move functions from mrcommomns

R/calcAttributes.R

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+#' @title calcAttributes
+#' @description provides attributes of different products
+#'
+#' @param subtype subtype of readProductAttributes function.
+#'
+#' @return List of magpie objects with results on global level, empty weight, unit and description.
+#' @author Benjamin Leon Bodirsky
+#' @seealso
+#' [readProductAttributes()]
+#' @examples
+#' \dontrun{
+#' calcOutput("Attributes")
+#' }
+#'
+calcAttributes <- function(subtype = "Products") {
+  attributes <- readSource("ProductAttributes", subtype = subtype)
+  return(list(x = attributes,
+              weight = NULL,
+              unit = "t X per t dry matter (DM), except generalizable energy (ge), where it is PJ/Mt DM.",
+              description = paste("Values from literature survey. See SVN:",
+                                  "tools/Nutrients/crop_specifications.ods or livestock_specifications.ods")))
+}

R/calcFAOLand.R

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+#' @title calcFAOLand
+#' @description Returns physical land areas from FAOSTAT
+#'
+#' @return land areas from FAOSTAT and weight
+#' @author Ulrich Kreidenweis, Kristine Karstens
+
+calcFAOLand <- function() {
+
+  data <- readSource("FAO_online", "Land")
+  data <- data[, , "1000_ha", pmatch = TRUE]   # subset all area information
+  data <- collapseDim(data / 10^3, dim = 3.2)  # transform unit, drop unit statement
+
+  return(list(x           = data,
+              weight      = NULL,
+              unit        = "mio. ha",
+              description = "land-use categories from FAOSTAT"))
+}

R/calcFAOharmonized.R

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+#' @title calcFAOharmonized
+#' @description Calculate harmonized FAO Commodity Balance and Food Supply data based on CB, only harvested areas
+#'              are taken from ProdSTAT. This functions adds the CBCrop, CBLive, FSCrop and FSLive data together.
+#'
+#' @return FAO harmonized data, weight as NULL, and a description as as a list of MAgPIE objects
+#' @author Ulrich Kreidenweis, David Chen, Kristine Karstens
+#' @examples
+#' \dontrun{
+#' a <- calcOutput("FAOharmonized")
+#' }
+#' @importFrom utils read.csv
+
+calcFAOharmonized <- function() {
+
+
+  # input data: Commodity Balance (Crops Primary + Livestock Primary), Food Supply (Crops Primary + Livestock Primary)
+  cbCrop <- readSource("FAO_online", "CBCrop")
+  cbLive <- readSource("FAO_online", "CBLive")
+  fsCrop <- readSource("FAO_online", "FSCrop")
+  fsLive <- readSource("FAO_online", "FSLive")
+
+  cb <- toolFAOcombine(cbLive, cbCrop, combine = "Item")
+  fs <- toolFAOcombine(fsLive, fsCrop, combine = "Item")
+  rm(cbCrop, cbLive, fsCrop, fsLive)
+
+  faoData <- mbind(cb, fs)
+
+   ## in addition harvested area from Crops Primary
+
+  prod <- readSource("FAO_online", "Crop", convert = TRUE)
+
+  ## aggregate Prod to CB units
+  aggregation <- toolGetMapping("FAOitems_online.csv", type = "sectoral", where = "mappingfolder")
+
+    # remove  aggregate categories
+  remove <- setdiff(getNames(prod, dim = 1), aggregation$ProductionItem)
+  prod <- prod[, , remove, invert = TRUE]
+
+  areaHarvested <- toolAggregate(prod, rel = aggregation, from = "ProductionItem", to = "FoodBalanceItem",
+                                  dim = 3.1, partrel = TRUE)[, , "area_harvested"]
+
+  commonyears <- intersect(getYears(areaHarvested), getYears(faoData))
+
+  faoData <- mbind(faoData[, commonyears, ], areaHarvested[, commonyears, ])
+
+  rm(areaHarvested)
+
+
+  ### add Fodder data ###
+
+  fodder <- readSource("FAO", "Fodder")
+  fodder <- toolExtrapolateFodder(fodder, endyear = max(getYears(faoData, as.integer = TRUE)))
+  fodder <- add_columns(x = fodder, addnm = "domestic_supply", dim = 3.2)
+  fodder[, , "domestic_supply"] <- fodder[, , "feed"]
+  fodderAggregated <- toolAggregate(fodder, rel = aggregation, from = "ProductionItem",
+                                    to = "FoodBalanceItem", dim = 3.1, partrel = TRUE)
+  cyears <- intersect(getYears(faoData), getYears(fodderAggregated))
+  faoData <- mbind(faoData[, cyears, ], fodderAggregated[, cyears, ])
+  rm(fodder, fodderAggregated)
+gc()
+
+  faoData[is.na(faoData)] <- 0
+
+  ## check if there is data without an element name
+
+  ## what to do? In case there is data these dimensions should not be deleted
+
+  if (any(getItems(faoData, dim = 3.1) == "")) {
+    if (sum(faoData[, , ""]) == 0) {
+      faoData <- faoData[, , "", invert = TRUE]
+    } else  {
+      vcat(1, 'Aggregation created entries without name (""), but containing information. This should not be the case.')
+    }
+  }
+
+  if (any(getNames(faoData) == "remaining.production")) {
+    remainProd <- mean(dimSums(faoData[, , "remaining.production"], dim = 1) /
+                         dimSums(dimSums(faoData[, , "production"], dim = 3), dim = 1))
+    if (remainProd > 0.02) vcat(1, "Aggregation created a 'remaining' category. Production is",
+                                round(remainProd, digits = 3) * 100, "% of total \n")
+  }
+  if (any(getNames(faoData) == "remaining.area_harvested")) {
+    remainArea <- mean(dimSums(faoData[, , "remaining.area_harvested"], dim = 1) /
+                         dimSums(dimSums(faoData[, , "area_harvested"], dim = 3), dim = 1))
+    if (remainArea > 0.02) vcat(1, "Aggregation created a 'remaining' category. The area harvested is",
+                                round(remainArea, digits = 3) * 100, "% of total \n")
+  }
+
+  # conversion from tonnes to Mt, hectares to Mha and 10^6kcal to 10^12kcal.
+  faoData <- faoData / 10^6
+
+  return(list(x = faoData,
+              weight = NULL,
+              description = "FAO Commodity Balance and Food Supply data",
+              unit = "Unit in Mt/yr, for area Mha, calories in 10^12 kcal/yr",
+              note = "food_supply_kcal, protein_supply and fat_supply were calculated from per capita per day values"))
+}