Master mppalves #33
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,8 +1,8 @@ | ||
| Type: Package | ||
| Package: mrmagpie | ||
| Title: madrat based MAgPIE Input Data Library | ||
| Version: 1.35.8 | ||
| Date: 2023-07-17 | ||
| Authors@R: c( | ||
| person("Kristine", "Karstens", , "[email protected]", role = c("aut", "cre")), | ||
| person("Jan Philipp", "Dietrich", , "[email protected]", role = "aut"), | ||
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| Original file line number | Diff line number | Diff line change |
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| @@ -1,6 +1,9 @@ | ||
| #' @title calcPastureSuit | ||
| #' @description Calculate glassland suitable for pasture management based | ||
| #' on population and aridity criteria. | ||
| #' @param datasource Document | ||
| #' @param climatetype Document | ||
| #' @param lpjml Document | ||
| #' @param smoothPrecipitation Smooth precipitation climate data over time | ||
| #' @param smoothOut smooth the Pasture suitability areas variations over time | ||
| #' @return List of magpie object with results on cluster level | ||
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@@ -11,58 +14,54 @@ | |
| #' } | ||
| #' @importFrom raster area rasterFromXYZ | ||
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| calcPastureSuit <- function(datasource = "ISIMIP3bv2", climatetype = "MRI-ESM2-0:ssp126", | ||
| lpjml = "LPJmL4_for_MAgPIE_44ac93de", smoothPrecipitation = 10, smoothOut = 10) { | ||
|
There was a problem hiding this comment. You don't need 'smoothPrecipitation' and 'smoothOut' anymore. Also the datasource argument is a bit unclear to me. It isn't used anymore, right? |
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| x <- toolSplitSubtype(climatetype, list(climatemodel = NULL, scenario = NULL)) | ||
| # Drivers of managed pastures | ||
| population <- calcOutput("GridPop", subtype = "all", cellular = TRUE, FiveYear = TRUE, | ||
| harmonize_until = 2015, | ||
| aggregate = FALSE)[, , toupper(substring(x$scenario, first = 0, last = 4))] | ||
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| cellPrep <- calcOutput("LPJmLClimateInput", climatetype = climatetype, | ||
| variable = "precipitation:monthlySum", | ||
| stage = "smoothed", | ||
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There was a problem hiding this comment. stage has to be 'harmonized2020' (as this is future data, right?) |
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| lpjmlVersion = lpjml, | ||
| aggregate = FALSE) | ||
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| cellPet <- calcOutput(type = "LPJmL_new", climatetype = climatetype, | ||
| subtype = "mpet", | ||
| stage = "smoothed", | ||
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There was a problem hiding this comment. stage has to be 'harmonized2020' (as this is future data, right?) |
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| version = lpjml, | ||
| aggregate = FALSE) | ||
| cellPrep <- mrwater::toolLPJcell2MAgPIEcell(cellPrep) | ||
| cellPet <- mrwater::toolLPJcell2MAgPIEcell(cellPet) | ||
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| yearsCellPet <- intersect(getYears(cellPet), findset("time")) | ||
| yearsCellPrep <- intersect(findset("time"), getYears(cellPrep)) | ||
| years <- intersect(yearsCellPet, yearsCellPrep) | ||
| cellPrep <- dimSums(cellPrep[, years, ], dim = 3) | ||
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There was a problem hiding this comment. It seems you only need yearly precipitation and pet, is this correct? |
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| cellPet <- dimSums(cellPet[, years, ], dim = 3) | ||
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| # Cell area calculation | ||
| landcoords <- as.data.frame(toolGetMapping("magpie_coord.rda", type = "cell", where = "mappingfolder")) | ||
| landcoords <- cbind(landcoords, rep(1, nrow(landcoords))) | ||
| landcoords <- raster::rasterFromXYZ(landcoords) | ||
| raster::crs(landcoords) <- "+proj=longlat" # outputs cell are in km2 | ||
|
There was a problem hiding this comment. Do you really need cellsize or landarea size of a given cell? there is a function already calculating this: |
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| cellSize <- raster::area(landcoords) | ||
| cellSize <- cellSize * landcoords | ||
| cellSize <- as.magpie(cellSize) | ||
| cellSize <- toolOrderCells(collapseDim(addLocation(cellSize), dim = c("x", "y"))) | ||
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| # population density | ||
| population <- population[getCells(cellPet), , ] # fixing the order of the population cells (should not be necessary!) | ||
| popDensity <- (population * 1e6) / cellSize # population density in number of people per km2 | ||
| popDensity[is.infinite(popDensity)] <- 0 | ||
| popDensity[is.nan(popDensity)] <- 0 | ||
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| years <- intersect(getYears(popDensity), getYears(cellPrep)) | ||
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| aridity <- cellPrep[, years, ] / cellPet[, years, ] | ||
| aridity[is.infinite(aridity) | is.nan(aridity)] <- 0 | ||
| # 0.5 aridity threshold for managed pastures. Same from HYDE 3.2. | ||
| aridity[aridity < 0.5] <- 0 | ||
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@@ -90,9 +89,11 @@ calcPastureSuit <- function(subtype = "ISIMIP3bv2:IPSL-CM6A-LR:1850-2100", smoot | |
| map <- toolGetMapping("CountryToCellMapping.csv", type = "cell") | ||
| pastureSuitAreaReg <- toolAggregate(pastureSuitArea, rel = map, from = "celliso", to = "iso") | ||
| histPastrReg <- toolAggregate(histPastr, rel = map, from = "celliso", to = "iso") | ||
| calibReg <- histPastrReg[, pastLy, ] / pastureSuitAreaReg[, pastLy, ] | ||
| calibReg[is.infinite(calibReg)] <- 1 | ||
| calibReg[is.nan(calibReg)] <- 0 | ||
| pastureSuitArea[, future, ] <- toolAggregate(calibReg, rel = map, | ||
| from = "iso", to = "celliso") * pastureSuitArea[, future, ] | ||
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| pastureSuitArea[is.infinite(pastureSuitArea) | is.nan(pastureSuitArea) | is.na(pastureSuitArea)] <- 0 | ||
| pastureSuitArea[pastureSuitArea < 0] <- 0 | ||
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@@ -106,7 +107,7 @@ calcPastureSuit <- function(subtype = "ISIMIP3bv2:IPSL-CM6A-LR:1850-2100", smoot | |
| pastureSuitArea <- toolHoldConstant(pastureSuitArea, findset("time")) | ||
| pastureSuitArea <- collapseNames(pastureSuitArea) | ||
| pastureSuitArea[, pastAll, ] <- histPastr[, pastAll, ] | ||
| pastureSuitArea <- setNames(pastureSuitArea, "yields") | ||
| return(list( | ||
| x = pastureSuitArea, | ||
| weight = NULL, | ||
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@@ -206,12 +206,13 @@ fullCELLULARMAGPIE <- function(rev = 0.1, dev = "", | |
| subtype = "/co2/Nreturn0p5", # nolint | ||
| lsu_levels = c(seq(0, 2.2, 0.2), 2.5), past_mngmt = "mdef", | ||
| file = paste0("f31_grassl_yld.mz"), years = magYears, aggregate = FALSE) | ||
| calcOutput("PastureSuit", datasource = "ISIMIP3bv2", climatetype = "MRI-ESM2-0:ssp126", | ||
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There was a problem hiding this comment. climatetype and lpjml argument has to be set to the flexible arguments as they change with the preprocessing settings. See e.g.: mrmagpie/R/fullCELLULARMAGPIE.R Line 322 in 5b6edca My guess how the call should look like: Check which years make most sense (magYears or lpjYears) and the lpjml version ('natveg' or 'grass'). |
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| lpjml = "LPJmL4_for_MAgPIE_44ac93de", | ||
| file = paste0("f31_pastr_suitability_", ctype, ".mz"), years = magYears, aggregate = "cluster") | ||
| calcOutput("PastureSuit", datasource = "ISIMIP3bv2", climatetype = "MRI-ESM2-0:ssp126", | ||
| lpjml = "LPJmL4_for_MAgPIE_44ac93de", | ||
| file = "f31_pastr_suitability.mz", years = magYears, aggregate = FALSE) | ||
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| if (grepl("+PastrMngtLevels", dev)) { | ||
| calcOutput("PastrMngtLevels", climatetype = paste0("MRI-ESM2-0", ":", climatescen), | ||
| options = c("brazil_1", "brazil_2", "brazil_4"), cost_level = c(1, 2, 3), | ||
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What does the "Document" here stands for? ^^'