update validProcessing to reflect summation changes in rerporting

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '50848968'
+ValidationKey: '50927856'
 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  # gms, goxygen, GDPuc) will usually have an outdated binary version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: 'mrvalidation: madrat data preparation for validation purposes'
-version: 2.56.8
-date-released: '2024-03-19'
+version: 2.56.9
+date-released: '2024-04-11'
 abstract: Package contains routines to prepare data for validation exercises.
 authors:
 - family-names: Bodirsky

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: mrvalidation
 Title: madrat data preparation for validation purposes
-Version: 2.56.8
-Date: 2024-03-19
+Version: 2.56.9
+Date: 2024-04-11
 Authors@R: c(
  person("Benjamin Leon", "Bodirsky", , "[email protected]", role = c("aut", "cre")),
  person("Stephen", "Wirth", role = "aut"),

R/calcValidPovertyLine.R

@@ -26,7 +26,7 @@ calcValidPovertyLine <- function(datasource = "WBPoverty", subtype = "320Poverty
  # Fill interpolating values when there are 2 or more points reported
  for (i in getCells(rawPer)) {
  if (length(where(rawPer[i, , ] != 0)$true$years) >= 2 &&
- length(where(rawPer[i, , ] != 0)$true$years) < length(getYears(rawPer))) {
+  length(where(rawPer[i, , ] != 0)$true$years) < length(getYears(rawPer))) {
  yrInter <- where(rawPer[i, , ] == 0)$true$years
  rawPer[i, yrInter, ] <- time_interpolate(rawPer[i, , ][, yrInter, , invert = TRUE], yrInter)
  }
@@ -53,7 +53,7 @@ calcValidPovertyLine <- function(datasource = "WBPoverty", subtype = "320Poverty
  out <- magpiesort(setNames((round(rawPer * population[, years, ] * 1e6, digits = 0)) / 1e6, NULL))
  nameScenario <- if (subtype == "190PovertyLine") "1p90 USDppp11/day" else if (subtype == "320PovertyLine")
  "3p20 USDppp11/day" else if (subtype == "550PovertyLine")
-  "5p50 USDppp11/day"
+ "5p50 USDppp11/day"
 
  getNames(out) <- paste0("Income|Number of People Below ", nameScenario)
  out <- add_dimension(out, dim = 3.1, add = "scenario", nm = "historical")

R/calcValidProcessing.R

@@ -19,54 +19,57 @@
 #' @importFrom magpiesets reporthelper summationhelper reportingnames
 #' @importFrom magclass add_columns mbind getNames
 
-calcValidProcessing <- function(datasource = "FAO", detail = TRUE, nutrient = "dm", indicator = "secondary_from_primary") {
+calcValidProcessing <- function(datasource = "FAO", detail = TRUE, nutrient = "dm", indicator = "primary_to_process") {
 
- if (indicator == "primary_to_process") {
+  if (indicator == "primary_to_process") {
 
- if (datasource == "FAO") {
- mb <- collapseNames(calcOutput("FAOmassbalance", aggregate = FALSE)[, , nutrient])
+  if (datasource == "FAO") {
+  mb <- collapseNames(calcOutput("FAOmassbalance", aggregate = FALSE)[, , nutrient])
 
- processing <- setdiff(c(findset("processing20")), c("milling", "ginning", "breeding"))
+ processing <- setdiff(c(findset("processing20")), c("milling", "ginning", "breeding"))
+ mb2 <- mb[, , c(processing)]
+ getNames(mb2, dim = 2) <- reportingnames(getNames(mb2, dim = 2))
 
- mb2 <- mb[, , c(processing)]
- getNames(mb2, dim = 2) <- reportingnames(getNames(mb2, dim = 2))
+ mb3 <- dimOrder(mb2, c(2, 1))
 
- mb3 <- dimOrder(mb2, c(2, 1))
+ out <- reporthelper(x = mb3, dim = 3.2, level_zero_name = "_", detail = detail)
+ getNames(out) <- gsub("[^[:alnum:][:blank:]\\|]", "", getNames(out))
+ getNames(out) <- sub("\\|$", "", getNames(out))
+ getNames(out) <- paste0("Demand|Processing|", getNames(out))
 
- out <- reporthelper(x = mb3, dim = 3.2, level_zero_name = "_", detail = detail)
- getNames(out) <- gsub("[^[:alnum:][:blank:]\\|]", "", getNames(out))
- getNames(out) <- sub("\\|$", "", getNames(out))
- getNames(out) <- paste0("Demand|Processing|", getNames(out))
+ out <- summationhelper(out, sep = "+")
 
- out <- summationhelper(out, sep = "+")
+  getNames(out) <- sub(getNames(out), pattern = "Processing|+", replacement = "Processing|++", fixed = TRUE)
 
- getNames(out) <- sub(getNames(out), pattern = "Processing|+", replacement = "Processing|++", fixed = TRUE)
+ out <- out[, , which(dimSums(out, dim = c(1, 2)) > 0)]
+
+ out <- add_dimension(out, dim = 3.1, add = "scenario", nm = "historical")
+ out <- add_dimension(out, dim = 3.2, add = "model", nm = datasource)
 
- out <- out[, , which(dimSums(out, dim = c(1, 2)) > 0)]
+ } else {
 
- out <- add_dimension(out, dim = 3.1, add = "scenario", nm = "historical")
- out <- add_dimension(out, dim = 3.2, add = "model", nm = datasource)
+ stop("No data exist for the given datasource!")
 
- } else stop("No data exist for the given datasource!")
+  }
 
- names(dimnames(out))[3] <- "scenario.model.variable"
+  names(dimnames(out))[3] <- "scenario.model.variable"
 
- if (nutrient == "dm") {
-unit <- "Mt DM/yr"
- } else if (nutrient == "nr") {
-unit <- "Mt Nr/yr"
- } else if (nutrient == "p") {
-unit <- "Mt P/yr"
- } else if (nutrient == "k") {
-unit <- "Mt K/yr"
- } else if (nutrient == "ge") {
-unit <- "PJ/yr"
- } else if (nutrient == "wm") {
-unit <- "Mt WM/yr"
-}
+  if (nutrient == "dm") {
+ unit <- "Mt DM/yr"
+  } else if (nutrient == "nr") {
+ unit <- "Mt Nr/yr"
+  } else if (nutrient == "p") {
+ unit <- "Mt P/yr"
+  } else if (nutrient == "k") {
+ unit <- "Mt K/yr"
+  } else if (nutrient == "ge") {
+ unit <- "PJ/yr"
+  } else if (nutrient == "wm") {
+ unit <- "Mt WM/yr"
+ }
 
- getNames(out) <- paste0(getNames(out), " (", unit, ")")
- } else if (indicator == "secondary_from_primary") {
+  getNames(out) <- paste0(getNames(out), " (", unit, ")")
+  } else if (indicator == "secondary_from_primary") {
 
  if (datasource == "FAO") {
  mb <- collapseNames(calcOutput("FAOmassbalance", aggregate = FALSE)[, , nutrient])
@@ -85,38 +88,48 @@ unit <- "Mt WM/yr"
  getNames(out, dim = 1) <- substr(getNames(out, dim = 1), start = 1, stop = nchar(getNames(out, dim = 1)) - 1)
  getNames(out, dim = 1)[which(getNames(out, dim = 1) == "oil")] <- "oils"
  getNames(out, dim = 1) <- reportingnames(getNames(out, dim = 1))
- getNames(out) <- sub(getNames(out), pattern = "\\.", replacement = "|+|")
- getSets(out) <- c("region", "year", "data")
- getNames(out) <- paste0("Production|Secondary Products|", getNames(out))
 
- out <- out[, , which(dimSums(out, dim = c(1, 2)) > 0)]
+ getNames(out, dim = 1) <- paste0("Processing|Raw material|Processed into ", getNames(out, dim = 1))
+ out <- add_columns(out, addnm = "Processing|Raw material|Processed into Secondary products", dim = 3.1, fill = 0)
+ out[, , "Processing|Raw material|Processed into Secondary products"] <- dimSums(out, dim = 3.1)
+ out <- add_columns(out, addnm = "dummy", dim = 3.2, fill = 0)
+ out[, , "dummy"] <- dimSums(out, dim = 3.2)
+
+ getNames(out) <- sub(getNames(out), pattern = "\\.", replacement = "|")
+ out <- summationhelper(out)
+ getNames(out) <- sub(getNames(out), pattern = "\\|\\+\\|dummy", replacement = "")
+ getNames(out) <- paste(getNames(out), "(Mt DM/yr)", sep = " ")
+
+ out <- out[, , where(out != 0)$true$data]
 
  out <- add_dimension(out, dim = 3.1, add = "scenario", nm = "historical")
  out <- add_dimension(out, dim = 3.2, add = "model", nm = datasource)
 
- } else stop("No data exist for the given datasource!")
+ } else {
+ stop("No data exist for the given datasource!")
+ }
 
  names(dimnames(out))[3] <- "scenario.model.variable"
 
  if (nutrient == "dm") {
-unit <- "Mt DM/yr"
+ unit <- "Mt DM/yr"
  } else if (nutrient == "nr") {
-unit <- "Mt Nr/yr"
+ unit <- "Mt Nr/yr"
  } else if (nutrient == "p") {
-unit <- "Mt P/yr"
+ unit <- "Mt P/yr"
  } else if (nutrient == "k") {
-unit <- "Mt K/yr"
+ unit <- "Mt K/yr"
  } else if (nutrient == "ge") {
-unit <- "PJ/yr"
+ unit <- "PJ/yr"
  } else if (nutrient == "wm") {
-unit <- "Mt WM/yr"
-}
+ unit <- "Mt WM/yr"
+ }
 
  getNames(out) <- paste0(getNames(out), " (", unit, ")")
-}
-  return(list(x = out,
-  weight = NULL,
-  unit = unit,
-  description = "Agricultural Demand")
-  )
+ }
+ return(list(x = out,
+ weight = NULL,
+ unit = unit,
+ description = "Agricultural Demand")
+ )
 }

README.md

@@ -1,6 +1,6 @@
 # madrat data preparation for validation purposes
 
-R package **mrvalidation**, version **2.56.8**
+R package **mrvalidation**, version **2.56.9**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/mrvalidation)](https://cran.r-project.org/package=mrvalidation) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.4317826.svg)](https://doi.org/10.5281/zenodo.4317826) [![R build status](https://github.com/pik-piam/mrvalidation/workflows/check/badge.svg)](https://github.com/pik-piam/mrvalidation/actions) [![codecov](https://codecov.io/gh/pik-piam/mrvalidation/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/mrvalidation) [![r-universe](https://pik-piam.r-universe.dev/badges/mrvalidation)](https://pik-piam.r-universe.dev/builds)
 
@@ -39,7 +39,7 @@ In case of questions / problems please contact Benjamin Leon Bodirsky <bodirsky@
 
 To cite package **mrvalidation** in publications use:
 
-Bodirsky B, Wirth S, Karstens K, Humpenoeder F, Stevanovic M, Mishra A, Biewald A, Weindl I, Beier F, Chen D, Crawford M, Leip D, Molina Bacca E, Kreidenweis U, W. Yalew A, von Jeetze P, Wang X, Dietrich J, Alves M (2024). _mrvalidation: madrat data preparation for validation purposes_. doi:10.5281/zenodo.4317826 <https://doi.org/10.5281/zenodo.4317826>, R package version 2.56.8, <https://github.com/pik-piam/mrvalidation>.
+Bodirsky B, Wirth S, Karstens K, Humpenoeder F, Stevanovic M, Mishra A, Biewald A, Weindl I, Beier F, Chen D, Crawford M, Leip D, Molina Bacca E, Kreidenweis U, W. Yalew A, von Jeetze P, Wang X, Dietrich J, Alves M (2024). _mrvalidation: madrat data preparation for validation purposes_. doi: 10.5281/zenodo.4317826 (URL: https://doi.org/10.5281/zenodo.4317826), R package version 2.56.9, <URL: https://github.com/pik-piam/mrvalidation>.
 
 A BibTeX entry for LaTeX users is
 
@@ -48,7 +48,7 @@ A BibTeX entry for LaTeX users is
  title = {mrvalidation: madrat data preparation for validation purposes},
  author = {Benjamin Leon Bodirsky and Stephen Wirth and Kristine Karstens and Florian Humpenoeder and Mishko Stevanovic and Abhijeet Mishra and Anne Biewald and Isabelle Weindl and Felicitas Beier and David Chen and Michael Crawford and Debbora Leip and Edna {Molina Bacca} and Ulrich Kreidenweis and Amsalu {W. Yalew} and Patrick {von Jeetze} and Xiaoxi Wang and Jan Philipp Dietrich and Marcos Alves},
  year = {2024},
- note = {R package version 2.56.8},
+ note = {R package version 2.56.9},
  doi = {10.5281/zenodo.4317826},
  url = {https://github.com/pik-piam/mrvalidation},
 }