add correct weights

.buildlibrary

@@ -1,4 +1,4 @@
-ValidationKey: '11996656'
+ValidationKey: '12157300'
 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: 'mrland: MadRaT land data package'
-version: 0.60.2
-date-released: '2024-07-24'
+version: 0.61.0
+date-released: '2024-07-26'
 abstract: The package provides land related data via the madrat framework.
 authors:
 - family-names: Dietrich

DESCRIPTION

@@ -1,8 +1,8 @@
 Type: Package
 Package: mrland
 Title: MadRaT land data package
-Version: 0.60.2
-Date: 2024-07-24
+Version: 0.61.0
+Date: 2024-07-26
 Authors@R: c(
     person("Jan Philipp", "Dietrich", , "dietrich@pik-potsdam.de", role = c("aut", "cre")),
     person("Abhijeet", "Mishra", role = "aut"),

R/calcLossShare.R

@@ -1,27 +1,41 @@
-# maybe rename to loss?
+#' @title calcLossShare
+#' @description Calculates share of domestic supply wasted
+#'
+#' @return List of magpie object with results and weight on country or cellular level, unit and description.
+#' @author Benjamin Leon Bodirsky
+#' @examples
+#' \dontrun{
+#' calcOutput("LossShare")
+#' }
+#' @importFrom magpiesets findset
+
 calcLossShare <- function() {
+
   massbalance <- calcOutput("FAOmassbalance", aggregate = FALSE)
 
   # connected to domestic supply, as FAOSTATS flossary states that
   # "Waste is often estimated as a fixed percentage of availability, the latter
   # being defined as production plus imports plus stock withdrawals."
-  wasteshr <- dimSums(massbalance[, , "waste"][, , "dm"],
-                      dim = c(3.2, 3.3)) / dimSums(massbalance[, , "domestic_supply"][, , "dm"],
-                                                   dim = c(3.2, 3.3))
-  weight <- dimSums(massbalance[, , "domestic_supply"][, , "dm"], dim = c(3.2, 3.3))
+  wasteshr <-
+    dimSums(massbalance[, , "waste"][, , "dm"], dim = c(3.2, 3.3)) /
+    dimSums(massbalance[, , "domestic_supply"][, , "dm"], dim = c(3.2, 3.3))
+  weight <-
+    dimSums(massbalance[, , "domestic_supply"][, , "dm"], dim = c(3.2, 3.3))
   newproducts <- c("begr", "betr", "scp")
-  #assume a waste share of 1 percent for begr, betr and scp
+
+  # assume a waste share of 1 percent for begr, betr and scp
   wasteshr[, , newproducts] <- 0.01
-  weight[, , newproducts] <- 1
-  wasteshr[, , "pasture"] <- 0
+  weight[, , newproducts]   <- 1
+  wasteshr[, , "pasture"]   <- 0
   wasteshr[is.na(wasteshr)] <- 0
-  weight[wasteshr == Inf] <- 0
+  weight[wasteshr == Inf]   <- 0
   wasteshr[wasteshr == Inf] <- 0
 
   wasteshr <- toolHoldConstantBeyondEnd(wasteshr)
-  weight <- toolHoldConstantBeyondEnd(weight)
-
+  weight   <- toolHoldConstantBeyondEnd(weight) + 10^-10
 
-  return(list(x = wasteshr, weight = weight, unit = "DM share, weight: domestic supply",
+  return(list(x           = wasteshr,
+              weight      = weight,
+              unit        = "DM share, weight: domestic supply",
               description = "Share of domestic supply wasted"))
 }

R/calcNitrogenFixationNdfa.R

@@ -6,26 +6,25 @@
 #' @seealso
 #' \code{\link{calcNitrogenFixationPast}}
 #' @examples
-#' 
-#' \dontrun{ 
+#' \dontrun{
 #' calcOutput("calcNitrogenFixationNdfa")
 #' }
-#' 
-calcNitrogenFixationNdfa<-function(){
-  past   <- findset("past")
-
-  ndfa<-setYears(readSource("Herridge",subtype = "ndfa"),NULL)
-  harvest<-collapseNames(calcOutput("FAOmassbalance",aggregate = FALSE)[,,"nr"][,,"production"])
-  harvest<-add_dimension(harvest,dim = 3.1,add = "data1",nm = "organ")
-  res<-collapseNames(calcOutput("ResBiomass",aggregate = FALSE)[,past,"nr"])
-  biomass<-mbind(harvest[,,getNames(res,dim=2)],res)
-  weight<-dimSums(biomass,dim=3.1)
-  out<-weight<-toolHoldConstantBeyondEnd(weight)
-  out[,,]<-ndfa
-  weight[,,c("begr","betr")]<-10^-10
+#'
+calcNitrogenFixationNdfa <- function() {
+
+  past      <- findset("past")
+  ndfa      <- setYears(readSource("Herridge", subtype = "ndfa"), NULL)
+  harvest   <- collapseNames(calcOutput("FAOmassbalance", aggregate = FALSE)[, , "nr"][, , "production"])
+  harvest   <- add_dimension(harvest, dim = 3.1, add = "data1", nm = "organ")
+  res       <- collapseNames(calcOutput("ResBiomass", aggregate = FALSE)[, past, "nr"])
+  biomass   <- mbind(harvest[, , getNames(res, dim = 2)], res)
+  weight    <- dimSums(biomass, dim = 3.1)
+  out       <- weight <- toolHoldConstantBeyondEnd(weight)
+  out[, , ] <- ndfa
+  weight    <- weight + 10^-10
 
-  return(list(x=out,
-              weight=weight,
-              unit="share of N",
-              description="Share of N in biomass derived from biological fixation"))
+  return(list(x           = out,
+              weight      = weight,
+              unit        = "Share of N",
+              description = "Share of N in biomass derived from biological fixation"))
 }

R/calcSeedShare.R

@@ -1,19 +1,35 @@
+#' @title calcSeedShare
+#' @description Calculates Seed share (seed demand per production)
+#'
+#' @return List of magpie object with results and weight on country or cellular level, unit and description.
+#' @author Benjamin Leon Bodirsky
+#' @examples
+#' \dontrun{
+#' calcOutput("SeedShare")
+#' }
+#' @importFrom magpiesets findset
 
-calcSeedShare<-function(){
-  massbalance<-calcOutput("FAOmassbalance",aggregate=F)
-  kcr<-findset("kcr")
-  seedshr<-dimSums(massbalance[,,"seed"][,,"dm"][,,kcr],dim=c(3.2,3.3))/dimSums(massbalance[,,"production"][,,"dm"][,,kcr],dim=c(3.2,3.3))
-  weight<-dimSums(massbalance[,,"production"][,,"dm"][,,kcr],dim=c(3.2,3.3))
-
-  #assume a seed share of 1 percent for begr and betr
-  seedshr[,,c("begr","betr")]<-0.01
-  weight[,,c("begr","betr")]<-1
-  seedshr[is.nan(seedshr)]<-0
-  weight[seedshr==Inf]<-0
-  seedshr[seedshr==Inf]<-0
+calcSeedShare <- function() {
 
-  seedshr <- toolHoldConstantBeyondEnd(seedshr)
-  weight  <- toolHoldConstantBeyondEnd(weight)
-
-  return(list(x=seedshr,weight=weight,unit="DM share, weight: production quantity",description="Share of production used as seed"))
+  massbalance <- calcOutput("FAOmassbalance", aggregate = FALSE)
+  kcr         <- findset("kcr")
+  seedshr     <-
+    dimSums(massbalance[, , "seed"][, , "dm"][, , kcr], dim = c(3.2, 3.3)) /
+    dimSums(massbalance[, , "production"][, , "dm"][, , kcr], dim = c(3.2, 3.3))
+  weight      <- dimSums(massbalance[, , "production"][, , "dm"][, , kcr], dim = c(3.2, 3.3))
+
+  # assume a seed share of 1 percent for begr and betr
+  seedshr[, , c("begr", "betr")] <- 0.01
+  weight[, , c("begr", "betr")]  <- 1
+  seedshr[is.nan(seedshr)]       <- 0
+  weight[seedshr == Inf]         <- 0
+  seedshr[seedshr == Inf]        <- 0
+
+  seedshr <- mstools::toolHoldConstantBeyondEnd(seedshr)
+  weight  <- mstools::toolHoldConstantBeyondEnd(weight) + 10^-10
+
+  return(list(x           = seedshr,
+              weight      = weight,
+              unit        = "DM share, weight: production quantity",
+              description = "Share of production used as seed"))
 }

README.md

@@ -1,6 +1,6 @@
 # MadRaT land data package
 
-R package **mrland**, version **0.60.2**
+R package **mrland**, version **0.61.0**
 
 [![CRAN status](https://www.r-pkg.org/badges/version/mrland)](https://cran.r-project.org/package=mrland) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3822083.svg)](https://doi.org/10.5281/zenodo.3822083) [![R build status](https://github.com/pik-piam/mrland/workflows/check/badge.svg)](https://github.com/pik-piam/mrland/actions) [![codecov](https://codecov.io/gh/pik-piam/mrland/branch/master/graph/badge.svg)](https://app.codecov.io/gh/pik-piam/mrland) [![r-universe](https://pik-piam.r-universe.dev/badges/mrland)](https://pik-piam.r-universe.dev/builds)
 
@@ -39,7 +39,7 @@ In case of questions / problems please contact Jan Philipp Dietrich <dietrich@pi
 
 To cite package **mrland** in publications use:
 
-Dietrich J, Mishra A, Weindl I, Bodirsky B, Wang X, Baumstark L, Kreidenweis U, Klein D, Steinmetz N, Chen D, Humpenoeder F, von Jeetze P, Wirth S, Beier F, Hoetten D, Sauer P (2024). _mrland: MadRaT land data package_. doi:10.5281/zenodo.3822083 <https://doi.org/10.5281/zenodo.3822083>, R package version 0.60.2, <https://github.com/pik-piam/mrland>.
+Dietrich J, Mishra A, Weindl I, Bodirsky B, Wang X, Baumstark L, Kreidenweis U, Klein D, Steinmetz N, Chen D, Humpenoeder F, von Jeetze P, Wirth S, Beier F, Hoetten D, Sauer P (2024). _mrland: MadRaT land data package_. doi:10.5281/zenodo.3822083 <https://doi.org/10.5281/zenodo.3822083>, R package version 0.61.0, <https://github.com/pik-piam/mrland>.
 
 A BibTeX entry for LaTeX users is
 
@@ -48,8 +48,8 @@ A BibTeX entry for LaTeX users is
   title = {mrland: MadRaT land data package},
   author = {Jan Philipp Dietrich and Abhijeet Mishra and Isabelle Weindl and Benjamin Leon Bodirsky and Xiaoxi Wang and Lavinia Baumstark and Ulrich Kreidenweis and David Klein and Nele Steinmetz and David Chen and Florian Humpenoeder and Patrick {von Jeetze} and Stephen Wirth and Felicitas Beier and David Hoetten and Pascal Sauer},
   year = {2024},
-  note = {R package version 0.60.2},
-  url = {https://github.com/pik-piam/mrland},
+  note = {R package version 0.61.0},
   doi = {10.5281/zenodo.3822083},
+  url = {https://github.com/pik-piam/mrland},
 }
 ```