fix toolFixWeight

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '69584592'
+ValidationKey: '69669726'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

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: 'madrat: May All Data be Reproducible and Transparent (MADRaT) *'
-version: 3.37.2
-date-released: '2026-07-02'
+version: 3.37.4
+date-released: '2026-07-15'
 abstract: Provides a framework which should improve reproducibility and transparency
   in data processing. It provides functionality such as automatic meta data creation
   and management, rudimentary quality management, data caching, work-flow management

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: madrat
 Title: May All Data be Reproducible and Transparent (MADRaT) *
-Version: 3.37.2
-Date: 2026-07-02
+Version: 3.37.4
+Date: 2026-07-15
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "dietrich@pik-potsdam.de", role = c("aut", "cre"),
            comment = c(affiliation = "Potsdam Institute for Climate Impact Research", ORCID = "0000-0002-4309-6431")),

NAMESPACE

@@ -59,25 +59,17 @@ import(magclass)
 importFrom(callr,r)
 importFrom(igraph,"V<-")
 importFrom(igraph,V)
-importFrom(igraph,as_undirected)
-importFrom(igraph,cluster_edge_betweenness)
-importFrom(igraph,components)
 importFrom(igraph,ego)
 importFrom(igraph,graph_from_data_frame)
 importFrom(igraph,make_ego_graph)
-importFrom(igraph,membership)
 importFrom(igraph,subcomponent)
 importFrom(igraph,union)
 importFrom(magclass,"getCells<-")
-importFrom(magclass,"getComment<-")
-importFrom(magclass,"getYears<-")
 importFrom(magclass,as.magpie)
-importFrom(magclass,clean_magpie)
 importFrom(magclass,collapseNames)
 importFrom(magclass,dimExists)
 importFrom(magclass,dimSums)
 importFrom(magclass,getCells)
-importFrom(magclass,getComment)
 importFrom(magclass,getItems)
 importFrom(magclass,getNames)
 importFrom(magclass,getYears)
@@ -86,15 +78,11 @@ importFrom(magclass,magpie_expand)
 importFrom(magclass,mbind)
 importFrom(magclass,ncells)
 importFrom(magclass,new.magpie)
-importFrom(magclass,nregions)
-importFrom(magclass,nyears)
 importFrom(magclass,read.magpie)
 importFrom(magclass,setCells)
 importFrom(magclass,setYears)
 importFrom(magclass,time_interpolate)
 importFrom(magclass,where)
-importFrom(magclass,write.magpie)
-importFrom(magclass,write.report)
 importFrom(methods,formalArgs)
 importFrom(pkgload,is_dev_package)
 importFrom(renv,activate)
@@ -115,10 +103,7 @@ importFrom(utils,capture.output)
 importFrom(utils,download.file)
 importFrom(utils,installed.packages)
 importFrom(utils,modifyList)
-importFrom(utils,packageDescription)
 importFrom(utils,person)
-importFrom(utils,read.csv)
-importFrom(utils,read.csv2)
 importFrom(utils,sessionInfo)
 importFrom(utils,str)
 importFrom(utils,tail)

R/calcOutput.R

@@ -104,10 +104,6 @@
 #' a <- calcOutput(type = "TauTotal")
 #' }
 #'
-#' @importFrom magclass nyears nregions getComment<- getComment getYears clean_magpie write.report write.magpie
-#' getCells getYears<- is.magpie dimSums
-#' @importFrom utils packageDescription read.csv2 read.csv
-#' @importFrom withr defer local_dir
 #' @export
 calcOutput <- function(type, aggregate = TRUE, file = NULL, years = NULL, # nolint
                        round = NULL, signif = NULL, supplementary = FALSE,
@@ -205,7 +201,7 @@ calcOutput <- function(type, aggregate = TRUE, file = NULL, years = NULL, # noli
     if (x$isocountries) {
       .countrycheck <- function(datacountries, name) {
         datacountries <- robustSort(datacountries)
-        isoCountry <- read.csv2(system.file("extdata", "iso_country.csv", package = "madrat"), row.names = NULL)
+        isoCountry <- utils::read.csv2(system.file("extdata", "iso_country.csv", package = "madrat"), row.names = NULL)
         isoCountry1 <- as.vector(isoCountry[, "x"])
         names(isoCountry1) <- isoCountry[, "X"]
         isocountries <- robustSort(isoCountry1)
@@ -268,11 +264,11 @@ calcOutput <- function(type, aggregate = TRUE, file = NULL, years = NULL, # noli
   }
 
   startinfo <- toolstartmessage(callString, "+")
-  defer({
+  withr::defer({
     toolendmessage(startinfo, "-")
   })
 
-  local_dir(getConfig("outputfolder"))
+  withr::local_dir(getConfig("outputfolder"))
 
   functionname <- prepFunctionName(type = type, prefix = "calc", ignore = ifelse(is.null(years), "years", NA))
   extraArgs <- sapply(attr(functionname, "formals"), function(x) return(eval(parse(text = x))), simplify = FALSE) # nolint

R/getISOlist.R

@@ -25,7 +25,7 @@
 #' @importFrom magclass ncells
 #' @export
 getISOlist <- function(type = "all", threshold = 1) {
-  isoCountry <- read.csv2(system.file("extdata", "iso_country.csv", package = "madrat"), row.names = NULL)
+  isoCountry <- utils::read.csv2(system.file("extdata", "iso_country.csv", package = "madrat"), row.names = NULL)
   isoCountry1 <- as.vector(isoCountry[, "x"])
   names(isoCountry1) <- isoCountry[, "X"]
   ref <- robustSort(isoCountry1)

R/getMadratInfo.R

@@ -15,8 +15,6 @@
 #' @author Jan Philipp Dietrich
 #' @seealso \code{\link{getCalculations}}, \code{\link{getMadratGraph}}
 #' @family dependency graph
-#' @importFrom igraph graph_from_data_frame components V
-#' cluster_edge_betweenness as_undirected membership
 #' @export
 
 getMadratInfo <- function(graph = NULL, cutoff = 5, extended = FALSE, ...) {

R/readSource.R

@@ -112,7 +112,7 @@ readSource <- function(type, subtype = NULL, subset = NULL, # nolint: cyclocomp_
   }
 
   .testISO <- function(x, functionname = "function") {
-    isoCountry  <- read.csv2(system.file("extdata", "iso_country.csv", package = "madrat"), row.names = NULL)
+    isoCountry  <- utils::read.csv2(system.file("extdata", "iso_country.csv", package = "madrat"), row.names = NULL)
     isoCountry1 <- as.vector(isoCountry[, "x"])
     names(isoCountry1) <- isoCountry[, "X"]
     isocountries  <- robustSort(isoCountry1)

R/regionscode.R

@@ -49,7 +49,7 @@ regionscode <- function(mapping = NULL, label = FALSE, strict = TRUE) {
     if (ncol(mapping) >= 3) mapping[[1]] <- NULL
 
     # read list of ISO-countries
-    isCountry  <- read.csv2(system.file("extdata", "iso_country.csv", package = "madrat"), row.names = NULL)
+    isCountry  <- utils::read.csv2(system.file("extdata", "iso_country.csv", package = "madrat"), row.names = NULL)
     isCountry1 <- as.vector(isCountry[, "x"])
     names(isCountry1) <- isCountry[, "X"]
     isocountries <- robustSort(isCountry1)

R/toolAggregate.R

@@ -219,8 +219,9 @@ toolAggregateWeighted <- function(x, rel, weight, from, to, dim, wdim, partrel,
   }
 
   weightAndWeightSum <- toolZeroWeight(weight, rel, from, to, dim, wdim, partrel, zeroWeight)
-  weight <- weightAndWeightSum$weight
-  weight2 <- 1 / (weightAndWeightSum$weightSum + 10^-100)
+  weight <- weightAndWeightSum$weight # fine resolution
+  weight2 <- 1 / (weightAndWeightSum$weightSum + 10^-100) # coarse resolution
+  stopifnot(length(weight) >= length(weight2))
 
   if (mixedAggregation) {
     weight2[is.na(weight2)] <- 1
@@ -233,15 +234,17 @@ toolAggregateWeighted <- function(x, rel, weight, from, to, dim, wdim, partrel,
   }
 
   if (setequal(getItems(weight, dim = wdim), getItems(x, dim = dim))) {
+    # weighted mean aggregation
     out <- toolAggregate(x * weight, rel, from = from, to = to, dim = dim, partrel = partrel) * weight2
   } else {
+    # weighted disaggregation
     out <- toolAggregate(x * weight2, rel, from = from, to = to, dim = dim, partrel = partrel) * weight
+    if (zeroWeight == "fix" && !isTRUE(all.equal(sum(out), sum(x)))) {
+      warning("total sum is not the same after toolAggregate's weighted disaggregation ",
+              "despite zeroWeight = 'fix', please contact a madrat developer.")
+    }
   }
 
-  if (zeroWeight == "fix" && !isTRUE(all.equal(sum(out), sum(x)))) {
-    warning("total sum is not the same after toolAggregate despite zeroWeight = 'fix', ",
-            "please contact a madrat developer.")
-  }
 
   getComment(out) <- c(xComment, paste0("Data aggregated (toolAggregate): ", date()))
   return(out)
@@ -251,8 +254,7 @@ toolZeroWeight <- function(weight, rel, from, to, dim, wdim, partrel, zeroWeight
   weightSum <- toolAggregate(weight, rel, from = from, to = to, dim = wdim, partrel = partrel, verbosity = 10)
   if (zeroWeight != "allow" && any(weightSum == 0, na.rm = TRUE)) {
     if (zeroWeight == "warn") {
-      warning("Weight sum is 0, so cannot normalize and will return 0 for some ",
-              "aggregation targets. This changes the total sum of the magpie object! ",
+      warning("Weight sum is 0, so cannot normalize and will return 0 for some aggregation targets. ",
               'If this is really intended set zeroWeight = "allow", or "setNA" to return NA.')
     } else if (zeroWeight == "setNA") {
       weightSum[weightSum == 0] <- NA
@@ -263,7 +265,7 @@ toolZeroWeight <- function(weight, rel, from, to, dim, wdim, partrel, zeroWeight
         warning("Critical: toolAggregate zeroWeight = fix did not fix the weight! Please contact a madrat developer.")
       }
     } else {
-      stop("Weight sum is 0, so cannot normalize. This changes the total sum of the magpie object!")
+      stop("Weight sum is 0, so cannot normalize weights!")
     }
   }
   return(list(weight = weight, weightSum = weightSum))

R/toolCountry2isocode.R

@@ -25,8 +25,8 @@
 #' @export
 toolCountry2isocode <- function(country, warn = TRUE, ignoreCountries = NULL, type = NULL, mapping = NULL) {
   if (!is.null(type)) warning("\"type\" argument is deprecated and will be ignored! Don't use it!")
-  country2iso <- read.csv2(system.file("extdata", "country2iso.csv", package = "madrat"),
-                           row.names = NULL, encoding = "UTF-8")
+  country2iso <- utils::read.csv2(system.file("extdata", "country2iso.csv", package = "madrat"),
+                                  row.names = NULL, encoding = "UTF-8")
   country2iso1 <- as.vector(country2iso[, "x"])
   names(country2iso1) <- country2iso[, "X"]
   mapping <- c(country2iso1, mapping)

R/toolCountryFill.R

@@ -44,7 +44,7 @@ toolCountryFill <- function(x, fill = NA, no_remove_warning = NULL, overwrite =
                             countrylist = NULL, ...) {
   comment <- getComment(x)
   if (is.null(countrylist)) {
-    isoCountry <- read.csv2(system.file("extdata", "iso_country.csv", package = "madrat"), row.names = NULL)
+    isoCountry <- utils::read.csv2(system.file("extdata", "iso_country.csv", package = "madrat"), row.names = NULL)
     countrylist <- as.vector(isoCountry[, "x"])
     names(countrylist) <- isoCountry[, "X"]
   }
@@ -57,8 +57,8 @@ toolCountryFill <- function(x, fill = NA, no_remove_warning = NULL, overwrite =
     # warn only for countries which were not explicitly mentioned in argument "remove"
     countries2warn <- setdiff(additionalCountries, no_remove_warning)
     if (length(countries2warn) > 0) {
-      historicalCountries <- unique(read.csv2(system.file("extdata", "ISOhistorical.csv", package = "madrat"),
-                                              stringsAsFactors = FALSE)[["fromISO"]])
+      historicalCountries <- unique(utils::read.csv2(system.file("extdata", "ISOhistorical.csv", package = "madrat"),
+                                                     stringsAsFactors = FALSE)[["fromISO"]])
       removedHistoricalCountries <- intersect(countries2warn, historicalCountries)
       historicalHint <- if (length(removedHistoricalCountries) > 0) {
         paste(" - By using madrat::toolISOhistorical the data for the following countries can usually still be used:",

R/toolFixWeight.R

@@ -8,8 +8,8 @@
 #' @param weight magclass object containing weights to be used for a weighted
 #' (dis)aggregation. The provided weight does not need to be normalized, any
 #' number >= 0 is allowed.
-#' @param map a data frame where the first column contains coarse resolution items
-#' and the second column contains fine resolution items; fine resolution items
+#' @param map a 2-column data frame where one column contains coarse resolution items
+#' and the other column contains fine resolution items; fine resolution items
 #' must match items in weight
 #' @param dim which dim to fix (e.g. 1 or 3.2 or "region")
 #' @return weight, with weights set to 10^-30 only where otherwise the total
@@ -44,7 +44,11 @@ toolFixWeight <- function(weight, map, dim) {
   dim <- dimCode(dim, weight)
   stopifnot(length(dim) == 1,
             weight >= 0,
-            setequal(map[[2]], getItems(weight, dim)))
+            ncol(map) == 2)
+  if (!setequal(map[[2]], getItems(weight, dim))) {
+    map <- map[, 2:1]
+  }
+  stopifnot(setequal(map[[2]], getItems(weight, dim)))
   originalDimnames <- dimnames(weight)
 
   extramap <- NULL
@@ -55,17 +59,20 @@ toolFixWeight <- function(weight, map, dim) {
     } else {
       # merge all subdims into one dim, and replace back at the end using extramap
       originalMap2 <- map[[2]]
-      map[[1]] <- sub(".", "p", map[[1]], fixed = TRUE)
-      map[[2]] <- sub(".", "p", map[[2]], fixed = TRUE)
-      extramap <- stats::setNames(nm = map[[2]], originalMap2)
-      getItems(weight, dim, full = TRUE) <- sub(".", "p", getItems(weight, dim, full = TRUE), fixed = TRUE)
+      map[[1]] <- gsub(".", "p", map[[1]], fixed = TRUE)
+      map[[2]] <- gsub(".", "p", map[[2]], fixed = TRUE)
+      extramap <- originalMap2
+      names(extramap) <- map[[2]]
+      getItems(weight, dim, full = TRUE) <- gsub(".", "p", getItems(weight, dim, full = TRUE), fixed = TRUE)
     }
     dim <- dim + 0.1
     stopifnot(dim %in% c(1.1, 2.1, 3.1))
   }
   stopifnot(dim >= 1, dim < 4)
   mainDim <- floor(dim)
-  map <- stats::setNames(nm = map[[2]], object = map[[1]])
+  mapnames <- map[[2]]
+  map <- map[[1]]
+  names(map) <- mapnames
 
   # append subdim for coarse items according to map
   weight <- add_dimension(weight, dim + 0.1, "placeholder_dimname",

R/toolGetMapping.R

@@ -129,7 +129,7 @@ toolGetMapping <- function(name, type = NULL, where = NULL,
   filetype <- tolower(file_ext(fname))
   if (filetype == "csv") {
     sep <- if (grepl(pattern = ";", x = readLines(fname, 1))) ";" else ","
-    return(read.csv(fname, sep = sep, stringsAsFactors = FALSE, comment.char = "*"))
+    return(utils::read.csv(fname, sep = sep, stringsAsFactors = FALSE, comment.char = "*"))
   } else if (filetype == "rda") {
     data <- NULL
     load(fname)

R/toolISOhistorical.R

@@ -39,9 +39,10 @@ toolISOhistorical <- function(m, mapping = NULL, additional_mapping = NULL, over
   # mapping of historical countries and regions to the standard ISO-Country-List
   #            and last year of existence of the historical countries
   if (is.null(mapping)) {
-    mapping <- read.csv2(system.file("extdata", "ISOhistorical.csv", package = "madrat"), stringsAsFactors = FALSE)
+    mapping <- utils::read.csv2(system.file("extdata", "ISOhistorical.csv", package = "madrat"),
+                                stringsAsFactors = FALSE)
   } else if (is.character(mapping)) {
-    mapping <- read.csv(mapping, sep = ";", as.is = TRUE)
+    mapping <- utils::read.csv(mapping, sep = ";", as.is = TRUE)
   }
   # add additional mapping, if provided
   if (!is.null(additional_mapping)) {

README.md

@@ -1,6 +1,6 @@
 # May All Data be Reproducible and Transparent (MADRaT) *
 
-R package **madrat**, version **3.37.2**
+R package **madrat**, version **3.37.4**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/madrat)](https://cran.r-project.org/package=madrat) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1115490.svg)](https://doi.org/10.5281/zenodo.1115490) [![R build status](https://github.com/pik-piam/madrat/workflows/check/badge.svg)](https://github.com/pik-piam/madrat/actions) [![codecov](https://codecov.io/gh/pik-piam/madrat/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/madrat) [![r-universe](https://pik-piam.r-universe.dev/badges/madrat)](https://pik-piam.r-universe.dev/builds)
 
@@ -55,7 +55,7 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **madrat** in publications use:
 
-Dietrich J, Sauer P, Baumstark L, Wirth S, Giannousakis A, Rodrigues R, Bodirsky B, Leip D, Crawford M, Kreidenweis U, Klein D, Rein P (2026). "madrat: May All Data be Reproducible and Transparent (MADRaT) *." doi:10.5281/zenodo.1115490 <https://doi.org/10.5281/zenodo.1115490>, Version: 3.37.2, <https://github.com/pik-piam/madrat>.
+Dietrich J, Sauer P, Baumstark L, Wirth S, Giannousakis A, Rodrigues R, Bodirsky B, Leip D, Crawford M, Kreidenweis U, Klein D, Rein P (2026). "madrat: May All Data be Reproducible and Transparent (MADRaT) *." doi:10.5281/zenodo.1115490 <https://doi.org/10.5281/zenodo.1115490>. Version: 3.37.4, <https://github.com/pik-piam/madrat>.
 
 A BibTeX entry for LaTeX users is
 
@@ -64,9 +64,9 @@ A BibTeX entry for LaTeX users is
   title = {madrat: May All Data be Reproducible and Transparent (MADRaT) *},
   author = {Jan Philipp Dietrich and Pascal Sauer and Lavinia Baumstark and Stephen Wirth and Anastasis Giannousakis and Renato Rodrigues and Benjamin Leon Bodirsky and Debbora Leip and Michael Crawford and Ulrich Kreidenweis and David Klein and Patrick Rein},
   doi = {10.5281/zenodo.1115490},
-  date = {2026-07-02},
+  date = {2026-07-15},
   year = {2026},
   url = {https://github.com/pik-piam/madrat},
-  note = {Version: 3.37.2},
+  note = {Version: 3.37.4},
 }
 ```

tests/testthat/test-toolAggregate.R

@@ -260,7 +260,7 @@ test_that("trivial renaming works with weight", {
   expect_silent(toolAggregate(pm, mapping, from = "a", to = "b", dim = 3, weight = weight))
 })
 
-test_that("zeroWeight = fix works", {
+test_that("zeroWeight = fix works for disaggregation", {
   x <- new.magpie(c("A", "B"), fill = 100)
   rel <- data.frame(c("A", "A", "B", "B"),
                     c("A1", "A2", "B1", "B2"))
@@ -283,6 +283,21 @@ test_that("zeroWeight = fix works", {
   expect_true(as.vector(y["B2", , ]) == 0) # and this is also still 0
 })
 
+test_that("zeroWeight = fix works for weighted mean aggregation", {
+  rel <- data.frame(c("A", "A", "B", "B"),
+                    c("A.A1", "A.A2", "B.B1", "B.B2"))
+  x <- new.magpie(rel[[2]], fill = 100)
+  weight <- new.magpie(rel[[2]], fill = 0)
+  weight["B1", , ] <- 1
+
+  expect_warning(y <- toolAggregate(x, rel, weight),
+                 "Weight sum is 0")
+  expect_true(as.vector(y["A", , ]) == 0)
+
+  expect_silent(y <- toolAggregate(x, rel, weight, zeroWeight = "fix"))
+  expect_true(as.vector(y["A", , ]) == 100)
+})
+
 test_that("empty cells in a to column do not result in aggregated data", {
 
   empty <- ""

tests/testthat/test-toolFixWeight.R

@@ -44,8 +44,8 @@ test_that("toolFixWeight works with subdims", {
 })
 
 test_that("toolFixWeight works with multi subdims map", {
-  map <- data.frame(c("X.CC", "X.CC", "X.CC", "X.DD", "X.DD"),
-                    c("X.CC1", "X.CC2", "X.CC3", "X.DD1", "X.DD2"))
+  map <- data.frame(c("X.CC.U", "X.CC.U", "X.CC.U", "X.DD.U", "X.DD.U"),
+                    c("X.CC1.U", "X.CC2.U", "X.CC3.U", "X.DD1.U", "X.DD2.U"))
   weight <- new.magpie(c("A", "B"), map[[2]], c("EEE", "FFF"), fill = 0)
   weight["B", "CC3", "EEE"] <- 1
 
@@ -58,7 +58,6 @@ test_that("toolFixWeight works with multi subdims map", {
 })
 
 test_that("toolFixWeight can handle large objects", {
-  skip("to save time skip test whether toolFixWeight can handle large objects")
   to <- Reduce(x = 1:26, init = NULL, f = function(total, i) {
     return(c(total, paste0(LETTERS[i], seq_len(1000 * i))))
   })