first commit of biosphere integrity metrics package

DESCRIPTION

+Package: biospheremetrics
+Type: Package
+Title: Biosphere integrity metrics for LPJmL
+Version: 0.1.1
+Author: Fabian Stenzel, Johanna Braun, Jannes Breier
+Maintainer: Fabian Stenzel <stenzel@pik-potsdam.de>
+Description: Functions to compute Biosphere integrity metrics M-COL and M-ECO based on output from LPJmL
+License: GPL-3
+Encoding: UTF-8
+LazyData: true
+RoxygenNote: 7.2.2
+Depends:
+    lpjmliotools

NAMESPACE

+# Generated by roxygen2: do not edit by hand
+
+export(calcDeltaV)
+export(calcGamma)
+export(calcMCOL)
+export(classify_biomes)
+export(disaggregateGammaIntoBiomes)
+export(evaluateGamma)
+export(gammaCrossTable)
+export(list_needed_outputs)
+export(plotBiomes)
+export(plotBiomesAverage)
+export(plotBiomesAveragesToScreen)
+export(plotBiomesToScreen)
+export(plotGammaCrossTable)
+export(plotGammaCrossTableToScreen)
+export(plotGammaMap)
+export(plotGammaMapToScreen)
+export(plotGammaRadial)
+export(plotGammaRadial4)
+export(plotGammaRadialToScreen)
+export(plotMCOL)
+export(plotMCOLmap)
+export(plotMCOLovertime)
+export(plot_biomes)
+export(readGammaData)
+export(readMCOLdata)

R/list_needed_outputs.R

+# output timesteps have to be added (monthly / yearly)
+# differentiation between required and optional outputs (prec, temp)
+
+#' Returns LPJmL outputs required for given metric
+#'
+#' Function to return a list of strings with the LPJmL output names required for
+#' the computation of the metrics M-COL, M-ECO, the biome classification
+#' and/or planetary boundary calculations
+#'
+#' @param metric string/list of strings, containing name of metric to get
+#'        required outputs for. Pick from "meco", "mcol", "biome", "all_pbs",
+#'               "pb_n", "pb_w", "pb_b", "pb_lsc", "all" (default)
+#'
+#' @param withNitrogen logical: include nitrogen outputs? default: TRUE
+#'
+#' @return List of strings with LPJmL variable names
+#'
+#' @examples
+#' \dontrun{
+#'
+#' }
+#' @export
+list_needed_outputs <- function(metric = "all", with_nitrogen = TRUE) {
+
+  optional_metrics <- c("meco", "mcol", "biome", "all_pbs", "pb_n",
+                        "pb_w", "pb_b", "pb_lsc", "all")
+  notin <- metric[!metric %in% optional_metrics]
+  if (length(notin) > 0) {
+    stop(paste("Metrics not available:", notin, collapse = ", "))
+  }
+  varsGAMMA <- c("grid", "fpc", "fpc_bft", "cftfrac", "firec", "rh_harvest",
+                 "npp", "runoff", "transp", "vegc", "firef", "rh", "harvestc",
+                 "evap", "interc", "soilc", "litc", "swc")
+  varsGAMMAnitrogen <- c("vegn", "soilnh4", "soilno3", "leaching", "n2o_denit",
+                         "n2o_nit", "n2o_denit", "n2_emis", "bnf",
+                         "n_volatilization")
+  varsHANPP <- c("grid", "npp", "pft_npp", "pft_harvestc", "pft_rharvestc",
+                 "firec", "timber_harvestc", "cftfrac", "fpc")
+  varsBiome <- c("grid", "fpc", "vegc", "pft_lai", "temp")
+  vars_pb_n <- c("grid", "runoff", "leaching", "pet", "prec")
+  vars_pb_w <- c("grid", "discharge", "irrig", "drainage")
+  vars_pb_lsc <- varsBiome
+  vars_pb_b <- c()
+
+  outs <- c()
+  tsteps <- c() # todo: add timestep functionality - needs to be clever
+
+  if ("all" %in% metric) {
+    if (with_nitrogen) {
+      outs <- c(outs,varsGAMMA, varsGAMMAnitrogen, varsHANPP, varsBiome,
+                           vars_pb_n, vars_pb_w, vars_pb_lsc, vars_pb_b)
+    } else {
+      outs <- c(outs,varsGAMMA, varsHANPP, varsBiome, vars_pb_w, vars_pb_lsc,
+                vars_pb_b)
+    }
+  }
+  if ("meco" %in% metric) {
+    if (with_nitrogen) {
+      outs <- c(outs,varsGAMMA, varsGAMMAnitrogen)
+    } else {
+      outs <- c(outs,varsGAMMA)
+    }
+  }
+  if ("biome" %in% metric) {
+    outs <- c(outs,varsBiome)
+  }
+  if ("mcol" %in% metric) {
+    outs <- c(outs,varsHANPP)
+  }
+  if ("all_pbs" %in% metric) {
+    if (with_nitrogen) {
+      outs <- c(outs,varsBiome, vars_pb_n, vars_pb_w, vars_pb_lsc, vars_pb_b)
+    } else {
+      outs <- c(outs,varsBiome, vars_pb_w, vars_pb_lsc, vars_pb_b)
+    }
+  }
+  if ("pb_n" %in% metric) {
+    outs <- c(outs,vars_pb_n)
+  }
+  if ("pb_w" %in% metric) {
+    outs <- c(outs,vars_pb_w)
+  }
+  if ("pb_lsc" %in% metric) {
+    outs <- c(outs,vars_pb_lsc)
+  }
+  if ("pb_b" %in% metric ) {
+    outs <- c(outs,vars_pb_b)
+  }
+  return(list(outputs = unique(sort(outs)), timesteps = tsteps))
+}

R/plot_biomes.R

+#' Plot global distribution of lpjml simulated biomes
+#'
+#' Plots a map with the biome distribution as derived from a lpjml run based
+#' on the "classify_biomes" function
+#'
+#' @param biome_data output (list) from classify_biomes()
+#'
+#' @param plotpath directory for saving the plot (character string)
+#'
+#' @param to_robinson logical to define if robinson projection should be used
+#' for plotting
+#'
+#' @param bg_col character, specify background possible (`NA` for transparent)#
+#'
+#' @examples
+#' \dontrun{
+#'  plot_biomes(biome_data = biomes,
+#'              file_name ="/p/projects/open/Johanna/R/biomes.pfd")
+#' }
+#'
+#' @md
+#' @export
+
+plot_biomes <- function(biome_data,
+                        file_name = NULL,
+                        to_robinson = TRUE,
+                        bg_col = NA) {
+
+  # load required data: bbox, countries
+  lpjml_extent <- c(-180, 180, -60, 85)
+
+  bounding_box <- system.file("extdata", "ne_110m_wgs84_bounding_box.shp",
+                              package = "pbfunctions") %>%
+      rgdal::readOGR(layer = "ne_110m_wgs84_bounding_box", verbose = FALSE) %>%
+      { if(to_robinson) sp::spTransform(., sp::CRS("+proj=robin")) else . } # nolint
+
+  countries <- system.file("extdata", "ne_110m_admin_0_countries.shp",
+                              package = "pbfunctions") %>%
+      rgdal::readOGR(layer = "ne_110m_admin_0_countries", verbose = FALSE) %>%
+      crop(., lpjml_extent) %>%
+      { if(to_robinson) sp::spTransform(., CRS("+proj=robin")) else . } # nolint
+
+  biome_cols <-  c("#993404", "#D95F0E", "#004529", "#238443",
+                   "#78C679", "#D9F0A3", "#4EB3D3", "#2B8CBE",
+                   "#FE9929", "#FEC44F", "#FEE391", "#A8DDB5",
+                   "#E0F3DB", "#F7FCF0", "#c79999", "#0868AC",
+                   "#FFFFD4", "white", "#dad4d4")
+
+  biome_mapping <- system.file("extdata", "biomes.csv",
+                              package = "pbfunctions") %>%
+                   readr::read_csv2()
+  names(biome_cols) <- biome_mapping$short_name
+
+  order_legend <- c(1, 2, 9, 10, 11, 3, 4, 5, 6, 12, 13, 14, 7, 8, 15, 16, 17,
+                      18, 19)
+
+  biome_cols_legend <- biome_cols[order_legend]
+
+  biome_names_legend <- biome_mapping$short_name[order_legend]
+
+  biomes_lpjml <- to_raster(lpjml_array = biome_data$biome_id,
+                         boundary_box = bounding_box,
+                         ext = lpjml_extent,
+                         to_robinson = to_robinson)
+
+  if (!is.null(file_name)) {
+    file_extension <- strsplit(file_name, split = "\\.")[[1]][-1]
+    switch(file_extension,
+      `png` = {
+        png(file_name,
+            width = 8 * 1.8,
+            height = 4 * 2,
+            units = "cm",
+            res = 600,
+            pointsize = 7)
+      },
+      `pdf` = {
+        pdf(file_name,
+            width = 8 * 1.8 / 2.54,
+            height = (4 * 2) / 2.54,
+            pointsize = 7)
+      }, {
+        stop("File extension ", dQuote(file_extension), " not supported.")
+      }
+    )
+  }
+  brk <- seq(0.5, 19.5, 1)
+  par(mar = c(4, 0, 0, 0), xpd = T, bg = bg_col)
+  image(biomes_lpjml, asp = 1, xaxt = "n", yaxt = "n",
+          xlab = "", ylab = "", col = biome_cols, breaks = brk, lwd = 0.1,
+          bty = "n")
+  plot(countries, add = TRUE, lwd = 0.3,
+         border = "#5c565667", usePolypath = FALSE)
+  legend(0, y = -6736039, xjust = 0.45, yjust = 1, cex = 0.8,
+    biome_names_legend[1:19],
+    fill = biome_cols_legend[1:19],
+    horiz = F, border = NULL, bty = "o", box.col = "white",
+    bg = bg_col, ncol = 4)
+  if (!is.null(file_name)) dev.off()
+}
\ No newline at end of file

biospheremetrics.Rproj

+Version: 1.0
+
+RestoreWorkspace: Default
+SaveWorkspace: Default
+AlwaysSaveHistory: Default
+
+EnableCodeIndexing: Yes
+UseSpacesForTab: Yes
+NumSpacesForTab: 2
+Encoding: UTF-8
+
+RnwWeave: Sweave
+LaTeX: pdfLaTeX
+
+BuildType: Package
+PackageUseDevtools: Yes
+PackageInstallArgs: --no-multiarch --with-keep.source
+PackageRoxygenize: rd,collate,namespace,vignette

man/calcDeltaV.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/MECO.R
+\name{calcDeltaV}
+\alias{calcDeltaV}
+\title{Calculates changes in vegetation structure (deltaV)}
+\usage{
+calcDeltaV(fpcRef, fpcScen, bftRef, bftScen, cftRef, cftScen, weighting)
+}
+\arguments{
+\item{fpcRef}{reference fpc array (dim: [ncells,npfts+1])}
+
+\item{fpcScen}{scenario fpc array (dim: [ncells,npfts+1])}
+
+\item{bftRef}{reference bft array (dim: [ncells,nbfts])}
+
+\item{bftScen}{scenario bft array (dim: [ncells,nbfts])}
+
+\item{cftRef}{reference cft array (dim: [ncells,ncfts])}
+
+\item{cftScen}{scenario cft array (dim: [ncells,ncfts])}
+
+\item{weighting}{apply "old" (Ostberg-like), "new", or "equal" weighting of deltaV weights (default "old")}
+}
+\value{
+deltaV array of size ncells with the deltaV value [0,1] for each cell
+}
+\description{
+Utility function to calculate changes in vegetation structure (deltaV)
+for calculation of gamma
+}
+\examples{
+\dontrun{
+deltaV <- calcDeltaV(fpcRef = fpc_ref_mean,fpcScen = apply(fpc_scen,c(1,2),mean),
+          bftRef = bft_ref_mean,bftScen = apply(bft_scen,c(1,2),mean),
+          cftRef = cft_ref_mean, cftScen = apply(cft_scen,c(1,2),mean),
+          weighting = "new")
+}
+}

man/calcGamma.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/MECO.R
+\name{calcGamma}
+\alias{calcGamma}
+\title{Calculate the ecosystem change metric gamma between 2 simulations/timesteps}
+\usage{
+calcGamma(
+  folderRef,
+  folderRef2 = NULL,
+  folderScen,
+  readPreviouslySavedData = TRUE,
+  saveFileData = NULL,
+  saveFileGamma = NULL,
+  combined = FALSE,
+  nitrogen = FALSE,
+  weighting = "old",
+  varnames = NULL,
+  headerout = 0,
+  timespan_full_ref,
+  timespan_full_scen,
+  timespan_focus_ref,
+  timespan_focus_ref2 = NULL,
+  timespan_focus_scen,
+  npfts,
+  ncfts,
+  nbfts,
+  ncells,
+  dimensionsOnlyLocal = T
+)
+}
+\arguments{
+\item{folderRef}{folder of reference run}
+
+\item{folderRef2}{2nd folder of reference run, if split (default NULL -- no split)}
+
+\item{folderScen}{folder of scenario run}
+
+\item{saveFileData}{file to save read in data to (default NULL)}
+
+\item{saveFileGamma}{file to save gamma data to (default NULL)}
+
+\item{combined}{read in soilc+litc, evap+interc, rh+harvestc separate or as combined outputs (default F -- separate)}
+
+\item{nitrogen}{include nitrogen outputs for pools and fluxes into gamma calculation (default F)}
+
+\item{weighting}{apply "old" (Ostberg-like), "new", or "equal" weighting of deltaV weights (default "old")}
+
+\item{varnames}{data.frame with names of output files -- can be specified to account for variable file names (default NULL -- standard names are used)}
+
+\item{headerout}{headersize of the output files (default 0)}
+
+\item{timespan_full_ref}{full timespan of output files in reference period}
+
+\item{timespan_full_scen}{full timespan of output files in scenario period}
+
+\item{timespan_focus_ref}{specific years to use as reference period}
+
+\item{timespan_focus_ref2}{specific years to use as 2nd part of reference period in case this is split (default NULL)}
+
+\item{timespan_focus_scen}{specific years to use as scenario period}
+
+\item{npfts}{number of natural plant functional types (== bands in fpc - 1)}
+
+\item{ncfts}{number of crop functional types}
+
+\item{nbfts}{number of bfts (bioenergy functional types)}
+
+\item{ncells}{number of cells in lpjml grid}
+
+\item{exportGamma}{flag whether to export gamma data to global environment (default F)}
+}
+\value{
+list data object containing arrays of deltaV, local_change,
+        global_change, ecosystem_balance, carbon_fluxes, carbon_stocks,
+        water_fluxes, gamma_total (+ nitrogen_fluxes and nitrogen_stocks if used)
+}
+\description{
+Function to calculate the ecosystem change metric gamma according
+to Sykes (1999), Heyder (2011), and Ostberg (2015,2018).
+This is a reformulated version in R, not producing 100% similar values
+than the C/bash version from Ostberg 2018, but following their methodology.
+}
+\examples{
+\dontrun{
+gamma_today <- calcGamma(folderRef = "/p/projects/elis/ostberg/biome_shift/archive_Ostberg2018/simulations/scenario_PNV_trunkupdate_noCC/HadGEM2-ES/r1i1p1/",
+               folderScen = "/p/projects/elis/ostberg/biome_shift/archive_Ostberg2018/simulations/scenario_LUC_trunkupdate/rcp26/HadGEM2-ES/r1i1p1/luc_rcp26_50bg50btflexi/",
+               readPreviouslySavedData = TRUE, saveFileData = "/media/All/Gamma/Gamma_today_data.RData",
+               saveFileGamma = "/media/All/Gamma/Gamma_today_gamma.RData",
+               timespan_full_ref = c(1991,2099), timespan_full_scen = c(1991,2099),
+               timespan_focus_ref = c(2000,2029), timespan_focus_scen = c(2000,2029),
+               npfts = 9, ncfts = 32, nbfts = 12, ncells = 64240,
+               combined = TRUE, weighting = "old")
+}
+}

man/calcMCOL.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/MCOL.R
+\name{calcMCOL}
+\alias{calcMCOL}
+\title{Calculate the ecosystem change metric gamma between 2 simulations/timesteps}
+\usage{
+calcMCOL(
+  inFol_lu,
+  inFol_pnv,
+  startyr,
+  stopyr,
+  gridbased = T,
+  npp_threshold = 20,
+  pftbands = 11,
+  cftbands = 32,
+  readPreviouslySavedData = FALSE,
+  saveDataFile = FALSE,
+  dataFile = NULL,
+  ncells = 67420,
+  fileType = "clm",
+  headersize = 0,
+  varnames = NULL,
+  grass_scaling = T,
+  grass_harvest_file = "/p/projects/open/Fabian/LPJbox/grazing_data.RData"
+)
+}
+\arguments{
+\item{inFol_lu}{folder of landuse scenario run}
+
+\item{inFol_pnv}{folder of pnv reference run}
+
+\item{startyr}{first year of simulations}
+
+\item{stopyr}{last year of simulations}
+
+\item{gridbased}{logical are pft outputs gridbased or pft-based?}
+
+\item{npp_threshold}{lower threshold for npp (to mask out non-lu areas
+according to Haberl et al. 2007). Below MCOL will be set to 0.
+(default: 20 gC/m2)}
+
+\item{pftbands}{number of natural plant functional types (== bands in fpc - 1)}
+
+\item{cftbands}{number of crop functional types}
+
+\item{readPreviouslySavedData}{flag whether to read previously saved data
+instead of reading it in from output files (default FALSE)}
+
+\item{saveDataFile}{whether to save input data to file (default FALSE)}
+
+\item{dataFile}{file to save/read input data to/from (default NULL)}
+
+\item{ncells}{number of cells in lpjml grid}
+
+\item{fileType}{type of output files - one of "clm", "nc" (default: "clm")}
+
+\item{headersize}{headersize of the output files (default 0)}
+
+\item{varnames}{data.frame with names (outname) and timestep of output files
+-- can be specified to account for variable file names
+(default NULL -- standard names are used)}
+
+\item{grass_scaling}{whether to scale pasture harvest according to
+data given via grass_harvest_file (default T)}
+
+\item{grass_harvest_file}{file containing grazing data to rescale the
+grassland harvests according to Herrero et al. 2013. File contains:
+grazing_data list object with $name and $id of 29 world regions, and
+$Herrero_2000_kgDM_by_region containing for each of these regions and
+mapping_lpj67420_to_grazing_regions array with a mapping between 67420
+LPJmL cells and the 29 regions}
+}
+\value{
+list data object containing arrays of ...
+}
+\description{
+Function to calculate the ecosystem change metric gamma according
+to Sykes (1999), Heyder (2011), and Ostberg (2015,2018).
+This is a reformulated version in R, not producing 100% similar values
+than the C/bash version from Ostberg 2018, but following their methodology.
+}
+\examples{
+\dontrun{
+}
+}

man/classify_biomes.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/classify_biomes.R
+\name{classify_biomes}
+\alias{classify_biomes}
+\title{Classify biomes}
+\usage{
+classify_biomes(
+  path_data,
+  timespan,
+  input_files = NULL,
+  diff_output_files = NULL,
+  file_type = "raw",
+  savanna_proxy = list(pft_lai = 6),
+  montane_arctic_proxy = list(elevation = 1000),
+  tree_cover_thresholds = list(),
+  avg_nyear_args = list(),
+  read_args = list(header_size = 0, ncell = 67420, firstyear = 1901, fpc_nbands = 12,
+    size = 4)
+)
+}
+\arguments{
+\item{path_data}{output directory (character string) of the LPJmL run o read
+default outputs from (fpc, grid, vegc, pft_lai, temp)}
+
+\item{timespan}{time span to be used, defined as an integer vector, e.g.
+`c(1982,2011)`, to average over (default over all years, else see
+\link[pbfunctions]{average_nyear_window})}
+
+\item{input_files}{optional `list` containing additional input (!) files,
+not in the `path_data`, e.g. if temp was not written out:
+`list(grid=..., temp = ..., elevation = ...)`}
+
+\item{diff_output_files}{optional list for specification of output file names
+differing from default, which is list(grid = "grid.bin", fpc = "fpc.bin",# nolint
+vegc = "vegc.bin", pft_lai = "pft_lai.bin", temp = "temp.bin")}
+
+\item{savanna_proxy}{`list` with either "pft_lai" or "vegc" as
+name/key and value in m2/m2 for pft_lai (default = 6) and gC/m2 for
+vegc (default would be 7500), Set to `NULL` if no proxy is used.}
+
+\item{montane_arctic_proxy}{`list` with either "elevation" or "latitude" as
+name/key and value in m for elevation (default 1000) and degree for
+latitude (default would be 55), Set to `NULL` if no proxy is used.}
+
+\item{tree_cover_thresholds}{list with minimum tree cover thresholds for
+definition of forest, woodland, savanna and grassland. Only changes to
+the default have to be included in the list, for the rest the default
+is used. Default values:
+"boreal forest" = 0.6
+"temperate forest" = 0.6
+"temperate woodland" = 0.3
+"temperate savanna" = 0.1
+"tropical forest" = 0.6
+"tropical woodland" = 0.3
+"tropical savanna" = 0.1}
+
+\item{avg_nyear_args}{list of arguments to be passed to
+\link[pbfunctions]{average_nyear_window} (see for more info). To be used for # nolint
+time series analysis}
+
+\item{read_args}{list of arguments for reading input/output. only required
+for:
+nc output: specification of header_size and ncell to read in
+           lpjml grid input
+raw/clm output: specification of header_size, ncell, firstyear and 
+           fpc_nbands (12 or 10)}
+
+\item{file_ending}{replace default file ending. default: ".bin"}
+}
+\value{
+list object containing biome_id (main biome per grid cell [dim=c(ncells)]), # nolint
+and list of respective biome_names[dim=c(nbiomes)]
+}
+\description{
+Classify biomes based on foliage protected cover (FPC) and temperature
+LPJmL output plus either vegetation carbon or pft_lai depending on
+the savanna_proxy option and elevation if montane_arctic_proxy requires this
+}
+\examples{
+\dontrun{
+classify_biomes(
+  path_data = "/p/projects/open/Fabian/runs/Gamma/output/historic_gamma"
+  timespan = c(1982,2011))
+}
+
+}

man/disaggregateGammaIntoBiomes.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/MECO.R
+\name{disaggregateGammaIntoBiomes}
+\alias{disaggregateGammaIntoBiomes}
+\title{Returns the average gamma values across regions}
+\usage{
+disaggregateGammaIntoBiomes(
+  gamma,
+  biome_class,
+  type = "quantile",
+  classes = "4biomes"
+)
+}
+\arguments{
+\item{gamma}{gamma data object with dimension c(regions/biomes[4/16],gamma_components[10/8],minmeanmax/quantiles[3])}
+
+\item{biome_class}{path to save modified data to}
+
+\item{type}{return minimum,mean,maximum or Q10,Q50,Q90}
+
+\item{classes}{into which regions should be disaggregated? "4biomes" or "allbiomes" default "4biomes"}
+}
+\description{
+Returns the average value across either 4 regions or 19 biomes for gamma
+and each of the subcomponents for each
+}
+\examples{
+\dontrun{
+disaggregateGammaIntoBiomes(gamma = gamma_historic_nitrogen_classic_bnf,
+                   biome_class = gamma_historic_withNitrogen_biome_classes,
+                   type = "quantile",classes = "4biomes")
+}
+}

man/evaluateGamma.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/MECO.R
+\name{evaluateGamma}
+\alias{evaluateGamma}
+\title{Create modified gamma data}
+\usage{
+evaluateGamma(
+  dataFileIn,
+  dataFileOut,
+  temperature,
+  pft_lai,
+  elevation,
+  lat,
+  lon,
+  refBiom
+)
+}
+\arguments{
+\item{dataFileIn}{path to input data}
+
+\item{dataFileOut}{path to save modified data to}
+
+\item{temperature}{yearly average temperature}
+
+\item{refBiom}{}
+}
+\description{
+Function to create a modified gamma data file where each cell is compared
+to the average cell of the precribed reference biome refBiom
+}
+\examples{
+\dontrun{
+evaluateGamma(dataFileIn = "/media/All/Gamma/Gamma_today_data.RData",
+      dataFileOut = "/media/All/Gamma/Gamma_preind_compared_to_average_TrBD_data.RData",
+      temperature = temperature_1716, lat = lat64240, lon = lon64240, refBiom = 4)
+}
+}

man/gammaCrossTable.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/MECO.R
+\name{gammaCrossTable}
+\alias{gammaCrossTable}
+\title{Create modified gamma data for crosstable}
+\usage{
+gammaCrossTable(
+  dataFileIn,
+  dataFileOut,
+  temperature,
+  pft_lai,
+  elevation,
+  pickCells = NULL,
+  lat,
+  lon
+)
+}
+\arguments{
+\item{dataFileIn}{path to input data}
+
+\item{dataFileOut}{path to save modified data to}
+
+\item{temperature}{yearly average temperature}
+
+\item{pft_lai}{yearly pft_lai values for the biome classification}
+
+\item{elevation}{elevation input file for the biome classification}
+
+\item{lon}{}
+}
+\description{
+Function to create a modified gamma data file where for each present day biome
+the average cell is compared to the average cell of all other biomes. This
+can then be used to compute a crosstable with the average difference between
+each of them as in the SI of Ostberg et al. 2013
+(Critical impacts of global warming on land ecosystems)
+}
+\examples{
+\dontrun{
+gammaCrossTable(dataFileIn = "/media/All/Gamma/Gamma_today_data.RData",
+      dataFileOut = "/media/All/Gamma/Gamma_preind_compared_to_average_TrBD_data.RData",
+      temperature = temperature_1716, pft_lai = pft_lai_1996, elevation = elevation, lat = lat64240, lon = lon64240, refBiom = 4)
+}
+}

man/list_needed_outputs.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/list_needed_outputs.R
+\name{list_needed_outputs}
+\alias{list_needed_outputs}
+\title{Returns LPJmL outputs required for given metric}
+\usage{
+list_needed_outputs(metric = "all", with_nitrogen = TRUE)
+}
+\arguments{
+\item{metric}{string/list of strings, containing name of metric to get
+required outputs for. Pick from "meco", "mcol", "biome", "all_pbs",
+       "pb_n", "pb_w", "pb_b", "pb_lsc", "all" (default)}
+
+\item{withNitrogen}{logical: include nitrogen outputs? default: TRUE}
+}
+\value{
+List of strings with LPJmL variable names
+}
+\description{
+Function to return a list of strings with the LPJmL output names required for
+the computation of the metrics M-COL, M-ECO, the biome classification
+and/or planetary boundary calculations
+}
+\examples{
+\dontrun{
+
+}
+}

man/plotBiomes.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/MECO.R
+\name{plotBiomes}
+\alias{plotBiomes}
+\title{Plot radial gamma plot to file with 4/16 biomes}
+\usage{
+plotBiomes(
+  biome_ids,
+  biome_class_names,
+  file,
+  title,
+  titleSize = 2,
+  legYes = T,
+  leg_scale = 1,
+  eps = FALSE
+)
+}
+\arguments{
+\item{file}{to write into}
+
+\item{title}{character string title for plot}
+
+\item{eps}{write as eps or png}
+
+\item{data}{gamma data array c(4[biomes],[ngammacomponents],3[min,median,max])}
+}
+\value{
+None
+}
+\description{
+Function to plot an aggregated radial status of gamma values [0-1]
+for the different sub-categories to file
+}
+\examples{
+\dontrun{
+
+}
+}

man/plotBiomesAverage.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/MECO.R
+\name{plotBiomesAverage}
+\alias{plotBiomesAverage}
+\title{Plot radial gamma plot to file with 4/16 biomes}
+\usage{
+plotBiomesAverage(
+  data,
+  file,
+  biome_class_names,
+  title,
+  titleSize = 2,
+  leg_scale = 1,
+  eps = FALSE
+)
+}
+\arguments{
+\item{data}{gamma data array c(4[biomes],[ngammacomponents],3[min,median,max])}
+
+\item{file}{to write into}
+
+\item{biome_class_names}{to write into}
+
+\item{title}{character string title for plot}
+
+\item{titleSize}{character string title for plot}
+
+\item{leg_scale}{character string title for plot}
+
+\item{eps}{write as eps or png}
+}
+\value{
+None
+}
+\description{
+Function to plot an aggregated radial status of gamma values [0-1]
+for the different sub-categories to file
+}
+\examples{
+\dontrun{
+
+}
+}

man/plotBiomesAveragesToScreen.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/MECO.R
+\name{plotBiomesAveragesToScreen}
+\alias{plotBiomesAveragesToScreen}
+\title{Plot radial gamma plot to file with 4/16 biomes}
+\usage{
+plotBiomesAveragesToScreen(
+  data,
+  biome_class_names,
+  title,
+  titleSize = 2,
+  leg_scale = 0.5
+)
+}
+\arguments{
+\item{data}{input data with dimension c(nbiome_classes,3) -- Q10,Q50,Q90 each}
+
+\item{biome_class_names}{to write into}
+
+\item{title}{character string title for plot}
+
+\item{titleSize}{character string title for plot}
+
+\item{leg_scale}{character string title for plot}
+}
+\value{
+None
+}
+\description{
+Function to plot an aggregated radial status of gamma values [0-1]
+for the different sub-categories to file
+}
+\examples{
+\dontrun{
+
+}
+}

man/plotBiomesToScreen.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/MECO.R
+\name{plotBiomesToScreen}
+\alias{plotBiomesToScreen}
+\title{Plot radial gamma plot to file with 4/16 biomes}
+\usage{
+plotBiomesToScreen(
+  biome_ids,
+  biome_class_names,
+  title,
+  titleSize = 2,
+  legYes = T,
+  leg_scale = 0.5
+)
+}
+\arguments{
+\item{title}{character string title for plot}
+
+\item{data}{gamma data array c(4[biomes],[ngammacomponents],3[min,median,max])}
+
+\item{file}{to write into}
+
+\item{eps}{write as eps or png}
+}
+\value{
+None
+}
+\description{
+Function to plot an aggregated radial status of gamma values [0-1]
+for the different sub-categories to file
+}
+\examples{
+\dontrun{
+
+}
+}