correction of 10^3 mistake in nitrogen validation

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '50377148'
+ValidationKey: '50396896'
 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: 'mrvalidation: madrat data preparation for validation purposes'
-version: 2.55.1
+version: 2.55.2
 date-released: '2024-01-26'
 abstract: Package contains routines to prepare data for validation exercises.
 authors:

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: mrvalidation
 Title: madrat data preparation for validation purposes
-Version: 2.55.1
+Version: 2.55.2
 Date: 2024-01-26
 Authors@R: c(
  person("Benjamin Leon", "Bodirsky", , "[email protected]", role = c("aut", "cre")),

R/calcValidNitrogenBudgetCropland.R

@@ -3,7 +3,8 @@
 #'
 #' @param datasource Bodirsky for own calculations, Lassaletta2014 for a country dataset from
 #' Lassaletta, L., G. Billen, B. Grizzetti, J. Angalde, and J. Garnier. 2014.
-#' 50 Year Trends in Nitrogen Use Efficiency of World Cropping Systems: The Relationship between Yield and Nitrogen Input to Cropland.
+#' 50 Year Trends in Nitrogen Use Efficiency of World Cropping Systems: The Relationship
+#' between Yield and Nitrogen Input to Cropland.
 #' Environmental Research Letters.
 #' FAO for some N related parameters published in FAOSTAT.
 #'
@@ -12,7 +13,6 @@
 #' @seealso
 #' \code{\link{calcNitrogenBudgetCropland}}
 #' @examples
-#'
 #' \dontrun{
 #' calcOutput("ValidNitrogenBudgetCropland")
 #' }
@@ -58,24 +58,28 @@ calcValidNitrogenBudgetCropland <- function(datasource = "Bodirsky") {
 
  out <- add_dimension(out, dim = 3.1, add = "scenario", nm = "historical")
  } else if (datasource == "ACCMIP") {
- dep <- calcOutput("AtmosphericDeposition", datasource = "ACCMIP", scenario = c("rcp26", "rcp45", "rcp85"), aggregate = FALSE)
+ dep <- calcOutput("AtmosphericDeposition", datasource = "ACCMIP",
+ scenario = c("rcp26", "rcp45", "rcp85"), aggregate = FALSE)
  out <- dep
  out <- dimSums(out, dim = c(3.1, 3.3, 3.4))
- out <- add_dimension(out, dim = 3.2, add = "indicator", nm = "Resources|Nitrogen|Cropland Budget|Inputs|+|Atmospheric Deposition")
+ out <- add_dimension(out, dim = 3.2, add = "indicator",
+ nm = "Resources|Nitrogen|Cropland Budget|Inputs|+|Atmospheric Deposition")
  getSets(out)[3] <- "scenario"
  } else if (datasource == "Lassaletta2014") {
  budget <- readSource("Lassaletta2014", subtype = "budget")
  out <- mbind(
- setNames(budget[, , "harvest"], paste0("Resources|Nitrogen|Cropland Budget|Withdrawals|+|", reportingnames(getNames(budget[, , "harvest"])))),
- setNames(budget[, , "harvest", invert = T], paste0("Resources|Nitrogen|Cropland Budget|Inputs|+|", reportingnames(getNames(budget[, , "harvest", invert = T]))))
+ setNames(budget[, , "harvest"], paste0("Resources|Nitrogen|Cropland Budget|Withdrawals|+|",
+ reportingnames(getNames(budget[, , "harvest"])))),
+ setNames(budget[, , "harvest", invert = TRUE],
+ paste0("Resources|Nitrogen|Cropland Budget|Inputs|+|",
+ reportingnames(getNames(budget[, , "harvest", invert = TRUE]))))
  )
  out <- add_dimension(out, dim = 3.1, add = "scenario", nm = "historical")
  } else if (datasource == "FAO") {
  residues <- readSource("FAO_online", "EmisAgCropResid")
- # residues<-setNames(residues[,,"Residues_(Crop_residues)_(tonnes_of_nutrients)"][,,"1712|All Crops + (Total)"]/10^9,"ag_recycling")
- ## Previous conversion was 1e9 which would have converted from ton to Giga ton <--- Confirm with Benni
  ## New units are provided in kg by FAO so kg to Mt should be 1e9
- residues <- setNames(residues[, , "Residues_(Crop_residues)_(kg_of_nutrients)"][, , "1712|All Crops"] / 1e9, "ag_recycling")
+ residues <- setNames(residues[, , "Residues_(Crop_residues)_(kg_of_nutrients)"][, , "1712|All Crops"]
+ / 1e9, "ag_recycling")
 
  manure <- readSource("FAO_online", "EmisAgManureSoil")
  selection <- c(
@@ -97,12 +101,13 @@ calcValidNitrogenBudgetCropland <- function(datasource = "Bodirsky") {
  tmp2 <- collapseNames(manure[, , selection][, , "Manure_applied_to_soils_(N_content)_(kg)"])
  mapping <- toolGetMapping(type = "sectoral", name = "IPCCitems_fao_online.csv", where = "mappingfolder")
  tmp2 <- toolAggregate(tmp2, rel = mapping, from = "fao", to = "magpie", dim = 3.1)
- tmp2 <- tmp2 / 1e12
+ tmp2 <- tmp2 / 1e9
  manure <- setNames(dimSums(tmp2, dim = 3.1), "manure_conf")
 
  # fertilizer
- fertilizer <- readSource("FAO_online", "EmisAgSynthFerti")[, , c("3102|Nutrient nitrogen N (total).Agricultural_Use_in_nutrients_(kg_of_nutrients)")]
- fertilizer <- dimSums(fertilizer, dim = c(3)) / 1e12
+ fertilizer <- (readSource("FAO_online", "EmisAgSynthFerti")
+ )[, , c("3102|Nutrient nitrogen N (total).Agricultural_Use_in_nutrients_(kg_of_nutrients)")]
+ fertilizer <- dimSums(fertilizer, dim = c(3)) / 1e9
  fertilizer <- setNames(fertilizer, "fertilizer")
  commonyears <- intersect(intersect(getYears(fertilizer), getYears(residues)), getYears(manure))
 
@@ -114,19 +119,19 @@ calcValidNitrogenBudgetCropland <- function(datasource = "Bodirsky") {
 
  vcat(2, "instead of removing years with no data, each object should rather be blown up to full dimensionality")
 
- names_x <- reportingnames(getNames(out))
- names(names_x) <- NULL
- getNames(out) <- paste0("Resources|Nitrogen|Cropland Budget|Inputs|+|", names_x)
+ namesX <- reportingnames(getNames(out))
+ names(namesX) <- NULL
+ getNames(out) <- paste0("Resources|Nitrogen|Cropland Budget|Inputs|+|", namesX)
  out <- add_dimension(out, dim = 3.1, add = "scenario", nm = "historical")
  } else {
  stop("No data exist for the given datasource!")
  }
  out <- add_dimension(out, dim = 3.1, add = "model", nm = datasource)
  getNames(out) <- paste0(getNames(out), " (Mt Nr/yr)")
 
- return(list(x=out,
- weight=NULL,
- unit="Mt Nr/yr",
- description="Cropland Nitrogen Budget")
-  )
+  return(list(x = out,
+ weight = NULL,
+ unit = "Mt Nr/yr",
+ description = "Cropland Nitrogen Budget")
+ )
 }

README.md

@@ -1,6 +1,6 @@
 # madrat data preparation for validation purposes
 
-R package **mrvalidation**, version **2.55.1**
+R package **mrvalidation**, version **2.55.2**
 
 [![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 2.55.1, <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 <https://doi.org/10.5281/zenodo.4317826>, R package version 2.55.2, <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 2.55.1},
+ note = {R package version 2.55.2},
  doi = {10.5281/zenodo.4317826},
  url = {https://github.com/pik-piam/mrvalidation},
 }