Updated AEI validation data and lintering some functions

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '507885960'
+ValidationKey: '508110694'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

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: 'mrvalidation: madrat data preparation for validation purposes'
-version: 2.56.12
-date-released: '2024-04-17'
+version: 2.56.13
+date-released: '2024-04-25'
 abstract: Package contains routines to prepare data for validation exercises.
 authors:
 - family-names: Bodirsky

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: mrvalidation
 Title: madrat data preparation for validation purposes
-Version: 2.56.12
-Date: 2024-04-17
+Version: 2.56.13
+Date: 2024-04-25
 Authors@R: c(
     person("Benjamin Leon", "Bodirsky", , "[email protected]", role = c("aut", "cre")),
     person("Stephen", "Wirth", role = "aut"),

R/calcGMIA.R

@@ -1,66 +1,57 @@
-#'@title calcGMIA
-#' 
+#' @title calcGMIA
+#'
 #' @description Filling gaps in the Historical area equipped for irrigation from GMIA.
-#' 
+#'
 #' @return list of magpie object with data and weight
 #' @author Stephen Wirth, Anne Biewald
 #' @examples
-#' 
-#' \dontrun{ 
-#' a <- calcOutput("GMIA",aggregate="regglo")
+#' \dontrun{
+#' a <- calcOutput("GMIA", aggregate = "regglo")
 #' }
-calcGMIA <- function(){
+calcGMIA <- function() {
   x <- readSource("GMIA", "all_data_national", convert = TRUE)
-  
-  small_island_states <- c("ATG","BRB", "COK","NRU", "TUV","NIU", "MDV", "MLT", "GRD", 
-                           "VCT","PLW", "LCA", "SGP", "FSM", "BHR", "DMA", "TON",
-                           "KIR", "STP", "SYC")
-  
-  antarctica_or_arctic <- c("ATA", "ATF", "GRL", "SJM")
-  desserts_no_agg <-  c("ESH", "GIB")
-  
-  x[antarctica_or_arctic,,] <- 0
-  x[desserts_no_agg,,] <- 0
-  
+
+  smallIslandStates <- c("ATG", "BRB", "COK", "NRU", "TUV", "NIU", "MDV", "MLT", "GRD",
+                         "VCT", "PLW", "LCA", "SGP", "FSM", "BHR", "DMA", "TON",
+                         "KIR", "STP", "SYC")
+
+  antarcticORarctic <- c("ATA", "ATF", "GRL", "SJM")
+  desertNoAgg <-  c("ESH", "GIB")
+
+  x[antarcticORarctic, , ] <- 0
+  x[desertNoAgg, , ] <- 0
+
   area <- readSource("FAO_online", "Land")
-  sudan <- area[c("SDN","SSD"),1,"6600|Country area.Area_(1000_ha)"]
-  proportion_sudan <- sudan/as.numeric(as.numeric(sudan["SDN",,]) + as.numeric(sudan["SSD",,]))
-  x["SSD",,] <- as.numeric(x["SDN",,])*as.numeric(proportion_sudan["SSD",,])
-  x["SDN",,] <- as.numeric(x["SDN",,])*as.numeric(proportion_sudan["SDN",,])
+  sudan <- area[c("SDN", "SSD"), 1, "6600|Country area.Area_(1000_ha)"]
+  sudanRatio <- sudan / as.numeric(as.numeric(sudan["SDN", , ]) + as.numeric(sudan["SSD", , ]))
+  x["SSD", , ] <- as.numeric(x["SDN", , ]) * as.numeric(sudanRatio["SSD", , ])
+  x["SDN", , ] <- as.numeric(x["SDN", , ]) * as.numeric(sudanRatio["SDN", , ])
 
+  # Disaggregate values for China: Mainland, Hong Kong, Taiwan, and Macao
+  # Based on AEI shares the information from (http://www.fao.org/nr/water/aquastat/irrigationmap/CHN/index.stm)
+  x["HKG", , ] <- as.numeric(x["CHN", , ]) * 0.00003
+  x["TWN", , ] <- as.numeric(x["CHN", , ]) * 0.0078
+  x["CHN", , ] <- as.numeric(x["CHN", , ]) * 0.992
+  x["MAC", , ] <- 0
 
-  #Dissaggregate values for China: Mainland, Hong Kong, Tiwan, and Macao
-  #Based on AEI shares the information from (http://www.fao.org/nr/water/aquastat/irrigationmap/CHN/index.stm)
-  x["HKG",,] <- as.numeric(x["CHN",,]) * 0.00003
-  x["TWN",,] <- as.numeric(x["CHN",,]) * 0.0078
-  x["CHN",,] <- as.numeric(x["CHN",,]) * 0.992
-  x["MAC",,] <- 0
-
-
-  value_small_islands <- as.magpie(apply(x[small_island_states,,],MARGIN = c(2,3),FUN = "mean"))
-
-  for(i in getRegions(x))
-  {
-    tmp <- dimSums(x[i,,], dim=c(2,3))
-    if(is.na(tmp))
-    {
-      area_tmp <- area[i,length(getYears(area)),"6600|Country area.Area_(1000_ha)"]
-      if(area_tmp!=0)
-        {
-    x[i,,] <- value_small_islands 
-      }
-      else
-      {
-        x[i,,] <- 0
+
+  valSmallIslands <- as.magpie(apply(x[smallIslandStates, , ], MARGIN = c(2, 3), FUN = "mean"))
+
+  for (i in getItems(x, dim = 1.1)) {
+    tmp <- dimSums(x[i, , ], dim = c(2, 3))
+    if (is.na(tmp)) {
+      areaTMP <- area[i, length(getYears(area)), "6600|Country area.Area_(1000_ha)"]
+      if (areaTMP != 0) {
+        x[i, , ] <- valSmallIslands
+      } else      {
+        x[i, , ] <- 0
       }
     }
   }
-
-  return(list(x=x,
-              weight=NULL,
-              unit="ha",
-              min=0,
-              description="Area equipped for Irrigation in ha")
-         )
-
-  }
+
+  return(list(x = x,
+              weight = NULL,
+              unit = "ha",
+              min = 0,
+              description = "Area equipped for irrigation in ha"))
+}

R/calcValidAEI.R

@@ -11,7 +11,7 @@
 
 calcValidAEI <- function(datasource = "LUH2v2") {
 
-  if (datasource == "LUH2v2" || datasource == "Mehta2022") {
+  if (datasource == "LUH2v2" || datasource == "Mehta2024_Siebert2013" || datasource == "Mehta2024_Meier2018") {
     out <- collapseNames(calcOutput("AreaEquippedForIrrigation", cells = "lpjcell",
                                     cellular = FALSE, aggregate = FALSE)[, , datasource])
   } else if (datasource == "HID") {

R/fullVALIDATION.R

@@ -172,7 +172,7 @@ fullVALIDATION <- function(rev = 0.1) {
   # Area equipped for Irrigation
   calcOutput(type = "ValidAEI", datasource = "LUH2v2", aggregate = "REG+GLO",
              file = "validation.mif", append = TRUE, try = TRUE)
-  calcOutput(type = "ValidAEI", datasource = "Mehta2022", aggregate = "REG+GLO",
+  calcOutput(type = "ValidAEI", datasource = "Mehta2024_Siebert2013", aggregate = "REG+GLO",
              file = "validation.mif", append = TRUE, try = TRUE)
   calcOutput(type = "ValidAEI", datasource = "HID", aggregate = "REG+GLO",
              file = "validation.mif", append = TRUE, try = TRUE)

R/readWaterUsage.R

@@ -1,7 +1,7 @@
 #' @title readWaterUsage
 #' @description Read Historic and projcted Agricultural water consumption
-#' 
-#' 
+#'
+#'
 #' @param subtype Available subtypes are:
 #'  \itemize{
 #'  \item historical:
@@ -25,45 +25,39 @@
 #' @author Stephen Wirth
 #' @seealso \code{\link{readSource}}
 #' @examples
-#' 
-#' \dontrun{ 
+#' \dontrun{
 #' a <- readSource("foley_2011")
 #' a <- readSource("aquastat_2008_12")
 #' }
-#' #'@importFrom reshape2 dcast
+#' #' @importFrom reshape2 dcast
 #' @importFrom magclass read.magpie getSets
 
-readWaterUsage <- function(subtype=NULL){
-
-
-  files <- c(foley_2011= "Foley_2011.csv",
-             shiklomanov_2000="shiklomanov_2000.csv",
-             wada_2011="Wada_2011.csv",
-             wisser_2008="Wisser_2008.csv",
-             fischer_IIASA="Fischer_IIASA.csv",
-             hejazi_2013="Hejazi_2013.csv",
-             molden_IWMI="Molden_IWMI.csv",
-             seckler_IWMI="Seckler_IWMI.csv",
-             shiklomanov="Shiklomanov.csv",
-             aquastat_2008_12="aquastat_use_2008_12.csv"
-              )
-
-
+readWaterUsage <- function(subtype = NULL) {
+
+  files <- c(foley_2011 = "Foley_2011.csv",
+             shiklomanov_2000 = "shiklomanov_2000.csv",
+             wada_2011 = "Wada_2011.csv",
+             wisser_2008 = "Wisser_2008.csv",
+             fischer_IIASA = "Fischer_IIASA.csv",
+             hejazi_2013 = "Hejazi_2013.csv",
+             molden_IWMI = "Molden_IWMI.csv",
+             seckler_IWMI = "Seckler_IWMI.csv",
+             shiklomanov = "Shiklomanov.csv",
+             aquastat_2008_12 = "aquastat_use_2008_12.csv")
+
   file <- toolSubtypeSelect(subtype, files)
-
-  if(subtype== "aquastat_2008_12")
-    {
-    a <- read.csv(file, header = F, skip=2, stringsAsFactors = FALSE)
-    colnames(a) <- as.character(a[1,])
-    a <- a[c(2:372),c(1,3,5,6)]
+
+  if (subtype == "aquastat_2008_12") {
+    a <- read.csv(file, header = FALSE, skip = 2, stringsAsFactors = FALSE)
+    colnames(a) <- as.character(a[1, ])
+    a <- a[c(2:372), c(1, 3, 5, 6)]
     a$Value <- as.numeric(a$Value)
-    colnames(a)[2] <- "VariableName" 
-    b <- reshape2::dcast(a,Area+Year~a$VariableName)  
-    return(as.magpie(b, spatial=1, temporal=2))
-  }
-  else
-    x <- read.magpie(file_name = file)
-  getSets(x) <- c("region", "year", "data")
+    colnames(a)[2] <- "VariableName"
+    b <- reshape2::dcast(a, Area + Year ~ a$VariableName)
+    return(as.magpie(b, spatial = 1, temporal = 2))
+  } else {
+    x          <- read.magpie(file_name = file)
+    getSets(x) <- c("region", "year", "data")
     return(x)
-
+  }
 }

README.md

@@ -1,6 +1,6 @@
 # madrat data preparation for validation purposes
 
-R package **mrvalidation**, version **2.56.12**
+R package **mrvalidation**, version **2.56.13**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/mrvalidation)](https://cran.r-project.org/package=mrvalidation) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4317826.svg)](https://doi.org/10.5281/zenodo.4317826) [![R build status](https://github.com/pik-piam/mrvalidation/workflows/check/badge.svg)](https://github.com/pik-piam/mrvalidation/actions) [![codecov](https://codecov.io/gh/pik-piam/mrvalidation/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/mrvalidation) [![r-universe](https://pik-piam.r-universe.dev/badges/mrvalidation)](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 **mrvalidation** in publications use:
 
-Bodirsky B, Wirth S, Karstens K, Humpenoeder F, Stevanovic M, Mishra A, Biewald A, Weindl I, Beier F, Chen D, Crawford M, Leip D, Molina Bacca E, Kreidenweis U, W. Yalew A, von Jeetze P, Wang X, Dietrich J, Alves M (2024). _mrvalidation: madrat data preparation for validation purposes_. doi:10.5281/zenodo.4317826 <https://doi.org/10.5281/zenodo.4317826>, R package version 2.56.12, <https://github.com/pik-piam/mrvalidation>.
+Bodirsky B, Wirth S, Karstens K, Humpenoeder F, Stevanovic M, Mishra A, Biewald A, Weindl I, Beier F, Chen D, Crawford M, Leip D, Molina Bacca E, Kreidenweis U, W. Yalew A, von Jeetze P, Wang X, Dietrich J, Alves M (2024). _mrvalidation: madrat data preparation for validation purposes_. doi:10.5281/zenodo.4317826 <https://doi.org/10.5281/zenodo.4317826>, R package version 2.56.13, <https://github.com/pik-piam/mrvalidation>.
 
 A BibTeX entry for LaTeX users is
 
@@ -48,7 +48,7 @@ A BibTeX entry for LaTeX users is
   title = {mrvalidation: madrat data preparation for validation purposes},
   author = {Benjamin Leon Bodirsky and Stephen Wirth and Kristine Karstens and Florian Humpenoeder and Mishko Stevanovic and Abhijeet Mishra and Anne Biewald and Isabelle Weindl and Felicitas Beier and David Chen and Michael Crawford and Debbora Leip and Edna {Molina Bacca} and Ulrich Kreidenweis and Amsalu {W. Yalew} and Patrick {von Jeetze} and Xiaoxi Wang and Jan Philipp Dietrich and Marcos Alves},
   year = {2024},
-  note = {R package version 2.56.12},
+  note = {R package version 2.56.13},
   doi = {10.5281/zenodo.4317826},
   url = {https://github.com/pik-piam/mrvalidation},
 }