Merge pull request #312 from ahagen-pik/fixWarnings

Fix warnings lucode2::buildLibrary()

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '42568470'
+ValidationKey: '42588540'
 AutocreateReadme: yes
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'

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: 'edgeTransport: Prepare EDGE Transport Data for the REMIND model'
-version: 2.12.1
+version: 2.12.2
 date-released: '2024-12-13'
 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.

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: edgeTransport
 Title: Prepare EDGE Transport Data for the REMIND model
-Version: 2.12.1
+Version: 2.12.2
 Authors@R: c(
     person("Johanna", "Hoppe", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0009-0004-6753-5090")),

NAMESPACE

@@ -36,7 +36,11 @@ importFrom(gdxdt,writegdx)
 importFrom(gdxdt,writegdx.parameter)
 importFrom(gdxrrw,rgdx)
 importFrom(madrat,calcOutput)
+importFrom(madrat,getConfig)
+importFrom(madrat,readSource)
+importFrom(magclass,getComment)
 importFrom(magclass,lowpass)
+importFrom(magclass,time_interpolate)
 importFrom(magrittr,`%>%`)
 importFrom(reporttransport,reportEdgeTransport)
 importFrom(reporttransport,reportToREMINDcapitalCosts)
@@ -47,5 +51,6 @@ importFrom(rmndt,approx_dt)
 importFrom(rmndt,magpie2dt)
 importFrom(rootSolve,multiroot)
 importFrom(stats,approxfun)
+importFrom(stats,setNames)
 importFrom(utils,capture.output)
 importFrom(zoo,na.approx)

R/iterativeEDGETransport.R

@@ -10,6 +10,7 @@
 #' reportToREMINDenergyEfficiency reportToREMINDfinalEnergyShares
 #' @import data.table
 #' @export
+#'
 
 
 iterativeEdgeTransport <- function() {
@@ -19,6 +20,7 @@ iterativeEdgeTransport <- function() {
   #############################################################
   ## Settings
   #############################################################
+  cfg <- NULL
 
   # Set paths to folders
   edgeTransportFolder <- "EDGE-T"
@@ -31,7 +33,7 @@ iterativeEdgeTransport <- function() {
 
   # Set gdx
   gdx <- "input.gdx"
-  if(file.exists("fulldata.gdx"))
+  if (file.exists("fulldata.gdx"))
     gdx <- "fulldata.gdx"
 
   # Load config
@@ -48,7 +50,12 @@ iterativeEdgeTransport <- function() {
   #############################################################
   ## Load input data
   #############################################################
-  inputFolder = paste0("./")
+  inputFolder <- paste0("./")
+
+  # bind variables locally to prevent NSE notes in R CMD CHECK
+  period <- value <- unit <- univocalName <- iteration <- type <- variable <- . <- NULL
+
+
   # share of electricity in Hybrid electric vehicles
   hybridElecShare <- 0.4
   numberOfRegions <- length(readGDX(gdx, "all_regi"))
@@ -70,7 +77,7 @@ iterativeEdgeTransport <- function() {
   genModelPar <- inputs$genModelPar
   scenModelPar <- inputs$scenModelPar
   RDSinputs <- inputs$RDSfiles
-  
+
 
 
   # Data from previous REMIND iteration
@@ -101,8 +108,8 @@ iterativeEdgeTransport <- function() {
     REMINDfuelCostIterations <- rbind(REMINDfuelCostIterations, copy(REMINDfuelCost)[, iteration := iterationNumber])
     storeData(file.path(".", edgeTransportFolder), REMINDfuelCostIterations = REMINDfuelCostIterations)
     averagePricesOverIterations <- TRUE
-    if(averagePricesOverIterations) {
-      if(max(unique(REMINDfuelCostIterations$iteration)) >= 20 &
+    if (averagePricesOverIterations) {
+      if (max(unique(REMINDfuelCostIterations$iteration)) >= 20 &&
          max(unique(REMINDfuelCostIterations$iteration)) <= 30) {
         ## apply moving avg
         byCols <- names(REMINDfuelCostIterations)
@@ -247,15 +254,15 @@ iterativeEdgeTransport <- function() {
 
     ## CapCosts
     writegdx.parameter("p35_esCapCost.gdx", f35_esCapCost, "p35_esCapCost",
-                       valcol="value", uelcols = c("tall", "all_regi", "GDP_scenario", "DEM_scenario", "EDGE_scenario", "all_teEs"))
+                       valcol = "value", uelcols = c("tall", "all_regi", "GDP_scenario", "DEM_scenario", "EDGE_scenario", "all_teEs"))
 
     ## Intensities
     writegdx.parameter("p35_fe2es.gdx", f35_fe2es, "p35_fe2es",
-                       valcol="value", uelcols = c("tall", "all_regi", "GDP_scenario", "DEM_scenario", "EDGE_scenario", "all_teEs"))
+                       valcol = "value", uelcols = c("tall", "all_regi", "GDP_scenario", "DEM_scenario", "EDGE_scenario", "all_teEs"))
 
     ## Shares: demand can represent the shares since it is normalized
     writegdx.parameter("p35_shFeCes.gdx", f35_shFeCes, "p35_shFeCes",
-                       valcol="value",
+                       valcol = "value",
                        uelcols = c("tall", "all_regi", "GDP_scenario", "DEM_scenario", "EDGE_scenario", "all_enty", "all_in", "all_teEs"))
 
     print(paste("---", Sys.time(), "End of the EDGE-T iterative model run."))

R/supportFunctions.R

@@ -7,16 +7,36 @@
 #' @export
 
 toolNormalizePreferences <- function(preferenceTab) {
+  # bind variables locally to prevent NSE notes in R CMD CHECK
+  level <- value <- NULL
+
+  # S1S: logit level: distances (e.g. short-medium, long)
   preferenceTab[level == "S1S", max := max(value), by = c("region", "period", "sector")]
-  preferenceTab[level == "S1S" & max != 0, value := value/max(value), by = c("region", "period", "sector")] # S1S: logit level: distances (e.g. short-medium, long)
-  preferenceTab[level == "S2S1", max := max(value), by = c("region", "period", "sector", "subsectorL1")]
-  preferenceTab[level == "S2S1" & max != 0, value := value/max(value), by = c("region", "period", "sector", "subsectorL1")] # S2S1: logit level: modes/categories (e.g. walk, road, rail)
+  preferenceTab[level == "S1S" & max != 0, value := value / max(value), by = c("region", "period", "sector")]
+
+  # S2S1: logit level: modes/categories (e.g. walk, road, rail)
   preferenceTab[level == "S3S2", max := max(value), by = c("region", "period", "sector", "subsectorL1", "subsectorL2")]
-  preferenceTab[level == "S3S2" & max != 0, value := value/max(value), by = c("region", "period", "sector", "subsectorL1", "subsectorL2")] # S3S2: logit level: modes/technologies (e.g. LDV, bus, Liquids)
-  preferenceTab[level == "VS3", max := max(value), by = c("region", "period", "sector", "subsectorL1", "subsectorL2", "subsectorL3")]
-  preferenceTab[level == "VS3" & max != 0, value := value/max(value), by = c("region", "period", "sector", "subsectorL1", "subsectorL2", "subsectorL3")] # VS3: logit level: modes/technologies (e.g. cars, Liquids)
-  preferenceTab[level == "FV", max := max(value), by = c("region", "period", "sector", "subsectorL1", "subsectorL2", "subsectorL3", "vehicleType")]
-  preferenceTab[level == "FV" & max != 0, value := value/max(value), by = c("region", "period", "sector", "subsectorL1", "subsectorL2", "subsectorL3", "vehicleType")]  # FV: logit level: vehicle type (e.g. large car, moped)
+  preferenceTab[level == "S2S1", max := max(value), by = c("region", "period", "sector", "subsectorL1")]
+  preferenceTab[level == "S2S1" & max != 0, value := value / max(value),
+                by = c("region", "period", "sector", "subsectorL1")]
+
+  # S3S2: logit level: modes/technologies (e.g. LDV, bus, Liquids)
+  preferenceTab[level == "S3S2" & max != 0, value := value / max(value),
+                by = c("region", "period", "sector", "subsectorL1", "subsectorL2")]
+
+  # VS3: logit level: modes/technologies (e.g. cars, Liquids)
+  preferenceTab[level == "VS3", max := max(value),
+                by = c("region", "period", "sector", "subsectorL1", "subsectorL2", "subsectorL3")]
+  preferenceTab[level == "VS3" & max != 0, value := value / max(value),
+                by = c("region", "period", "sector", "subsectorL1", "subsectorL2", "subsectorL3")]
+
+
+  # FV: logit level: vehicle type (e.g. large car, moped)
+  preferenceTab[level == "FV", max := max(value),
+                by = c("region", "period", "sector", "subsectorL1", "subsectorL2", "subsectorL3", "vehicleType")]
+  preferenceTab[level == "FV" & max != 0, value := value / max(value),
+                by = c("region", "period", "sector", "subsectorL1", "subsectorL2", "subsectorL3", "vehicleType")]
+
   preferenceTab[, max := NULL]
 
   if (anyNA(preferenceTab)) stop("Something went wrong with the normalization of the preference trends. Please check toolNormalizePreferences()")
@@ -34,10 +54,11 @@ toolNormalizePreferences <- function(preferenceTab) {
 #' @export
 
 toolLoadDecisionTree <- function(regionAggregation = "iso") {
+  # bind variables locally to prevent NSE notes in R CMD CHECK
+  spatial <- present <- region <- sector <- subsectorL1 <- subsectorL2 <- subsectorL3 <- vehicleType <- technology <- univocalName <- NULL
 
   # decisionTree.csv contains all possible branches of the decision tree
-  decisionTree <- fread(system.file("extdata/helpersDecisionTree.csv",
-                                    package = "edgeTransport", mustWork = TRUE), header = TRUE)
+  decisionTree <- fread(system.file("extdata/helpersDecisionTree.csv", package = "edgeTransport", mustWork = TRUE), header = TRUE)
   decisionTree[, spatial := "all"]
   # Not all countries feature the same branches of the decision tree - Some vehicleTypes and modes are not
   # available in certain countries
@@ -99,7 +120,7 @@ toolLoadDecisionTree <- function(regionAggregation = "iso") {
 
 getFilterEntriesUnivocalName <- function(categories, decisionTree) {
 
-  findEntries <- function(category, dt){
+  findEntries <- function(category, dt) {
     test <- dt[, lapply(.SD, function(x) grepl(category, x))]
     entries <- unique(dt[rowSums(test) > 0]$univocalName)
   }
@@ -130,10 +151,10 @@ calculateShares <- function(totPrice, lambda, pref = NULL) {
     if (sum(totPrice) == 0) {
       share <- 1 # e.g. for active modes with totPrice of zero on FV level
     } else {
-      share <- pref * totPrice ^ lambda / (sum(pref * totPrice ^ lambda))
+      share <- pref * totPrice^lambda / (sum(pref * totPrice^lambda))
     }
   } else {
-    share <- totPrice ^ lambda / (sum(totPrice ^ lambda))
+    share <- totPrice^lambda / (sum(totPrice^lambda))
   }
 
   return(share)
@@ -152,6 +173,7 @@ calculateShares <- function(totPrice, lambda, pref = NULL) {
 #' @export
 
 toolTraverseDecisionTree <- function(data, upperLevel, decisionTree) {
+  share <- value <- . <- NULL
 
   decisionGroups <- names(decisionTree[, -c("region", "univocalName")])
   indexUpperLevel <- which(match(decisionGroups, upperLevel) == 1)
@@ -182,15 +204,17 @@ toolTraverseDecisionTree <- function(data, upperLevel, decisionTree) {
 #' @export
 
 toolApplyMixedTimeRes <- function(data, helpers, idcols = NULL) {
+  # bind variables locally to prevent NSE notes in R CMD CHECK
+  period <- level <- test <- univocalName <- . <- NULL
 
   highRes <- unique(helpers$dtTimeRes$period)
   highResUnivocalNames <- copy(helpers$dtTimeRes)
   highResUnivocalNames <- highResUnivocalNames[, .(test = all(highRes %in% period)), by = univocalName]
   highResUnivocalNames <- highResUnivocalNames[test == TRUE]$univocalName
 
-  if (c("level") %in% names(data)){
-    #in this data format there is no univocalName
-    #this needs to change temporarily
+  if (c("level") %in% names(data)) {
+    # in this data format there is no univocalName
+    # this needs to change temporarily
     dataFV <- merge(data[level == "FV"], helpers$decisionTree, by = intersect(names(data), names(helpers$decisionTree)))
     dataHighRes <- dataFV[univocalName %in% highResUnivocalNames][, univocalName := NULL]
     dataLowRes <- rbind(dataFV[!(univocalName %in% highResUnivocalNames)][, univocalName := NULL], data[!level == "FV"])
@@ -227,6 +251,8 @@ return(data)
 #' @export
 
 toolCheckAllLevelsComplete <- function(data, decisionTree, name) {
+  # bind variables locally to prevent NSE notes in R CMD CHECK
+  level <- univocalName <- technology <- NULL
 
   decisionFV <- copy(decisionTree)
   decisionFV[, univocalName := NULL][, level := "FV"]
@@ -272,15 +298,17 @@ toolCheckAllLevelsComplete <- function(data, decisionTree, name) {
 #' @export
 
 toolOrderandCheck <- function(data, decisionTree, yrs = NULL, checkCompleteness = FALSE, fleetVars = FALSE) {
+  # bind variables locally to prevent NSE notes in R CMD CHECK
+  period <- subsectorL3 <- allyears <- NULL
 
   data <- merge(data, decisionTree, by = c(intersect(names(data), names(decisionTree))))
   allCols <- c(names(decisionTree), "variable", "unit", "period", "value")
   isComplete <- all(names(data) %in% allCols) && all(allCols %in% names(data))
   if (isComplete == FALSE) stop(paste0(deparse(substitute(data), " misses columns or has additional columns")))
   if (anyNA(data) == TRUE) stop(paste0(deparse(substitute(data), " contains NAs")))
-  data <- data[, ..allCols]
+  data <- data[, allCols, with = FALSE]
 
-  if (checkCompleteness == TRUE){
+  if (checkCompleteness == TRUE) {
     data <- data[period %in% yrs]
     if (fleetVars == TRUE) decisionTree <- decisionTree[grepl("Bus.*|.*4W|.*freight_road.*", subsectorL3)]
     allTimesteps <- data.table(period = yrs)[, allyears := "All"]

R/supportFunctionsIterative.R

@@ -7,16 +7,22 @@
 #' @param demScenario demand scenario
 #' @param transportPolScenario Transport policy scenario
 #' @import data.table
+#' @importFrom stats setNames
 #' @export
 
 # Loads the csv input files chooses the correct scenario and
   # converts the files into RDS local files
-  csv2RDS <- function(filename, inputPath, SSPscenario, demScenario, transportPolScenario) {
-    if (filename == "scenSpecPrefTrends") colNames <- c("period", "region", "SSPscen", "demScen", "transportPolScen", "sector",
-                                                        "subsectorL1", "subsectorL2", "subsectorL3", "vehicleType", "technology",
-                                                        "level", "variable", "unit", "value")
-    else if (filename == "initialIncoCosts") colNames <- c("period", "region", "SSPscen", "demScen", "transportPolScen", "univocalName","technology","variable","unit","type","value")
-    else if (filename == "timeValueCosts") colNames <-  c("period", "region", "SSPscen", "demScen", "transportPolScen", "univocalName", "variable", "unit", "value")
+csv2RDS <- function(filename, inputPath, SSPscenario, demScenario, transportPolScenario) {
+    # bind variables locally to prevent NSE notes in R CMD CHECK
+    SSPscen <- demScen <- transportPolScen <- NULL
+
+    if (filename == "scenSpecPrefTrends") colNames <- c("period", "region", "SSPscen", "demScen", "transportPolScen",
+                                                        "sector", "subsectorL1", "subsectorL2", "subsectorL3",
+                                                        "vehicleType", "technology", "level", "variable", "unit", "value")
+    else if (filename == "initialIncoCosts") colNames <- c("period", "region", "SSPscen", "demScen", "transportPolScen",
+                                                           "univocalName", "technology", "variable", "unit", "type", "value")
+    else if (filename == "timeValueCosts") colNames <-  c("period", "region", "SSPscen", "demScen", "transportPolScen",
+                                                          "univocalName", "variable", "unit", "value")
     else if (filename == "f29_trpdemand") colNames <-  c("period", "region", "SSPscen", "demScen", "transportPolScen", "all_in", "value")
     else colNames <-  c("period", "region", "SSPscen", "demScen", "transportPolScen",
                         "univocalName", "technology", "variable", "unit", "value")
@@ -53,6 +59,8 @@ toolLoadRDSinputs <- function(edgeTransportFolder, inputFiles) {
 #' @export
 
 toolLoadIterativeInputs <- function(edgeTransportFolder, inputFolder, inputFiles, numberOfRegions, SSPscenario, transportPolScenario, demScenario) {
+  # bind variables locally to prevent NSE notes in R CMD CHECK
+  transportPolScen <- all_in <- period <- value <- unit <- sector <- variable <- . <- univocalName <- test <- SSPscen <- NULL
 
   # Model input parameters from the package
   ## Exponents discrete choice model
@@ -65,8 +73,9 @@ toolLoadIterativeInputs <- function(edgeTransportFolder, inputFolder, inputFiles
   annuityCalc <- fread(system.file("extdata/genParAnnuityCalc.csv", package = "edgeTransport", mustWork = TRUE), header = TRUE)
   # Interest Rate and vehicle service life for annuity calculation
   # NOTE: right now there is only "default". If we add scenario specific annuity parameters, we can shift annuityCalc to the scenPar's
-  if  (gsub("ICEban", "", transportPolScenario) %in% annuityCalc$transportPolScen){
-    annuityCalc <- annuityCalc[transportPolScen == gsub("ICEban", "", transportPolScenario)][, transportPolScen := NULL]} else {
+  if  (gsub("ICEban", "", transportPolScenario) %in% annuityCalc$transportPolScen) {
+    annuityCalc <- annuityCalc[transportPolScen == gsub("ICEban", "", transportPolScenario)][, transportPolScen := NULL]
+} else {
     annuityCalc <- annuityCalc[transportPolScen == "default"][, transportPolScen := NULL]
   }
 
@@ -99,8 +108,9 @@ toolLoadIterativeInputs <- function(edgeTransportFolder, inputFolder, inputFiles
 
   # Input from REMIND input data
   # In the first iteration input data needs to be loaded
-  if (!dir.exists(file.path(edgeTransportFolder)))  {
-    print("Loading csv data from input folder and creating RDS files...")}
+  if (!dir.exists(file.path(edgeTransportFolder))) {
+    print("Loading csv data from input folder and creating RDS files...")
+}
   RDSfiles <- list()
   for (filename in inputFiles) {
     if (length(list.files(file.path(".", edgeTransportFolder), paste0(filename, ".RDS"), recursive = TRUE, full.names = TRUE)) < 1) {