Merge branch 'master' of github.com:pik-piam/madrat

.buildlibrary

@@ -1,7 +1,8 @@
-ValidationKey: '7551376'
+ValidationKey: '61488500'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'
 AcceptedNotes: unable to verify current time
 AutocreateReadme: yes
 allowLinterWarnings: no
+enforceVersionUpdate: no

.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           # gms, goxygen, GDPuc) will usually have an outdated binary version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
 
@@ -49,6 +48,11 @@ jobs:
         shell: Rscript {0}
         run: lucode2:::validkey(stopIfInvalid = TRUE)
 
+      - name: Verify that lucode2::buildLibrary was successful
+        if: github.event_name == 'pull_request'
+        shell: Rscript {0}
+        run: lucode2:::isVersionUpdated()
+
       - name: Checks
         shell: Rscript {0}
         run: |

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: 3.8.2
-date-released: '2024-02-15'
+version: 3.10.0
+date-released: '2024-04-22'
 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: 3.8.2
-Date: 2024-02-15
+Version: 3.10.0
+Date: 2024-04-22
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "[email protected]", role = c("aut", "cre")),
     person("Lavinia", "Baumstark", , "[email protected]", role = "aut"),
@@ -33,7 +33,7 @@ Depends:
 Imports:
     callr,
     digest,
-    igraph (>= 1.0.1),
+    igraph (>= 2.0.0),
     Matrix,
     methods,
     pkgload,

NAMESPACE

@@ -129,7 +129,6 @@ importFrom(utils,download.file)
 importFrom(utils,head)
 importFrom(utils,installed.packages)
 importFrom(utils,modifyList)
-importFrom(utils,object.size)
 importFrom(utils,packageDescription)
 importFrom(utils,person)
 importFrom(utils,read.csv)

R/toolAggregate.R

@@ -63,14 +63,15 @@
 #' will lead to summation.
 #' @param verbosity Verbosity level of messages coming from the function: -1 = error,
 #' 0 = warning, 1 = note, 2 = additional information, >2 = no message
+#' @param zeroWeight Describes how a weight sum of 0 for a category/aggregation target should be treated.
+#' "allow" means it is accepted (dangerous), "warn" throws a warning, "stop" throws an error.
 #' @return the aggregated data in magclass format
 #' @author Jan Philipp Dietrich, Ulrich Kreidenweis
 #' @export
 #' @importFrom magclass wrap ndata fulldim clean_magpie mselect setCells getCells mbind
 #' @importFrom magclass setComment getNames getNames<- as.array
 #' @importFrom magclass is.magpie getComment getComment<- dimCode getYears getYears<-
 #' @importFrom magclass getDim getSets getSets<- as.magpie getItems collapseNames
-#' @importFrom utils object.size
 #' @importFrom Matrix Matrix t rowSums
 #' @importFrom withr local_options
 #' @seealso \code{\link{calcOutput}}
@@ -79,9 +80,9 @@
 #' # create example mapping
 #' p <- magclass::maxample("pop")
 #' mapping <- data.frame(from = magclass::getItems(p, dim = 1.1),
-#'   region = rep(c("REG1", "REG2"), 5),
-#'   global = "GLO")
-#' mapping
+#'                       region = rep(c("REG1", "REG2"), 5),
+#'                       global = "GLO")
+#' print(mapping)
 #'
 #' # run aggregation
 #' toolAggregate(p, mapping)
@@ -91,7 +92,7 @@
 #' toolAggregate(p, mapping, to = "region+global")
 #'
 toolAggregate <- function(x, rel, weight = NULL, from = NULL, to = NULL, dim = 1, wdim = NULL, partrel = FALSE, # nolint
-                          negative_weight = "warn", mixed_aggregation = FALSE, verbosity = 1) { # nolint
+                          negative_weight = "warn", mixed_aggregation = FALSE, verbosity = 1, zeroWeight = "warn") { # nolint
 
   if (!is.magpie(x)) stop("Input is not a MAgPIE object, x has to be a MAgPIE object!")
 
@@ -167,7 +168,7 @@ toolAggregate <- function(x, rel, weight = NULL, from = NULL, to = NULL, dim = 1
       regions <- as.character(unique(rel[, to]))
       countries <- as.character(unique(rel[, from]))
       m <- Matrix(data = 0, nrow = length(regions), ncol = length(countries),
-        dimnames = list(regions = regions, countries = countries))
+                  dimnames = list(regions = regions, countries = countries))
       m[cbind(match(rel[, to], rownames(m)), match(rel[, from], colnames(m)))] <- 1
       if (is.numeric(to)) to <- dimnames(rel)[[2]][to]
       if (is.numeric(from)) from <- dimnames(rel)[[2]][from]
@@ -216,7 +217,7 @@ toolAggregate <- function(x, rel, weight = NULL, from = NULL, to = NULL, dim = 1
 
     if (is.null(wdim)) {
       wdim <- union(getDim(rownames(rel), weight, fullmatch = TRUE),
-        getDim(colnames(rel), weight, fullmatch = TRUE))
+                    getDim(colnames(rel), weight, fullmatch = TRUE))
       # wdim must be in same main dimension as dim
       wdim <- wdim[floor(wdim) == floor(dim)]
     }
@@ -249,6 +250,15 @@ toolAggregate <- function(x, rel, weight = NULL, from = NULL, to = NULL, dim = 1
       }
     }
     tmp <- toolAggregate(weight, rel, from = from, to = to, dim = wdim, partrel = partrel, verbosity = 10)
+    if (zeroWeight != "allow" && any(tmp == 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! ",
+                'If this is really intended set zeroWeight = "allow".')
+      } else {
+        stop("Weight sum is 0, so cannot normalize. This changes the total sum of the magpie object!")
+      }
+    }
     weight2 <- 1 / (tmp + 10^-100)
     if (mixed_aggregation) {
       weight2[is.na(weight2)] <- 1
@@ -288,13 +298,13 @@ toolAggregate <- function(x, rel, weight = NULL, from = NULL, to = NULL, dim = 1
         maxdim <- nchar(gsub("[^\\.]", "", names[1])) + 1
 
         search <- paste0("^(", paste(rep("[^\\.]*\\.", subdim - 1), collapse = ""),
-          ")([^\\.]*)(", paste(rep("\\.[^\\.]*", maxdim - subdim), collapse = ""), ")$")
+                         ")([^\\.]*)(", paste(rep("\\.[^\\.]*", maxdim - subdim), collapse = ""), ")$")
         onlynames <- unique(sub(search, "\\2", names))
 
         if (!setequal(colnames(rel), onlynames)) {
           if (!setequal(rownames(rel), onlynames)) {
             stop("The provided mapping contains entries which could not be found in the data: ",
-              paste(setdiff(colnames(rel), onlynames), collapse = ", "))
+                 paste(setdiff(colnames(rel), onlynames), collapse = ", "))
           } else  {
             rel <- t(rel)
           }
@@ -312,8 +322,7 @@ toolAggregate <- function(x, rel, weight = NULL, from = NULL, to = NULL, dim = 1
         cnames <- .tmp(add, colnames(rel))
         rnames <- .tmp(add, rownames(rel))
 
-        newRel <- Matrix(0, nrow = length(rnames), ncol = length(cnames),
-          dimnames = list(rnames, cnames))
+        newRel <- Matrix(0, nrow = length(rnames), ncol = length(cnames), dimnames = list(rnames, cnames))
 
         for (i in seq_along(additions)) {
           newRel[seq_len(nrow(rel)) + (i - 1) * nrow(rel), seq_len(ncol(rel)) + (i - 1) * ncol(rel)] <- rel
@@ -327,7 +336,7 @@ toolAggregate <- function(x, rel, weight = NULL, from = NULL, to = NULL, dim = 1
     if (dim(x)[dim] != dim(rel)[2]) {
       if (dim(x)[dim] != dim(rel)[1]) {
         stop("Relation matrix has in both dimensions a different number of entries (",
-          dim(rel)[1], ", ", dim(rel)[2], ") than x has cells (", dim(x)[dim], ")!")
+             dim(rel)[1], ", ", dim(rel)[2], ") than x has cells (", dim(x)[dim], ")!")
       } else {
         rel <- t(rel)
       }
@@ -378,7 +387,7 @@ toolAggregate <- function(x, rel, weight = NULL, from = NULL, to = NULL, dim = 1
       # Compute region vector for outputs after aggregation via sending
       # factor values through the relation matrix
       regOut <- factor(as.vector(round(rel %*% as.numeric(regionList) /
-        (rel %*% rep(1, dim(rel)[2])))))
+                                         (rel %*% rep(1, dim(rel)[2])))))
       levels(regOut) <- levels(regionList)
     } else {
       stop("Missing dimnames for aggregated dimension")

README.md

@@ -1,6 +1,6 @@
 # May All Data be Reproducible and Transparent (MADRaT) *
 
-R package **madrat**, version **3.8.2**
+R package **madrat**, version **3.10.0**
 
 [![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, Baumstark L, Wirth S, Giannousakis A, Rodrigues R, Bodirsky B, Leip D, Kreidenweis U, Klein D, Sauer P (2024). _madrat: May All Data be Reproducible and Transparent (MADRaT)_. doi:10.5281/zenodo.1115490 <https://doi.org/10.5281/zenodo.1115490>, R package version 3.8.2, <https://github.com/pik-piam/madrat>.
+Dietrich J, Baumstark L, Wirth S, Giannousakis A, Rodrigues R, Bodirsky B, Leip D, Kreidenweis U, Klein D, Sauer P (2024). _madrat: May All Data be Reproducible and Transparent (MADRaT)_. doi:10.5281/zenodo.1115490 <https://doi.org/10.5281/zenodo.1115490>, R package version 3.10.0, <https://github.com/pik-piam/madrat>.
 
 A BibTeX entry for LaTeX users is
 
@@ -64,7 +64,7 @@ A BibTeX entry for LaTeX users is
   title = {madrat: May All Data be Reproducible and Transparent (MADRaT)},
   author = {Jan Philipp Dietrich and Lavinia Baumstark and Stephen Wirth and Anastasis Giannousakis and Renato Rodrigues and Benjamin Leon Bodirsky and Debbora Leip and Ulrich Kreidenweis and David Klein and Pascal Sauer},
   year = {2024},
-  note = {R package version 3.8.2},
+  note = {R package version 3.10.0},
   url = {https://github.com/pik-piam/madrat},
   doi = {10.5281/zenodo.1115490},
 }

tests/testthat/test-toolAggregate.R

@@ -218,3 +218,11 @@ test_that("Edge cases work", {
   expect_silent(b <- toolAggregate(a, rel, weight = a))
   expect_setequal(getCells(b), c("NLD", "BEL", "LUX"))
 })
+
+test_that("columns with only zeros in weight produce a warning", {
+  weight <- pm
+  weight[, , ] <- 0
+  expect_warning(toolAggregate(pm, rel, weight = weight), "Weight sum is 0")
+  expect_error(toolAggregate(pm, rel, weight = weight, zeroWeight = "stop"), "Weight sum is 0")
+  expect_silent(toolAggregate(pm, rel, weight = weight, zeroWeight = "allow"))
+})