Merge pull request #220 from caviddhen/master

fix toolAggregate warning in toolISOHistorical

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '62608680'
+ValidationKey: '62691330'
 AcceptedWarnings:
 - 'Warning: package ''.*'' was built under R version'
 - 'Warning: namespace ''.*'' is not available and has been replaced'

.github/workflows/check.yaml

@@ -23,14 +23,14 @@ jobs:
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
-            any::lucode2
-            any::covr
-            any::madrat
-            any::magclass
-            any::citation
-            any::gms
-            any::goxygen
-            any::GDPuc
+            lucode2
+            covr
+            madrat
+            magclass
+            citation
+            gms
+            goxygen
+            GDPuc
           # piam packages also available on CRAN (madrat, magclass, citation,
           # gms, goxygen, GDPuc) will usually have an outdated binary version
           # available; by using extra-packages we get the newest 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: 'madrat: May All Data be Reproducible and Transparent (MADRaT) *'
-version: 3.13.2
-date-released: '2024-09-24'
+version: 3.13.3
+date-released: '2024-10-14'
 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: 3.13.2
-Date: 2024-09-24
+Version: 3.13.3
+Date: 2024-10-14
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "[email protected]", role = c("aut", "cre"),
            comment = c(affiliation = "Potsdam Institute for Climate Impact Research", ORCID = "0000-0002-4309-6431")),

R/toolISOhistorical.R

@@ -149,7 +149,8 @@ toolISOhistorical <- function(m, mapping = NULL, additional_mapping = NULL, over
         }
 
         mTr <- toolAggregate(m[a$fromISO, subTime, ],
-                             mapping[is.element(mapping$toISO, a$toISO), c("fromISO", "toISO")], weight = weight,
+                             mapping[is.element(mapping$toISO, a$toISO), c("fromISO", "toISO")],
+                             weight = weight + 1e-12,
                              negative_weight = "allow")
         ## aggregation of countries
       } else {
@@ -241,15 +242,17 @@ toolISOhistorical <- function(m, mapping = NULL, additional_mapping = NULL, over
           # these countries are added below if missing, and given weight 0
           if (mainDim == 1.1) {
             addInd <- setdiff(as.vector(outer(
-              tr$toISO,
-              getItems(z[setNames(list(c(tr$fromISO)), mainDimName), subTime, ], dim = secdDim),
-              paste, sep = ".")),
-              getItems(weight, dim = 1))
+                                              tr$toISO,
+                                              getItems(z[setNames(list(c(tr$fromISO)), mainDimName), subTime, ],
+                                                       dim = secdDim),
+                                              paste, sep = ".")),
+            getItems(weight, dim = 1))
           } else if (mainDim == 1.2) {
             addInd <- setdiff(as.vector(outer(
-              getItems(z[setNames(list(c(tr$fromISO)), mainDimName), subTime, ], dim = secdDim),
-              tr$toISO, paste, sep = ".")),
-              getItems(weight, dim = 1))
+                                              getItems(z[setNames(list(c(tr$fromISO)), mainDimName), subTime, ],
+                                                       dim = secdDim),
+                                              tr$toISO, paste, sep = ".")),
+            getItems(weight, dim = 1))
           }
           if (length(addInd) > 0) {
             addR <- unique(c(addR, addInd))

README.md

@@ -1,6 +1,6 @@
 # May All Data be Reproducible and Transparent (MADRaT) *
 
-R package **madrat**, version **3.13.2**
+R package **madrat**, version **3.13.3**
 
 [![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 3.13.2, <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 (URL: https://doi.org/10.5281/zenodo.1115490), R package version 3.13.3, <URL: https://github.com/pik-piam/madrat>.
 
 A BibTeX entry for LaTeX users is
 
@@ -64,8 +64,8 @@ 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 3.13.2},
-  url = {https://github.com/pik-piam/madrat},
+  note = {R package version 3.13.3},
   doi = {10.5281/zenodo.1115490},
+  url = {https://github.com/pik-piam/madrat},
 }
 ```

tests/testthat/test-toolISOhistorical.R

@@ -6,7 +6,7 @@ test_that("Historic data is properly translated", {
   a["SUN", 1990, ] <- 240
   a[-1, 1991:1992, ] <- rep(1:15, 2)
   a <- toolISOhistorical(a)
-  expect_identical(as.vector(a[, 1990, ]), 2 * (1:15))
+  expect_equal(as.vector(a[, 1990, ]), 2 * (1:15))
   expect_identical(magclass::getItems(a, dim = 1.1), newcountries)
 })
 
@@ -23,8 +23,10 @@ test_that("Given mapping data is properly translated", {
 
   ref <- new("magpie", .Data = structure(c(2, 1, 1, 1, 2, 1, 1, 1, 2,
                                            1, 1, 1, 2, 1, 1, 1, 2, 1, 1, 1),
-              .Dim = c(4L, 5L, 1L), .Dimnames = list(region = c("A", "B1", "B2", "B3"),
-              year = c("y9", "y10", "y11", "y12", "y13"), data = NULL)))
+                                         .Dim = c(4L, 5L, 1L),
+                                         .Dimnames = list(region = c("A", "B1", "B2", "B3"),
+                                                          year = c("y9", "y10", "y11", "y12", "y13"),
+                                                          data = NULL)))
   expect_identical(toolISOhistorical(a, mapping = m), ref)
 
   mapfile <- tempfile()
@@ -41,9 +43,11 @@ test_that("Given mapping data is properly translated", {
   b[is.na(b)] <- 0
 
   ref2 <- new("magpie", .Data = structure(c(0, 0, 0, 0, 0, 0, 0, 0, 2,
-              0, 0, 0, 2, 0, 0, 0, 2, 1, 1, 1), .Dim = c(4L, 5L, 1L),
-              .Dimnames = list(region = c("A", "B1", "B2", "B3"),
-                               year = c("y9", "y10", "y11", "y12", "y13"), data = NULL)))
+                                            0, 0, 0, 2, 0, 0, 0, 2, 1, 1, 1),
+                                          .Dim = c(4L, 5L, 1L),
+                                          .Dimnames = list(region = c("A", "B1", "B2", "B3"),
+                                                           year = c("y9", "y10", "y11", "y12", "y13"),
+                                                           data = NULL)))
 
   expect_identical(toolISOhistorical(b, mapping = m, overwrite = TRUE), ref)
   expect_identical(toolISOhistorical(b, mapping = m, overwrite = FALSE), ref2)
@@ -52,15 +56,17 @@ test_that("Given mapping data is properly translated", {
   expect_warning(o <- toolISOhistorical(a, mapping = m), "Weight in toolISOhistorical contained NAs")
   ref3 <- new("magpie", .Data = structure(c(2, 0, 1.5, 1.5, 2, 0, 1.5,
                                             1.5, 2, 0, 1.5, 1.5, 2, 0, 1.5, 1.5, 2, NA, 1, 1),
-                                         .Dim = c(4L, 5L, 1L), .Dimnames = list(region = c("A", "B1", "B2", "B3"),
-                                          year = c("y9", "y10", "y11", "y12", "y13"), data = NULL)))
-  expect_identical(o, ref3)
+                                          .Dim = c(4L, 5L, 1L),
+                                          .Dimnames = list(region = c("A", "B1", "B2", "B3"),
+                                                           year = c("y9", "y10", "y11", "y12", "y13"),
+                                                           data = NULL)))
+  expect_equal(o, ref3)
 })
 
 test_that("Bilateral data is properly translated", {
   localConfig(.verbose = FALSE)
   newcountriesA <- as.vector(outer(c("ARM", "AZE", "BLR", "EST", "GEO", "KAZ", "KGZ",
-                    "LVA", "LTU", "MDA", "TJK", "TKM", "UKR", "UZB"), "USA", paste, sep = "."))
+                                     "LVA", "LTU", "MDA", "TJK", "TKM", "UKR", "UZB"), "USA", paste, sep = "."))
   missing <- "RUS.USA"
   a <- new.magpie(c("SUN.USA", newcountriesA), 1991:1993)
   a["SUN.USA", 1991, ] <- 240
@@ -72,24 +78,24 @@ test_that("Bilateral data is properly translated", {
   # when disagg in 2nd dim, and with all countries missing
   b <- new.magpie("USA.SUN", 1991:1993)
   b["USA.SUN", 1991, ] <- 240
-  for (ov in c(TRUE, FALSE)){
-  b1 <- toolISOhistorical(b, overwrite = ov)
-  expect_equal(as.vector(b1[, 1991, ]), rep(240 / 15, 15))
+  for (ov in c(TRUE, FALSE)) {
+    b1 <- toolISOhistorical(b, overwrite = ov)
+    expect_equal(as.vector(b1[, 1991, ]), rep(240 / 15, 15))
   }
   # when additional weighting is given
   expect_error(o <- toolISOhistorical(b, additional_weight = "2"),
                "Additional_weight is not supported for bilateral data.")
 
   # when aggregating
   mapping <- data.frame(fromISO = c("A1", "A2"),
-                  toISO = c("A", "A"),
-                  lastYear = c("y0010", "y0010"),
-                  stringsAsFactors = FALSE)
+                        toISO = c("A", "A"),
+                        lastYear = c("y0010", "y0010"),
+                        stringsAsFactors = FALSE)
 
-  d <- new.magpie(c("A1.Z", "A2.Z", "A.Z"), 9:11,)
-  d[c("A1.Z", "A2.Z"), c("y0009", "y0010") , ] <- 5
+  d <- new.magpie(c("A1.Z", "A2.Z", "A.Z"), 9:11, )
+  d[c("A1.Z", "A2.Z"), c("y0009", "y0010"), ] <- 5
   d <- toolISOhistorical(d, mapping = mapping, overwrite = FALSE)
-  expect_equal(as.vector(d[,c("y0009", "y0010"), ]), rep(10, 2))
+  expect_equal(as.vector(d[, c("y0009", "y0010"), ]), rep(10, 2))