
 
     colnames(povertyGDP) <- c("ISO", "Year", "Unit", "Value")

diff --git a/R/getReportFableScenathon.R b/R/getReportFableScenathon.R
@@ -20,7 +20,7 @@
 getReportFableScenathon <- function(gdx, file = NULL, iso = NULL) {
 
   # Income ------------------------------------------------------------------
-  GDP <- reportIncome(gdx)[iso,,"Total income (million US$05 PPP/yr)"]
+  GDP <- reportIncome(gdx)[iso,,"Total income (million US$2017 PPP/yr)"]
   GDP <- setNames(GDP, "GPD")
 
 

diff --git a/R/income.R b/R/income.R
@@ -14,7 +14,7 @@
 #'                    TRUE is using the endogeenous real income that takes into account food price change on real income
 #' @return annual income as MAgPIE object
 #'         (unit depends on per_capita:
-#'         US$2005 MER/cap/yr (TRUE), US$2005 MER/yr (FALSE))
+#'         US$2017 MER/cap/yr (TRUE), US$2017 MER/yr (FALSE))
 #' @author Florian Humpenoeder, Benjamin Bodirsky, Felicitas Beier
 #' @importFrom magclass colSums mbind
 #' @examples

diff --git a/R/laborCosts.R b/R/laborCosts.R
@@ -11,7 +11,7 @@
 #' use factorCosts())
 #' @param dir for gridded outputs: magpie output directory which contains
 #' a mapping file (rds) for disaggregation
-#' @return MAgPIE object containing labor costs [million US$05]
+#' @return MAgPIE object containing labor costs [million US$17]
 #' @author Debbora Leip
 #' @importFrom magclass add_dimension getNames mbind
 #' @importFrom luscale superAggregate

diff --git a/R/land_price.R b/R/land_price.R
@@ -10,7 +10,7 @@
 #' @param absolute Should the absolute value of all the marginals be taken into calculations? \code{TRUE} (default) of \code{FALSE}. See Details.
 #' @param digits rounding accuracy for the output
 #' @details The land price is obtained through marginals of the "oq_cropland" constraint. The majority of these marginals are negative values, and a negligible number of them are positive. This is the consequence of the constraint binding either on upper or lower level. The parameter \code{ignore_lowbound} removes all the positive marginals from land price calculation (negligible), and parameter \code{absolute} transforms them into negative values (to be all together reported as positive values at the final calculation).
-#' @return A MAgPIE object containing the land shadow prices (US$05/ha).
+#' @return A MAgPIE object containing the land shadow prices (US$2017/ha).
 #' @author Markus Bonsch, Misko Stevanovic
 #' @examples
 #'

diff --git a/R/reportAgGDP.R b/R/reportAgGDP.R
@@ -16,6 +16,6 @@
 reportAgGDP <- function(gdx) {
   # Value added Agricultural GDP
   x <- AgGDP(gdx, level = "regglo")
-  getNames(x) <- "Value|Agriculture GDP (million US$05/yr)"
+  getNames(x) <- "Value|Agriculture GDP (million US$2017/yr)"
   return(x)
 }
diff --git a/R/reportConsumVal.R b/R/reportConsumVal.R
@@ -17,7 +17,7 @@ reportConsumVal <- function(gdx) {
   # Consumption value calculation
   x <- consumptionValue(gdx, level = "regglo")
 
-  getNames(x) <- "Value|Consumption Value (million US$05/yr)"
+  getNames(x) <- "Value|Consumption Value (million US$2017/yr)"
 
 
   return(x)

diff --git a/R/reportCostCapitalInvestment.R b/R/reportCostCapitalInvestment.R
@@ -19,6 +19,6 @@ reportCostCapitalInvestment <- function(gdx) {
     message("Info only available for sticky cost implementation")
     return(NULL)
   }
-  getNames(x) <- "Costs|Capital Investments (million US$05)"
+  getNames(x) <- "Costs|Capital Investments (million US$2017)"
   return(x)
 }
diff --git a/R/reportCostCapitalStocks.R b/R/reportCostCapitalStocks.R
@@ -20,6 +20,6 @@ reportCostCapitalStocks <- function(gdx) {
     message("Info only available for sticky cost implementation")
     return(NULL)
   }
-  getNames(x) <- "Costs|Capital Stocks (million US$05)"
+  getNames(x) <- "Costs|Capital Stocks (million US$2017)"
   return(x)
 }
diff --git a/R/reportCostInputsCrop.R b/R/reportCostInputsCrop.R
@@ -28,7 +28,7 @@ reportCostInputsCrop <- function(gdx) {
 
   }
 
-   getNames(out) <- "Costs|Inputs for crops (million US$05/yr)"
+   getNames(out) <- "Costs|Inputs for crops (million US$2017/yr)"
 
 
   return(out)

diff --git a/R/reportCostOverall.R b/R/reportCostOverall.R
@@ -20,7 +20,7 @@ reportCostOverall<-function(gdx){
   getNames(x)<-"Costs|Gross value of production"
 
 
-  getNames(x) <- paste0(getNames(x)," (million US$05/yr)")
+  getNames(x) <- paste0(getNames(x)," (million US$2017/yr)")
 
   return(x)
 

diff --git a/R/reportCostTC.R b/R/reportCostTC.R
@@ -15,6 +15,6 @@
 #'
 reportCostTC <- function(gdx) {
   tcCost <- CostTC(gdx, level = "regglo")
-  getNames(tcCost) <- "Costs|TC (million US$05/yr)"
+  getNames(tcCost) <- "Costs|TC (million US$2017/yr)"
   return(tcCost)
 }
diff --git a/R/reportCostTransport.R b/R/reportCostTransport.R
@@ -20,7 +20,7 @@ a <- CostTransport(gdx,level = "regglo",sum = FALSE)
 a <- reporthelper(a, dim=3.1, level_zero_name = "Costs|Transport", detail=FALSE)
 a <- summationhelper(a)
 
-getNames(a) <- paste0(getNames(a)," (million US$05/yr)")
+getNames(a) <- paste0(getNames(a)," (million US$2017/yr)")
 
 
 return(a)

diff --git a/R/reportCosts.R b/R/reportCosts.R
@@ -23,7 +23,7 @@ reportCosts<-function(gdx){
   x <- mbind(x,a)
   x <- mbind(x,setNames(dimSums(a[,,c("Costs|GHG Emissions","Costs|Reward for Afforestation"),invert=TRUE],dim=3),"Costs|MainSolve w/o GHG Emissions"))
 
-  getNames(x) <- paste0(getNames(x)," (million US$05/yr)")
+  getNames(x) <- paste0(getNames(x)," (million US$2017/yr)")
 
   return(x)
 }
diff --git a/R/reportCostsAEI.R b/R/reportCostsAEI.R
@@ -16,7 +16,7 @@ reportCostsAEI <- function(gdx) {
   AEI_costs <- CostsAEI(gdx, level = "regglo")
 
   getNames(AEI_costs)<-"Costs|AEI"
-  getNames(AEI_costs) <- paste0(getNames(AEI_costs)," (million US$05/yr)")
+  getNames(AEI_costs) <- paste0(getNames(AEI_costs)," (million US$2017/yr)")
 
   return(AEI_costs)
 }
diff --git a/R/reportCostsAccounting.R b/R/reportCostsAccounting.R
@@ -16,11 +16,11 @@
 reportCostsAccounting <- function(gdx) {
 
   a <- costs(gdx, level = "regglo", type = "investment", sum = FALSE)
-  getNames(a) <- paste0("Costs Accounting|", getNames(a), " (million US$05/yr)")
+  getNames(a) <- paste0("Costs Accounting|", getNames(a), " (million US$2017/yr)")
   a <- summationhelper(x = a, sep = "+")
 
   x <- NULL
-  x <- mbind(x, setNames(dimSums(a, dim = 3), paste0("Costs Accounting (million US$05/yr)")))
+  x <- mbind(x, setNames(dimSums(a, dim = 3), paste0("Costs Accounting (million US$2017/yr)")))
   x <- mbind(x, a)