replace unit conversion functions with madrat tool wrappers

pik-piam · Oct 14, 2024 · f00f6e4 · f00f6e4
1 parent eaea127
commit f00f6e4
Show file tree

Hide file tree

Showing 13 changed files with 63 additions and 62 deletions.
diff --git a/.buildlibrary b/.buildlibrary
@@ -1,4 +1,4 @@
-ValidationKey: '12520000'
+ValidationKey: '12546270'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

diff --git a/.github/workflows/check.yaml b/.github/workflows/check.yaml
@@ -23,14 +23,14 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
-            any::lucode2
-            any::covr
-            any::madrat
-            any::magclass
-            any::citation
-            any::gms
-            any::goxygen
-            any::GDPuc
+            lucode2
+            covr
+            madrat
+            magclass
+            citation
+            gms
+            goxygen
+            GDPuc
           # piam packages also available on CRAN (madrat, magclass, citation,
           # gms, goxygen, GDPuc) will usually have an outdated binary version
           # available; by using extra-packages we get the newest version

diff --git a/CITATION.cff b/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: 'mrland: MadRaT land data package'
-version: 0.62.6
-date-released: '2024-10-04'
+version: 0.62.7
+date-released: '2024-10-14'
 abstract: The package provides land related data via the madrat framework.
 authors:
 - family-names: Dietrich

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Type: Package
 Package: mrland
 Title: MadRaT land data package
-Version: 0.62.6
-Date: 2024-10-04
+Version: 0.62.7
+Date: 2024-10-14
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "dietrich@pik-potsdam.de", role = c("aut", "cre")),
     person("Abhijeet", "Mishra", role = "aut"),
@@ -34,12 +34,12 @@ Depends:
     mrfactors (>= 0.4.0),
     mrfaocore (>= 1.0.0),
     mrlandcore (>= 1.0.0),
+    GDPuc (>= 1.3.0),
     R (>= 2.10.0)
 Imports:
     countrycode,
     data.table,
     dplyr,
-    GDPuc,
     magpiesets,
     mstools (>= 0.6.0),
     ncdf4,

diff --git a/NAMESPACE b/NAMESPACE
@@ -21,6 +21,7 @@ export(readEvapotranspiration)
 export(readPYieldCoeff)
 export(spatial_header)
 export(toolPatternScaling)
+import(GDPuc)
 import(countrycode)
 import(madrat)
 import(magclass)
@@ -30,7 +31,7 @@ import(mrfaocore)
 import(mrlandcore)
 import(readxl)
 import(utils)
-importFrom(GDPuc,convertGDP)
+importFrom(GDPuc,toolConvertGDP)
 importFrom(SPEI,thornthwaite)
 importFrom(data.table,fread)
 importFrom(dplyr,left_join)

diff --git a/R/calcGDPdeflator.R b/R/calcGDPdeflator.R
@@ -6,7 +6,7 @@
 #' @param currency "PPP" or "MER"
 #' @return List of magpie objects with results on country level, weight on country level, unit and description.
 #' @author David Chen
-#' @importFrom GDPuc convertGDP
+#' @importFrom GDPuc toolConvertGDP
 
 calcGDPdeflator <- function(yearFrom = 2017, yearTo = 2005, currency = "PPP") {
 
@@ -25,10 +25,10 @@ calcGDPdeflator <- function(yearFrom = 2017, yearTo = 2005, currency = "PPP") {
     unit <- "US$MER"
   }
 
-  defl2017 <- convertGDP(defl2017,
-                         unit_in = paste("constant", yearFrom, unit, sep = " "),
-                         unit_out = paste("constant", yearTo, unit, sep = " "),
-                         replace_NAs = c("linear", "no_conversion"))
+  defl2017 <- toolConvertGDP(defl2017,
+                             unit_in = paste("constant", yearFrom, unit, sep = " "),
+                             unit_out = paste("constant", yearTo, unit, sep = " "),
+                             replace_NAs = c("linear", "no_conversion"))
   getNames(defl2017) <- NULL
 
   return(list(x = defl2017,

diff --git a/R/calcGHGPrices.R b/R/calcGHGPrices.R
@@ -70,8 +70,8 @@ calcGHGPrices <- function(emissions = "pollutants", datasource = "REMMAG", rev =
     description <- "GHG certificate prices for different scenarios based on data from REMIND-MAgPIE coupling"
 
     #convert from USD05MER to USD17MER based on USA values for all countries as the CO2 price is global.
-    x <- x * round(GDPuc::convertSingle(1, "USA", unit_in = "constant 2005 US$MER",
-                                        unit_out = "constant 2017 US$MER"), 2)
+    x <- x * round(GDPuc::toolConvertSingle(1, "USA", unit_in = "constant 2005 US$MER",
+                                            unit_out = "constant 2017 US$MER"), 2)
 
   } else if (datasource == "Strefler2021") {
     x <- readSource("Strefler2021", subtype = paste0("intensive_", rev))
@@ -103,8 +103,8 @@ calcGHGPrices <- function(emissions = "pollutants", datasource = "REMMAG", rev =
     getNames(x) <- gsub("^([^\\.]*)\\.(.*$)", "\\2.\\1", getNames(x))
 
     #convert from USD05MER to USD17MER based on USA values for all countries as the CO2 price is global.
-    x <- x * round(GDPuc::convertSingle(1, "USA", unit_in = "constant 2005 US$MER",
-                                        unit_out = "constant 2017 US$MER"), 2)
+    x <- x * round(GDPuc::toolConvertSingle(1, "USA", unit_in = "constant 2005 US$MER",
+                                            unit_out = "constant 2017 US$MER"), 2)
 
     description <- paste("GHG certificate prices for different scenarios taken",
                          "from Strefler et al 2021 (DOI 10.1038/s41467-021-22211-2)")
@@ -124,8 +124,8 @@ calcGHGPrices <- function(emissions = "pollutants", datasource = "REMMAG", rev =
     }
 
     #convert from USD05MER to USD17MER based on USA values for all countries as the CO2 price is global.
-    x <- x * round(GDPuc::convertSingle(1, "USA", unit_in = "constant 2005 US$MER",
-                                        unit_out = "constant 2017 US$MER"), 2)
+    x <- x * round(GDPuc::toolConvertSingle(1, "USA", unit_in = "constant 2005 US$MER",
+                                            unit_out = "constant 2017 US$MER"), 2)
 
     description <- "ghg certificate prices for different scenarios based on data from REMIND-MAgPIE-coupling"
 
@@ -202,8 +202,8 @@ calcGHGPrices <- function(emissions = "pollutants", datasource = "REMMAG", rev =
     x <- time_interpolate(x, seq(1995, 2150, 5), extrapolation_type = "constant")
 
     #convert from USD05MER to USD17MER based on USA values for all countries as the CO2 price is global.
-    x <- x * round(GDPuc::convertSingle(1, "USA", unit_in = "constant 2005 US$MER",
-                                        unit_out = "constant 2017 US$MER"), 2)
+    x <- x * round(GDPuc::toolConvertSingle(1, "USA", unit_in = "constant 2005 US$MER",
+                                            unit_out = "constant 2017 US$MER"), 2)
 
     description <- "ghg certificate prices for different scenarios based on CO2 prices provided by IMAGE"
 

diff --git a/R/calcIrrigationInvCosts.R b/R/calcIrrigationInvCosts.R
@@ -23,30 +23,30 @@ calcIrrigationInvCosts <- function() {
   # Investment costs for expanding irrigation infrastructure in 1000 US$ per hectare
   # Note: in World Bank report (William I. Jones, 1991), p. 98, given in US$ per hectare
   # But: csv table has transformed values (in 1000 US$ per hectare)
-  WBirrigation           <- readSource("WBirrigation")
-  getYears(WBirrigation) <- NULL
+  wBirrigation           <- readSource("WBirrigation")
+  getYears(wBirrigation) <- NULL
 
   # irrigation cost constant until 2015
-  data              <- new.magpie(cells_and_regions = getRegions(WBirrigation),
+  data              <- new.magpie(cells_and_regions = getItems(wBirrigation, dim = 1),
                                   years = 1995:2050,
                                   names = "ad_unit_cost",
                                   fill = NA)
-  data[, 1995:2050, ] <- WBirrigation
+  data[, 1995:2050, ] <- wBirrigation
 
   # Transform fromm 1000 USD$ per hectare to US$ per hectare
   data <- data * 1000
 
   # conversion: $1995 to $2004
-  data <- convertGDP(data,
-                     unit_in = "constant 1995 US$MER",
-                     unit_out = "constant 2017 US$MER",
-                     replace_NAs = "no_conversion")
+  data <- toolConvertGDP(data,
+                         unit_in = "constant 1995 US$MER",
+                         unit_out = "constant 2017 US$MER",
+                         replace_NAs = "no_conversion")
 
   # from 2015 onwards, data converges to value of Germany until 2050
-  dataDEU <- new.magpie(cells_and_regions = getRegions(WBirrigation),
-                         years = 1995:2050,
-                         names = "ad_unit_cost",
-                         fill = as.numeric(data["DEU", "y1995", ]))
+  dataDEU <- new.magpie(cells_and_regions = getItems(wBirrigation, dim = 1),
+                        years = 1995:2050,
+                        names = "ad_unit_cost",
+                        fill = as.numeric(data["DEU", "y1995", ]))
 
   data <- convergence(origin = data, aim = dataDEU,
                       start_year = "y2015", end_year = "y2050",

diff --git a/R/calcTradeMargin.R b/R/calcTradeMargin.R
@@ -17,7 +17,7 @@
 #' }
 #' @importFrom magpiesets findset
 #' @importFrom magclass is.magpie
-#' @importFrom GDPuc convertGDP
+#' @importFrom GDPuc toolConvertGDP
 #' @importFrom mstools toolCountryFillBilateral
 
 calcTradeMargin <- function(gtap_version = "GTAP9", bilateral = FALSE, producer_price = "FAOini") { # nolint
@@ -143,10 +143,10 @@ calcTradeMargin <- function(gtap_version = "GTAP9", bilateral = FALSE, producer_
   weight[, , "distillers_grain"] <- weight[, , "tece"]
 
   if (gtap_version == "GTAP9") {
-      out <- GDPuc::convertGDP(out, unit_in = "current US$MER",
-                               unit_out = "constant 2017 US$MER",
-                               replace_NAs = "no_conversion")
-    
+    out <- GDPuc::toolConvertGDP(out, unit_in = "current US$MER",
+                                 unit_out = "constant 2017 US$MER",
+                                 replace_NAs = "no_conversion")
+
     out <- setYears(out[, 2011, ], NULL)
     weight <- setYears(weight[, 2011, ], NULL)
   } else {

diff --git a/R/calcTradeTariff.R b/R/calcTradeTariff.R
@@ -23,7 +23,7 @@
 #' @importFrom reshape2 acast
 #' @importFrom magclass as.data.frame add_columns
 #' @importFrom magpiesets findset
-#' @importFrom GDPuc convertGDP
+#' @importFrom GDPuc toolConvertGDP
 #' @importFrom mstools toolCountryFillBilateral
 #'
 
@@ -112,10 +112,10 @@ calcTradeTariff<- function(gtap_version = "GTAP9", type_tariff = "total", bilate
     p <- add_dimension(p, dim = 1.2,   nm = getItems(p, dim = 1))
   }
   if (gtap_version == "GTAP9") {
-      y <- GDPuc::convertGDP(y, unit_in = "current US$MER",
-                             unit_out = "constant 2017 US$MER",
-                             replace_NAs = "no_conversion")
-    
+    y <- GDPuc::toolConvertGDP(y, unit_in = "current US$MER",
+                               unit_out = "constant 2017 US$MER",
+                               replace_NAs = "no_conversion")
+
     y <- setYears(y[, 2011, ], NULL)
   }
 

diff --git a/R/convertSathayeForest.R b/R/convertSathayeForest.R
@@ -1,22 +1,22 @@
 #' Convert Sathaye Forest data
-#' 
+#'
 #' Convert Sathaye Forest data on ISO country level.
-#' 
-#' 
+#'
+#'
 #' @param x MAgPIE object containing Sathaye Forest data region resolution
 #' @return Sathaye Forest data as MAgPIE object aggregated/disaggregated to
 #' country level
 #' @author Lavinia Baumstark
 #' @examples
-#' 
+#'
 #' \dontrun{ a <- convertSathayeForest(x)
 #' }
-#' 
+#'
 convertSathayeForest <- function(x) {
 
   # convert data from $US-2000 into $US-2017
-  y <- toolAggregate(x, "regionmappingSathayeForest.csv", weight=NULL )
-  y <- convertGDP(y, unit_in = "constant 2000 US$MER",
+  y <- toolAggregate(x, "regionmappingSathayeForest.csv", weight = NULL)
+  y <- toolConvertGDP(y, unit_in = "constant 2000 US$MER",
                       unit_out = "constant 2017 US$MER",
                       replace_NAs = "no_conversion")
 

diff --git a/R/imports.R b/R/imports.R
@@ -1,4 +1,4 @@
 # Generated by lucode2: do not edit by hand
 
-#' @import madrat magclass mrcommons mrfactors mrfaocore mrlandcore
+#' @import madrat magclass mrcommons mrfactors mrfaocore mrlandcore GDPuc
 NULL
diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # MadRaT land data package
 
-R package **mrland**, version **0.62.6**
+R package **mrland**, version **0.62.7**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/mrland)](https://cran.r-project.org/package=mrland) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3822083.svg)](https://doi.org/10.5281/zenodo.3822083) [![R build status](https://github.com/pik-piam/mrland/workflows/check/badge.svg)](https://github.com/pik-piam/mrland/actions) [![codecov](https://codecov.io/gh/pik-piam/mrland/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/mrland) [![r-universe](https://pik-piam.r-universe.dev/badges/mrland)](https://pik-piam.r-universe.dev/builds)
 
@@ -39,7 +39,7 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **mrland** in publications use:
 
-Dietrich J, Mishra A, Weindl I, Bodirsky B, Wang X, Baumstark L, Kreidenweis U, Klein D, Steinmetz N, Chen D, Humpenoeder F, von Jeetze P, Wirth S, Beier F, Hoetten D, Sauer P (2024). _mrland: MadRaT land data package_. doi:10.5281/zenodo.3822083 <https://doi.org/10.5281/zenodo.3822083>, R package version 0.62.6, <https://github.com/pik-piam/mrland>.
+Dietrich J, Mishra A, Weindl I, Bodirsky B, Wang X, Baumstark L, Kreidenweis U, Klein D, Steinmetz N, Chen D, Humpenoeder F, von Jeetze P, Wirth S, Beier F, Hoetten D, Sauer P (2024). _mrland: MadRaT land data package_. doi: 10.5281/zenodo.3822083 (URL: https://doi.org/10.5281/zenodo.3822083), R package version 0.62.7, <URL: https://github.com/pik-piam/mrland>.
 
 A BibTeX entry for LaTeX users is
 
@@ -48,8 +48,8 @@ A BibTeX entry for LaTeX users is
   title = {mrland: MadRaT land data package},
   author = {Jan Philipp Dietrich and Abhijeet Mishra and Isabelle Weindl and Benjamin Leon Bodirsky and Xiaoxi Wang and Lavinia Baumstark and Ulrich Kreidenweis and David Klein and Nele Steinmetz and David Chen and Florian Humpenoeder and Patrick {von Jeetze} and Stephen Wirth and Felicitas Beier and David Hoetten and Pascal Sauer},
   year = {2024},
-  note = {R package version 0.62.6},
-  url = {https://github.com/pik-piam/mrland},
+  note = {R package version 0.62.7},
   doi = {10.5281/zenodo.3822083},
+  url = {https://github.com/pik-piam/mrland},
 }
 ```