update mrtutorial

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '514404'
+ValidationKey: '533624'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

.zenodo.json

@@ -1,6 +1,6 @@
 {
   "title": "mrtutorial: Tutorial Package For Madrat Package Library",
-  "version": "0.2.7",
+  "version": "0.2.8",
   "description": "<p>Example package of mr- world libraries, in conjunction with MAgPIE MADRat tutorial. For more information please see: https://github.com/magpiemodel/tutorials/tree/master/madrat .<\/p>",
   "creators": [
     {

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: mrtutorial
 Type: Package
 Title: Tutorial Package For Madrat Package Library
-Date: 2022-03-01
-Version: 0.2.7
+Date: 2022-03-07
+Version: 0.2.8
 Authors@R: 
     person("David Meng-Chuen",  "Chen", email = "[email protected]", role = c("aut","cre"))
 Description: Example package of mr- world libraries, in conjunction with MAgPIE MADRat tutorial. For more information please see: https://github.com/magpiemodel/tutorials/tree/master/madrat .
@@ -20,6 +20,9 @@ Imports:
     countrycode,
     lucode2,
     reshape2,
-    magpiesets
+    magpiesets,
+    dplyr,
+    tidyr,
+    rlang
 Suggests: 
     covr

NAMESPACE

@@ -6,6 +6,9 @@ importFrom(WDI,WDI)
 importFrom(WDI,WDIcache)
 importFrom(WDI,WDIsearch)
 importFrom(countrycode,countrycode)
+importFrom(dplyr,"%>%")
+importFrom(dplyr,filter)
+importFrom(dplyr,select)
 importFrom(lucode2,path)
 importFrom(madrat,calcOutput)
 importFrom(madrat,getConfig)
@@ -27,5 +30,6 @@ importFrom(magclass,getRegions)
 importFrom(magclass,getSets)
 importFrom(magclass,getYears)
 importFrom(magpiesets,findset)
-importFrom(reshape2,melt)
+importFrom(rlang,.data)
+importFrom(tidyr,pivot_longer)
 importFrom(utils,read.csv)

R/calcAgGDP.R

@@ -15,6 +15,7 @@
 calcAgGDP <- function(){
 
   gdp <- readSource("TutorialWDI", subtype="NY.GDP.MKTP.CD")
+
   ag_gdp <- readSource("TutorialWDI", subtype="NV.AGR.TOTL.CD")
 
   x <- ag_gdp/gdp
@@ -24,9 +25,12 @@ calcAgGDP <- function(){
   ## some division by 0 happening
   x[is.na(x)] <- 0
 
+  #population weight
+  weight <- readSource("TutorialWDI", subtype = "SP.POP.TOTL")
+
   return(list(
     x=x,
-    weight=NULL,
+    weight=weight,
     unit="share",
     description="Ag GDP as percentage of total GDP"))
 }

R/convertTutorialWDI.R

@@ -17,46 +17,28 @@
 #' @importFrom madrat toolCountryFill
 
 
-convertTutorialWDI<-function(x,subtype){
-  WDI_data <- WDI::WDI_data
-
-  # changing scale of indicators
-  if (subtype %in% c("SP.POP.TOTL",
-                     "NY.GDP.MKTP.PP.KD", 
-                     "NV.AGR.TOTL.CD", 
-                     "NY.GDP.MKTP.PP.CD",
-                     "NY.GDP.MKTP.CD",
-                     "NY.GDP.MKTP.KD",
-                     "NY.GDP.MKTP.KN")) {
-    x <- x/1000000
-
-#Kosovo added to Serbia
-    x["RS",,] <- dimSums(x[c("RS","XK"),,],dim=1,na.rm=T)
-  }else if (subtype %in%  WDI_data$series[,"indicator"]){
-
-    vcat("Warning: Kosovo left out of conversion and has differing population values from FAO", verbosity=2)
-    x <- x
-  }else {
-    stop("subtype does not exist in the dataset!")
-  }
-  y <- x
-
-## Channel Islands add to JEY
-  JG <- "JEY"
-  names(JG) <- "JG"
-  getCells(y)<-countrycode::countrycode(getCells(y),"iso2c","iso3c", custom_match = JG)
-  y<-y[!is.na(getCells(y)),,]
-  y<-clean_magpie(y)
-
-  y<-y["ANT",,,invert=TRUE]
-
-  y<-toolCountryFill(y,fill = 0)
-  y[is.na(y)]<-0
-  y <- y[,sort(getYears(y)),]
-
-  #remove years which only contain 0s as entries
-  y <- y[,!apply(y,2,function(x) return(all(x==0))),]
-
-  y<-y[,sort(getYears(y)),]
-  return(y)
+convertTutorialWDI<-function(x, subtype){
+
+  # change scale of absolute indicators, MAgPIE runs in Million scale for Pop and GDP drivers
+if (subtype %in% c("NY.GDP.MKTP.CD",
+                     "SP.POP.TOTL",
+                     "NV.AGR.TOTL.CD")){
+
+       out <- x/1e6 } else
+
+ if (subtype == "SL.AGR.EMPL.ZS"){
+        # don't change for percentage of ag employment
+
+      out <- x } else{
+
+      stop("subtype does not exist in the dataset!")}
+
+  # toolCountryFill fills in missing countries - 249 required for aggregation
+
+  x<-toolCountryFill(out,fill = 0)
+
+  x[is.na(x)] <- 0  #remove NAs
+
+
+  return(x)
 }

R/fullTUTORIALVALIDATION.R

@@ -0,0 +1,33 @@
+#' fullTUTORIALVALIDATION
+#'
+#' Function that produces the complete validation data set used for evaluation of MAgPIE outputs
+#'
+#' @param rev data revision which should be used as input (positive numeric).
+#' @author Jan Philipp Dietrich, Kristine Karstens
+#' @seealso
+#' \code{\link{readSource}}, \code{\link{getCalculations}}, \code{\link{calcOutput}}
+#' @examples
+#' \dontrun{
+#' retrieveData("VALIDATION")
+#' }
+#' @importFrom madrat getConfig calcOutput
+#' @importFrom lucode2 path
+
+fullTUTORIALVALIDATION <- function(rev = 0.1) {
+
+  # all validation data regional aggregations happens here
+
+  # exitsting "validation.mif" file is loaded if all functions are set to append=TRUE
+  # Please put the validation.mif into your output folder.
+  # Use retrieveData("VALIDATION") to create a .tgz
+
+  file.copy(lucode2::path(paste0(getConfig("mainfolder"), "/output/"), "validation.mif"),
+            lucode2::path(getConfig("outputfolder"), "validation.mif"))
+
+  valfile <- "validation.mif"
+
+  # Add your validation scripts here
+  calcOutput(type = "ValidPopulation", datasource = "WDI", aggregate = "REG+GLO",
+             file = valfile, append = TRUE, na_warning = FALSE, try = TRUE)
+
+}

R/readTutorialWDI.R

@@ -5,32 +5,40 @@
 #'
 #'
 #' @param subtype Type of WDI data that should be read. Please use the
-#' worldbank indicator abbreviation. Available types are e.g.: \itemize{ \item
-#' \code{SP.POP.TOTL}: Population, total \item \code{NY.GDP.MKTP.PP.KD}: GDP,
-#' PPP (constant 2011 international Dollar) \item \code{NY.GDP.MKTP.PP.CD}:
-#' GDP, PPP (current international Dollar) \item \code{NY.GDP.MKTP.CD}: GDP MER
-#' (current USDollar) \item \code{NY.GDP.MKTP.KD}: GDP MER (constant 2005
-#' USDollar) \item \code{NY.GDP.MKTP.KN}: GDP LCU (constant LCU)
-#' \item \code{SP.URB.TOTL.IN.ZS}: Urban population (peccentage of total)
-#' \item \code{ NV.AGR.TOTL.CD}: GDP (current USD)}
+#' worldbank indicator abbreviation. Available types are e.g.: \itemize{
+#' \item \code{SP.POP.TOTL}: Population, total
+#' \item \code{NY.GDP.MKTP.PP.CD}: GDP, PPP (current international Dollar)
+#' \item \code{SL.AGR.EMPL.ZS}: Employment in agriculture as % of total employment
+#' \item \code{NV.AGR.TOTL.CD}: Agricultural GDP (current international Dollar) }
 #' @return magpie object of the WDI data
 #' @author David Chen
 #' @seealso \code{\link{readSource}} \code{\link{downloadTutorialWDI}}
 #' @examples
 #'
 #' \dontrun{ a <- readSource(type="WDI",subtype="SP.POP.TOTL")
 #' }
-#' @importFrom reshape2 melt
+#' @importFrom dplyr select filter %>%
+#' @importFrom tidyr pivot_longer
 #' @importFrom magclass as.magpie
+#' @importFrom rlang .data
 
 readTutorialWDI<-function(subtype){
+
   load("WDI.rda")
-   wdi$country <- NULL
-  wdi <- as.magpie(melt(wdi,id.vars = c("iso2c","year")),
-                   spatial=1,temporal=2,tidy=TRUE,replacement =".")
+
+  #convert the iso2c to iso3c using madrat tool
+  wdi$iso2c <- toolCountry2isocode(wdi$iso2c)
+
+  wdi <- wdi %>%
+         dplyr::select(!.data$country)  %>%
+         filter(!is.na(.data$iso2c)) %>%
+         pivot_longer(cols=3:6) %>%
+         as.magpie(spatial = 1, temporal = 2, replacement =".")
+
   wdi <- wdi[,,subtype]
 
-  getNames(wdi) <- gsub("\\.", "_", getNames(wdi)) ## Replace . with _
+  getNames(wdi) <- gsub("\\.", "_", getNames(wdi))
+  # Replacement of . with _ in dimension is also done automatically in as.magpie()
 
   return(wdi)
 }

README.md

@@ -1,6 +1,6 @@
 # Tutorial Package For Madrat Package Library
 
-R package **mrtutorial**, version **0.2.7**
+R package **mrtutorial**, version **0.2.8**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/mrtutorial)](https://cran.r-project.org/package=mrtutorial)  [![R build status](https://github.com/pik-piam/mrtutorial/workflows/check/badge.svg)](https://github.com/pik-piam/mrtutorial/actions) [![codecov](https://codecov.io/gh/pik-piam/mrtutorial/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/mrtutorial) [![r-universe](https://pik-piam.r-universe.dev/badges/mrtutorial)](https://pik-piam.r-universe.dev/ui#builds)
 
@@ -38,7 +38,7 @@ In case of questions / problems please contact David Meng-Chuen Chen <david.chen
 
 To cite package **mrtutorial** in publications use:
 
-Chen D (2022). _mrtutorial: Tutorial Package For Madrat Package Library_. R package version 0.2.7.
+Chen D (2022). _mrtutorial: Tutorial Package For Madrat Package Library_. R package version 0.2.8.
 
 A BibTeX entry for LaTeX users is
 
@@ -47,6 +47,6 @@ A BibTeX entry for LaTeX users is
   title = {mrtutorial: Tutorial Package For Madrat Package Library},
   author = {David Meng-Chuen Chen},
   year = {2022},
-  note = {R package version 0.2.7},
+  note = {R package version 0.2.8},
 }
 ```