Add integration with piamPlotComparison for compareScenarios

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '3069465'
+ValidationKey: '3092076'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

.github/workflows/check.yaml

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -23,7 +23,6 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
-            gamstransfer=?ignore
             any::lucode2
             any::covr
             any::madrat
@@ -36,7 +35,7 @@ jobs:
           # gms, goxygen, GDPuc) will usually have an outdated binary version
           # available; by using extra-packages we get the newest version
 
-      - uses: actions/setup-python@v4
+      - uses: actions/setup-python@v5
         with:
           python-version: 3.9
 

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: 'edgeTransport: Prepare EDGE Transport Data for the REMIND model'
-version: 1.5.5
-date-released: '2024-03-21'
+version: 1.5.6
+date-released: '2024-04-08'
 abstract: EDGE-T is a fork of the GCAM transport module https://jgcri.github.io/gcam-doc/energy.html#transportation
   with a high level of detail in its representation of technological and modal options.
   It is a partial equilibrium model with a nested multinomial logit structure and

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: edgeTransport
 Title: Prepare EDGE Transport Data for the REMIND model
-Version: 1.5.5
+Version: 1.5.6
 Authors@R: c(
     person("Alois", "Dirnaichner", email = "[email protected]", role = c("aut", "cre")),
     person("Marianna", "Rottoli", email = "[email protected]", role = "aut"),
@@ -15,7 +15,7 @@ Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.3.1
 VignetteBuilder: knitr
-Date: 2024-03-21
+Date: 2024-04-08
 Config/testthat/edition: 3
 Imports:
     rmndt,
@@ -32,9 +32,7 @@ Imports:
     gdxrrw,
     gdxdt,
     remind2,
-    rlang,
-    yaml,
-    ymlthis
+    piamPlotComparison
 Suggests:
     testthat,
     knitr,

NAMESPACE

@@ -62,7 +62,6 @@ importFrom(quitte,as.quitte)
 importFrom(quitte,write.mif)
 importFrom(readxl,read_excel)
 importFrom(remind2,toolRegionSubsets)
-importFrom(rlang,parse_expr)
 importFrom(rmarkdown,render)
 importFrom(rmndt,aggregate_dt)
 importFrom(rmndt,approx_dt)
@@ -74,10 +73,5 @@ importFrom(rootSolve,multiroot)
 importFrom(stats,complete.cases)
 importFrom(stats,na.omit)
 importFrom(utils,read.csv)
-importFrom(yaml,yaml.load)
-importFrom(ymlthis,as_yml)
-importFrom(ymlthis,use_rmarkdown)
-importFrom(ymlthis,yml_params_code)
-importFrom(ymlthis,yml_replace)
 importFrom(zoo,na.approx)
 importFrom(zoo,na.spline)

R/compareScenarios_EDGET.R

@@ -1,9 +1,6 @@
 #' Render CompareScenarios EDGE Transport
 #'
-#' Renders the *.Rmd-files associated to CompareScenarios EDGE TRansport. In the Rmds,
-#' scenario- and historical .mif-files are loaded. Then plots are created from
-#' this data. The result may be rendered to PDF or HTML. Alternatively one can
-#' choose Rmd as output format and obtain a copy of the *.Rmd-files.
+#' A wrapper for piamPlotComparison::compareScenarios
 #'
 #' @param mifScen \code{character(n)}, optionally named. Paths to scenario mifs.
 #'   If the vector has names, those are used to refer to the scenarios in the
@@ -15,149 +12,24 @@
 #'   and intermediary files are created.
 #' @param outputFormat \code{character(1)}, not case-sensitive. \code{"html"},
 #'   \code{"pdf"}, or \code{"rmd"}.
-#' @param ... YAML parameters, see below.
-#' @importFrom yaml yaml.load
-#' @importFrom rlang parse_expr
-#' @importFrom ymlthis yml_params_code yml_replace as_yml use_rmarkdown
-#' @importFrom rmarkdown render
 #' @return The value returned by \code{\link[rmarkdown:render]{render()}}.
-#' @section YAML Parameters:
-#' \describe{
-#'   \item{\code{yearsScen}}{
-#'     \code{numeric(n)}.
-#'     Default: \code{c(seq(2005, 2060, 5), seq(2070, 2100, 10))}.
-#'     Years to show for scenario data.}
-#'   \item{\code{yearsHist}}{
-#'     \code{numeric(n)}.
-#'     Default: \code{c(seq(1990, 2020, 1), seq(2025, 2100, 5))}.
-#'     Years to show for historical data.}
-#'   \item{\code{yearsBarPlot}}{
-#'     \code{numeric(n)}.
-#'     Default: \code{c(2010, 2030, 2050, 2100)}.
-#'     Years to show in bar plots of scenario data.}
-#'   \item{\code{reg}}{
-#'     \code{NULL} or \code{character(n)}.
-#'     Default: \code{NULL}.
-#'     Regions to show. \code{NULL} means all.}
-#'   \item{\code{modelsHistExclude}}{
-#'     \code{character(n) or NULL}.
-#'     Default: \code{c()}.
-#'     Models in historical data to exclude.}
-#'   \item{\code{sections}}{
-#'     \code{character(n)}.
-#'     Default: \code{"all"}.
-#'     Names of sections to include. A subset of
-#'     \code{c("01_energy_demand", "02_energy_services", "03_stock_and_sales", "04_costs_and_shareweight_trends")}
-#'     or \code{"all"} for all available sections.}
-#'   \item{\code{userSectionPath}}{
-#'     \code{NULL} or \code{character(n)}.
-#'     Default: \code{NULL}.
-#'     Path to a *.Rmd-file that may be included as additional section.}
-#'   \item{\code{mainReg}}{
-#'     \code{character(1)}.
-#'     Default: \code{"World"}.
-#'     A region for which larger plots are shown.}
-#'   \item{\code{figWidth, figHeight}}{
-#'     \code{numeric(1)}.
-#'     Default: \code{15} and \code{10}, respectively.
-#'     Size of plots in inches.}
-#'   \item{\code{warning}}{
-#'     \code{logical(1)}.
-#'     Default: \code{TRUE}.
-#'     Show warnings in output?}
-#' }
-#' @author Christof Schoetz, Johanna Hoppe
-#' @examples
-#' \dontrun{
-#' compareScenarios2(
-#'   mifScen = c("path/to/Base.mif", "path/to/NDC.mif"),
-#'   mifHist = "path/to/historical.mif",
-#'   outputFile = "CompareScenarios2Example1",
-#'   userSectionPath = "path/to/myPlots.Rmd")
-#' compareScenarios2(
-#'   mifScen = c(ScenarioName1 = "path/to/scen1.mif", ScenarioName2 = "path/to/scen2.mif"),
-#'   mifHist = "path/to/historical.mif",
-#'   outputFile = "CompareScenarios2Example2",
-#'   figWidth = 18, figHeight = 10)
-#' }
 #' @export
 compareScenarios_EDGET <- function(
-  mifScen, mifHist,
-  outputDir = getwd(),
-  outputFile = "CompareScenarios_EDGE-Transport",
-  outputFormat = "PDF",
-  ...
-) {
-  yamlParams <- c(
-    list(
-      mifScen = normalizePath(mifScen, mustWork = TRUE),
-      mifScenNames = names(mifScen),
-      mifHist = normalizePath(mifHist, mustWork = TRUE)),
-    list(...))
+    mifScen, mifHist,
+    outputDir = getwd(),
+    outputFile = "CompareScenarios_EDGE-Transport",
+    outputFormat = "PDF") {
 
-  # convert relative to absolute paths
-  if ("userSectionPath" %in% names(yamlParams)) {
-    yamlParams$userSectionPath <- normalizePath(yamlParams$userSectionPath,
-                                                mustWork = TRUE)
-  }
-
-  outputFormat <- tolower(outputFormat)
-  if (outputFormat == "pdf") outputFormat <- "pdf_document"
-  if (outputFormat == "html") outputFormat <- "html_document"
-  if (identical(tolower(outputFormat), "rmd")) {
-    return(.compareScenarios2Rmd(yamlParams, outputDir, outputFile))
-  }
-  # copy the template directory from the package to the outputDir because rmarkdown writes to the folder
-  # containing the template.
-  templateInOutputDir <- file.path(outputDir, "compareScenarios_Transport", "csEDGET_main.Rmd")
-  file.copy(system.file("Rmd/compareScenarios_Transport/", package = "edgeTransport"),
-            outputDir, recursive = TRUE)
-  render(
-    templateInOutputDir,
-    intermediates_dir = outputDir,
-    output_dir = outputDir,
-    output_file = outputFile,
-    output_format = outputFormat,
-    params = yamlParams,
-    envir = new.env())
-  unlink(file.path(outputDir, "compareScenarios_Transport"), recursive = TRUE)
-}
-
-# Copies the CompareScenarios2-Rmds to the specified location and modifies
-# their YAML header according to \code{yamlParams}.
-.compareScenarios2Rmd <- function(yamlParams, outputDir, outputFile) {
-  pathMain <- system.file("Rmd/compareScenarios_Transport/csEDGET_main.Rmd", package = "edgeTransport")
-  linesMain <- readLines(pathMain)
-  delimiters <- grep("^(---|\\.\\.\\.)\\s*$", linesMain)
-  headerMain <- linesMain[(delimiters[1]):(delimiters[2])]
-  yml <- yaml.load(
-    headerMain,
-    handlers = list(r = function(x) yml_params_code(!!parse_expr(x))))
-  baseYaml <- as_yml(yml)
-  newYamlParams <- baseYaml$params
-  newYamlParams[names(yamlParams)] <- yamlParams
-  if (!is.null(names(yamlParams$mifScen))) {
-    newYamlParams$mifScenNames <- names(yamlParams$mifScen)
-  }
-  newYaml <- yml_replace(
-    baseYaml,
-    params = newYamlParams,
-    date = format(Sys.Date()))
-  pathDir <- file.path(outputDir, paste0(outputFile, "_Rmd"))
-  if (!dir.exists(pathDir)) dir.create(pathDir)
-  dirFiles <- dir(
-    system.file("Rmd/compareScenarios_Transport", package = "edgeTransport"),
-    full.names = TRUE)
-  rmdDirFiles <- grep(
-    dirFiles,
-    pattern = "csEDGET_main\\.Rmd$",
-    invert = TRUE, value = TRUE)
-  file.copy(rmdDirFiles, pathDir)
-  use_rmarkdown(
-    newYaml,
-    path = file.path(pathDir, "cs2_main.Rmd"),
-    template = system.file(
-      "Rmd/compareScenarios_Transport/csEDGET_main.Rmd",
-      package = "edgeTransport"),
-    include_yaml = FALSE)
+  piamPlotComparison::compareScenarios(
+    projectLibrary = "edgeTransport",
+    mifScen = mifScen,
+    mifHist = mifHist,
+    outputFormat = outputFormat,
+    outputFile = outputFile,
+    sections = "all",
+    docTitle = "Edge Transport Compare Scenarios",
+    outputDir = outputDir,
+    reg = c("OAS", "MEA", "SSA", "LAM", "REF", "CAZ", "CHA", "IND", "JPN", "USA", "NEU", "EUR", "World"),
+    yearsHist = c(seq(2010, 2020, 1), seq(2025, 2100, 5))
+  )
 }

R/generateEDGEdata.R

@@ -449,7 +449,6 @@ toolGenerateEDGEdata <- function(input_folder, output_folder, cache_folder = NUL
     if(nrow(nas) > 0) {
       print("NAs found in FV vintage shares.")
       nas
-      browser()
     }
     shares$FV_shares = vintages[["shares"]]$FV_shares
     prices = vintages[["prices"]]
@@ -474,7 +473,6 @@ toolGenerateEDGEdata <- function(input_folder, output_folder, cache_folder = NUL
     if(nrow(nas) > 0) {
       print("NAs found in final demand output.")
       nas
-      browser()
     }
 
     num_veh_stations = toolVehicleStations(

R/incotrend.R

@@ -93,7 +93,6 @@ toolPreftrend <- function(SWS, ptab, calibdem, incocost, years, GDP_POP_MER,
   nas <- FVtarget[is.na(sw)]
   if(nrow(nas) > 0){
     print("Warning: NAs in SWs found.")
-    browser()
   }
 
   setnames(FVtarget, "sw", "value")
@@ -221,31 +220,27 @@ toolPreftrend <- function(SWS, ptab, calibdem, incocost, years, GDP_POP_MER,
   nas <- S3target[is.na(sw)]
   if(nrow(nas) > 0){
     print("Warning: NAs in SWs found.")
-    browser()
   }
 
   S2target[, sw := sw/max(sw),
            by = c("region", "year", "subsector_L3")]
   nas <- S2target[is.na(sw)]
   if(nrow(nas) > 0){
     print("Warning: NAs in SWs found.")
-    browser()
   }
 
   S1target[, sw := sw/max(sw),
            by = c("region", "year", "subsector_L2")]
   nas <- S1target[is.na(sw)]
   if(nrow(nas) > 0){
     print("Warning: NAs in SWs found.")
-    browser()
   }
 
   VStarget[, sw := sw/max(sw),
            by = c("region", "year", "subsector_L1")]
   nas <- VStarget[is.na(sw)]
   if(nrow(nas) > 0){
     print("Warning: NAs in SWs found.")
-    browser()
   }
 
 
@@ -332,7 +327,6 @@ Hybrid Electric,Liquids")
     nas <- FVtarget[logit_type != "pchar" & is.na(value)]
     if(nrow(nas) > 0){
       print(sprintf("NAs found in FV shareweight trends for %s scenario.", tech_scen))
-      browser()
     }
     ## level S2: Bus vs LDV
     S2target[, regioncat := ifelse(region %in% richregions, "rich", "poor")]
@@ -350,7 +344,6 @@ Hybrid Electric,Liquids")
     nas <- S2target[is.na(sw)]
     if(nrow(nas) > 0){
       print(sprintf("NAs found in S2 shareweight trends for %s scenario.", tech_scen))
-      browser()
     }
 
     ## level S3: all other mode shares
@@ -369,7 +362,6 @@ Hybrid Electric,Liquids")
     nas <- S3target[is.na(sw)]
     if(nrow(nas) > 0){
       print(sprintf("NAs found in S3 shareweight trends for %s scenario.", tech_scen))
-      browser()
     }
 
   }else{

R/logit.R

@@ -66,7 +66,6 @@ toolCalculateLogitSW <- function(prices,
     nas <- df[is.na(share)]
     if(nrow(nas) > 0) {
       print("NAs found in SWs.")
-      browser()
     }
     MJ_km <- merge(df, mj_km_data, by=intersect(names(df),names(mj_km_data)), all = FALSE)
 
@@ -237,7 +236,6 @@ toolCalculateLogitSW <- function(prices,
   if(nrow(nas) > 0){
     print("NAs found in FV shares.")
     nas
-    browser()
   }
   # VS1
   VS1_all <- X2Xcalc(prices = FV,

R/reportEDGET.R

@@ -418,14 +418,12 @@ toolReportEDGET <- function(output_folder = ".",
 
     vars <- varlist[[aggrname]]
     #access the first element in vars
-    
+
 
     if (length(unique(datatable[variable %in% vars]$variable)) < length(vars)){
-      browser()
       print(paste0("Missing variables to aggregate data to ", aggrname))
       }
     else if (length(unique(datatable[variable %in% vars]$variable)) > length(vars)) {
-      browser()
       print(paste0('duplicates from: ', aggrname, 'not summed up'))
       }
     else {
@@ -992,11 +990,11 @@ toolReportEDGET <- function(output_folder = ".",
 
   #Calculate useful energy
   UE <- toMIF[grepl("FE", variable) & grepl("Electric|Liquids|Hydrogen", variable)] #select only FE for electricity, liquids and hydrogen
-  
-  
+
+
   #create new column named technology and assign values based on variables in UE.varialbe: if the variable contains "Electricity" then technology is "Electric", if the variable contains "Liquids" then technology is "Liquids", if the variable contains "Hydrogen" then technology is "Hydrogen"
   UE[, technology := ifelse(grepl("Electricity", variable), "Electric", ifelse(grepl("Liquids", variable), "Liquids", ifelse(grepl("Hydrogen", variable), "Hydrogen", NA)))]
-  
+
   UE <- merge(UE, Mapp_UE, technology) #merge with efficiencies
   UE[, value:= value*UE_efficiency][, c("variable", "technology", "UE_efficiency"):= list(gsub("FE","UE", variable), NULL, NULL)] #calculate useful energy