roxygenized, incremented version number and removed old sav_files

DESCRIPTION

 Package: biospheremetrics
 Type: Package
 Title: Biosphere integrity metrics for LPJmL
-Version: 0.1.2
+Version: 0.1.3
 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

NAMESPACE

@@ -4,13 +4,17 @@ export(average_nyear_window)
 export(calcDeltaV)
 export(calcMCOL)
 export(calcMECO)
+export(calculateWithinBiomeDiffs)
 export(classify_biomes)
-export(disaggregateMECOintoBiomes)
+export(disaggregateIntoBiomes)
 export(get_biome_names)
 export(list_needed_outputs)
 export(mecoCrossTable)
+export(mecoWrapper)
 export(plotBiomeAverages)
 export(plotBiomeAveragesToScreen)
+export(plotBiomeInternalDistribution)
+export(plotBiomeInternalDistributionToScreen)
 export(plotBiomes)
 export(plotBiomesToScreen)
 export(plotMCOL)
@@ -20,9 +24,11 @@ export(plotMECOcrossTable)
 export(plotMECOcrossTableToScreen)
 export(plotMECOmap)
 export(plotMECOmapToScreen)
+export(plotMECOovertimePanel)
 export(plotMECOradial)
 export(plotMECOradialPanel)
 export(plotMECOradialToScreen)
+export(plotOvertimeToScreen)
 export(plot_biomes)
 export(readMCOLdata)
 export(readMECOData)

man/calcDeltaV.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/MECO.R
+% Please edit documentation in R/MECO.R, R/MECO_sav.R
 \name{calcDeltaV}
 \alias{calcDeltaV}
 \title{Calculates changes in vegetation structure (deltaV)}
 \usage{
-calcDeltaV(fpcRef, fpcScen, bftRef, bftScen, cftRef, cftScen, weighting)
+calcDeltaV(
+  fpcRef,
+  fpcScen,
+  bftRef,
+  bftScen,
+  cftRef,
+  cftScen,
+  weighting = "equal"
+)
+
+calcDeltaV(
+  fpcRef,
+  fpcScen,
+  bftRef,
+  bftScen,
+  cftRef,
+  cftScen,
+  weighting = "equal"
+)
 }
 \arguments{
 \item{fpcRef}{reference fpc array (dim: [ncells,npfts+1])}
@@ -19,12 +37,17 @@ calcDeltaV(fpcRef, fpcScen, bftRef, bftScen, cftRef, cftScen, weighting)
 
 \item{cftScen}{scenario cft array (dim: [ncells,ncfts])}
 
-\item{weighting}{apply "old" (Ostberg-like), "new", or "equal" weighting of deltaV weights (default "old")}
+\item{weighting}{apply "old" (Ostberg-like), "new", or "equal" weighting of deltaV weights (default "equal")}
 }
 \value{
+deltaV array of size ncells with the deltaV value [0,1] for each cell
+
 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 MECO
+
 Utility function to calculate changes in vegetation structure (deltaV)
 for calculation of MECO
 }
@@ -33,6 +56,12 @@ for calculation of MECO
 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")
+          weighting = "equal")
+}
+\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 = "equal")
 }
 }

man/calcMCOL.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/MCOL.R
+% Please edit documentation in R/MCOL.R, R/MCOL_sav.R
 \name{calcMCOL}
 \alias{calcMCOL}
-\title{Calculate the ecosystem change metric gamma between 2 simulations/timesteps}
+\title{Calculate MCOL}
 \usage{
 calcMCOL(
   inFol_lu,
@@ -13,10 +13,30 @@ calcMCOL(
   npp_threshold = 20,
   pftbands = 11,
   cftbands = 32,
-  readPreviouslySavedData = FALSE,
+  dataFile = NULL,
+  ncells = 67420,
   saveDataFile = FALSE,
+  readPreviouslySavedData = FALSE,
+  fileType = "clm",
+  headersize = 0,
+  varnames = NULL,
+  grass_scaling = T,
+  grass_harvest_file = "/p/projects/open/Fabian/LPJbox/grazing_data.RData"
+)
+
+calcMCOL(
+  inFol_lu,
+  inFol_pnv,
+  startyr,
+  stopyr,
+  gridbased = T,
+  npp_threshold = 20,
+  pftbands = 11,
+  cftbands = 32,
   dataFile = NULL,
   ncells = 67420,
+  saveDataFile = FALSE,
+  readPreviouslySavedData = FALSE,
   fileType = "clm",
   headersize = 0,
   varnames = NULL,
@@ -43,15 +63,15 @@ according to Haberl et al. 2007). Below MCOL will be set to 0.
 
 \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{saveDataFile}{whether to save input data to file (default FALSE)}
+
+\item{readPreviouslySavedData}{flag whether to read previously saved data
+instead of reading it in from output files (default FALSE)}
+
 \item{fileType}{type of output files - one of "clm", "nc" (default: "clm")}
 
 \item{headersize}{headersize of the output files (default 0)}
@@ -71,15 +91,28 @@ mapping_lpj67420_to_grazing_regions array with a mapping between 67420
 LPJmL cells and the 29 regions}
 }
 \value{
-list data object containing arrays of ...
+list data object containing MCOL and components as arrays: mcol, 
+        mcol_overtime, mcol_overtime_perc_piref, mcol_perc, mcol_perc_piref, 
+        ynpp_potential, npp_act_overtime, npp_pot_overtime, npp_eco_overtime, 
+        harvest_cft_overtime, npp_luc_overtime, rharvest_cft_overtime, 
+        fire_overtime, timber_harvest_overtime, harvest_cft, mcol_harvest,
+        grassland_scaling_factor_cellwise,  mcol_luc, mcol_luc_piref
+
+list data object containing MCOL and components as arrays: mcol, 
+        mcol_overtime, mcol_overtime_perc_piref, mcol_perc, mcol_perc_piref, 
+        ynpp_potential, npp_act_overtime, npp_pot_overtime, npp_eco_overtime, 
+        harvest_cft_overtime, npp_luc_overtime, rharvest_cft_overtime, 
+        fire_overtime, timber_harvest_overtime, harvest_cft, mcol_harvest,
+        grassland_scaling_factor_cellwise,  mcol_luc, mcol_luc_piref
 }
 \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.
+Function to calculate MCOL
+
+Function to calculate MCOL
 }
 \examples{
 \dontrun{
 }
+\dontrun{
+}
 }

man/calcMECO.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/MECO.R
+% Please edit documentation in R/MECO.R, R/MECO_sav.R
 \name{calcMECO}
 \alias{calcMECO}
-\title{Calculate the ecosystem change metric MECO between 2 simulations/timesteps}
+\title{Calculate the ecosystem change metric MECO between 2 sets of states}
 \usage{
 calcMECO(
-  folderRef,
-  folderRef2 = NULL,
-  folderScen,
-  readPreviouslySavedData = FALSE,
-  saveFileData = NULL,
-  saveFileMECO = 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,
-  soillayers = 6,
-  dimensionsOnlyLocal = F
+  fpc_ref,
+  fpc_scen,
+  bft_ref,
+  bft_scen,
+  cft_ref,
+  cft_scen,
+  state_ref,
+  state_scen,
+  weighting = "equal",
+  lat,
+  lon,
+  cellArea,
+  dimensionsOnlyLocal = F,
+  nitrogen = T
+)
+
+calcMECO(
+  fpc_ref,
+  fpc_scen,
+  bft_ref,
+  bft_scen,
+  cft_ref,
+  cft_scen,
+  state_ref,
+  state_scen,
+  weighting = "equal",
+  lat,
+  lon,
+  cellArea,
+  dimensionsOnlyLocal = F,
+  nitrogen = T
 )
 }
 \arguments{
-\item{folderRef}{folder of reference run}
+\item{fpc_ref}{reference run data for fpc}
 
-\item{folderRef2}{optional 2nd reference run folder (default NULL - no split)}
+\item{fpc_scen}{scenario run data for fpc}
 
-\item{folderScen}{folder of scenario run}
+\item{bft_ref}{reference run data for fpc_bft}
 
-\item{readPreviouslySavedData}{whether to read in previously saved data 
-(default: FALSE)}
+\item{bft_scen}{scenario run data for fpc_bft}
 
-\item{saveFileData}{file to save read in data to (default NULL)}
+\item{cft_ref}{reference run data for cftfrac}
 
-\item{saveFileMECO}{file to save MECO data to (default NULL)}
+\item{cft_scen}{scenario run data for cftfrac}
 
-\item{combined}{read in soilc+litc, evap+interc, rh+harvestc separate or as 
-combined outputs (default F -- separate)}
+\item{state_ref}{reference run data for state variables}
 
-\item{nitrogen}{include nitrogen outputs for pools and fluxes into MECO 
-calculation (default F)}
+\item{state_scen}{scenario run data for state variables}
 
 \item{weighting}{apply "old" (Ostberg-like), "new", or "equal" weighting of 
-deltaV weights (default "old")}
-
-\item{varnames}{data.frame with names of output files (outname) and time res.
-(timestep) -- can be specified to account for variable file names 
-(default NULL -- standard names as below)
-varnames <- data.frame(row.names = c("grid",    "fpc",    "fpc_bft",    "cftfrac",    "firec",    "rh_harvest",    "npp",    "evapinterc",    "runoff",    "transp",    "soillitc",    "vegc",    "swcsum",    "firef",    "rh",    "harvestc",    "evap",    "interc",    "soilc",    "litc",    "swc",    "vegn",    "soilnh4",    "soilno3",    "leaching",    "n2o_denit",    "n2o_nit",    "n2o_denit",    "n2_emis",    "bnf",    "n_volatilization"),
-outname = c("grid.bin","fpc.bin","fpc_bft.bin","cftfrac.bin","firec.bin","rh_harvest.bin","npp.bin","evapinterc.bin","runoff.bin","transp.bin","soillitc.bin","vegc.bin","swcsum.bin","firef.bin","rh.bin","harvestc.bin","evap.bin","interc.bin","soilc.bin","litc.bin","swc.bin","vegn.bin","soilnh4.bin","soilno3.bin","leaching.bin","n2o_denit.bin","n2o_nit.bin","n2o_denit.bin","n2_emis.bin","bnf.bin","n_volatilization.bin"),
-timestep = c("Y",       "Y",      "Y",          "Y",          "Y",        "Y",             "Y",      "Y",             "Y",         "Y",         "Y",           "Y",       "Y",         "Y",        "Y",     "Y",           "Y",       "Y",         "Y",        "Y",       "Y",      ,"Y",      "Y",          "Y",          "Y",           "Y",            "Y",          "Y",            "Y",          "Y",      "Y"))}
-
-\item{headerout}{headersize of the output files (default: 0 bytes)}
-
-\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)}
+deltaV weights (default "equal")}
 
-\item{ncfts}{number of crop bands (rainfed+irrigated)}
+\item{lat}{latitude array}
 
-\item{nbfts}{number of bands in fpc_bft (bioenergy functional types)}
+\item{lon}{longitude array}
 
-\item{ncells}{number of cells in lpjml grid}
-
-\item{soillayers}{number of soil layers (default: 6)}
+\item{cellArea}{cellarea array}
 
 \item{dimensionsOnlyLocal}{flag whether to use only local change component
 for water/carbon/nitrogen fluxes and pools, or use an average of
 local change, global change and ecosystem balance (default F)}
+
+\item{nitrogen}{include nitrogen outputs (default: TRUE)}
 }
 \value{
-list data object containing arrays of deltaV, local_change,
-        global_change, ecosystem_balance, carbon_fluxes, carbon_stocks,
-        water_fluxes, meco_total (+ nitrogen_fluxes and nitrogen_stocks)
+list data object containing arrays of meco_total, deltaV, local_change,
+        global_change, ecosystem_balance, carbon_stocks, carbon_fluxes,
+        water_fluxes (+ nitrogen_stocks and nitrogen_fluxes)
+
+list data object containing arrays of meco_total, deltaV, local_change,
+        global_change, ecosystem_balance, carbon_stocks, carbon_fluxes,
+        water_fluxes (+ nitrogen_stocks and nitrogen_fluxes)
 }
 \description{
+Function to calculate the ecosystem change metric MECO, based on gamma/deltaV
+work from 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 et al. 2018, but similar the methodology
+
 Function to calculate the ecosystem change metric MECO, based on gamma/deltaV
 work from Sykes (1999), Heyder (2011), and Ostberg (2015,2018).
 This is a reformulated version in R, not producing 100% similar values
@@ -100,4 +93,6 @@ than the C/bash version from Ostberg et al. 2018, but similar the methodology
 \examples{
 \dontrun{
 }
+\dontrun{
+}
 }

man/calculateWithinBiomeDiffs.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/MECO.R, R/MECO_sav.R
+\name{calculateWithinBiomeDiffs}
+\alias{calculateWithinBiomeDiffs}
+\title{Calculate meco with each biomes average cell}
+\usage{
+calculateWithinBiomeDiffs(
+  biome_classes,
+  dataFile_base,
+  intra_biome_distrib_file,
+  create = FALSE,
+  res = 0.05,
+  plotting = FALSE
+)
+
+calculateWithinBiomeDiffs(
+  biome_classes,
+  dataFile_base,
+  intra_biome_distrib_file,
+  create = FALSE,
+  res = 0.05,
+  plotting = FALSE
+)
+}
+\arguments{
+\item{biome_classes}{biome classes object as returned by classify biomes, 
+calculated for dataFile_base}
+
+\item{dataFile_base}{base MECO to compute differences with (only ref is relevant)}
+
+\item{intra_biome_distrib_file}{file to additionally write results to}
+
+\item{create}{create new modified files, or read already existing ones?}
+
+\item{res}{how finegrained the distribution should be (resolution)}
+
+\item{plotting}{whether plots for each biome should be created}
+}
+\value{
+data object with distibution - dim: c(biomes,meco_variables,bins)
+
+data object with distibution - dim: c(biomes,meco_variables,bins)
+}
+\description{
+Function to calculate meco with each biomes average cell
+as a measure of internal variability
+
+Function to calculate meco with each biomes average cell
+as a measure of internal variability
+}
+\examples{
+\dontrun{
+
+}
+\dontrun{
+
+}
+}

man/disaggregateMECOintoBiomes.Rd → man/disaggregateIntoBiomes.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/MECO.R
-\name{disaggregateMECOintoBiomes}
-\alias{disaggregateMECOintoBiomes}
+% Please edit documentation in R/MECO.R, R/MECO_sav.R
+\name{disaggregateIntoBiomes}
+\alias{disaggregateIntoBiomes}
 \title{Averages MECO values across regions}
 \usage{
-disaggregateMECOintoBiomes(
-  meco,
+disaggregateIntoBiomes(
+  data,
+  biome_class,
+  type = "quantile",
+  classes = "4biomes"
+)
+
+disaggregateIntoBiomes(
+  data,
   biome_class,
   type = "quantile",
   classes = "4biomes"
 )
 }
 \arguments{
-\item{meco}{MECO list object as returned by calcMECO}
+\item{data}{List object, of which every item should be disaggregated}
 
 \item{biome_class}{biome class list object as returned by classify_biomes}
 
@@ -23,12 +30,20 @@ disaggregateMECOintoBiomes(
 "4biomes" (tropics/temperate/boreal/arctic) or "allbiomes"}
 }
 \description{
+Returns the average value across either 4 regions or all (19) biomes for MECO
+and each of the subcomponents for each
+
 Returns the average value across either 4 regions or all (19) biomes for MECO
 and each of the subcomponents for each
 }
 \examples{
 \dontrun{
-disaggregateMECOintoBiomes(meco = meco,
+disaggregateIntoBiomes(meco = meco,
+                   biome_class = biome_classes,
+                   type = "quantile",classes = "4biomes")
+}
+\dontrun{
+disaggregateIntoBiomes(meco = meco,
                    biome_class = biome_classes,
                    type = "quantile",classes = "4biomes")
 }

man/get_biome_names.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/MECO.R
+% Please edit documentation in R/MECO.R, R/MECO_sav.R
 \name{get_biome_names}
 \alias{get_biome_names}
 \title{Get biome names}
 \usage{
+get_biome_names(biomeNameLength = 2)
+
 get_biome_names(biomeNameLength = 2)
 }
 \arguments{
@@ -11,9 +13,13 @@ get_biome_names(biomeNameLength = 2)
 or full biome names}
 }
 \description{
+Returns biome names with variable length (abbreviated, short, or full)
+
 Returns biome names with variable length (abbreviated, short, or full)
 }
 \examples{
 \dontrun{
 }
+\dontrun{
+}
 }

man/list_needed_outputs.Rd

@@ -4,12 +4,16 @@
 \alias{list_needed_outputs}
 \title{Returns LPJmL outputs required for given metric}
 \usage{
-list_needed_outputs(metric = "all", with_nitrogen = TRUE)
+list_needed_outputs(
+  metric = "all",
+  with_nitrogen = TRUE,
+  only_first_filename = 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)}
+  required outputs for. Pick from "meco", "mcol", "biome", "nitrogen",
+"lsc", "bluewater", "greenwater", "water", "biosphere", "all" (default)}
 
 \item{withNitrogen}{logical: include nitrogen outputs? default: TRUE}
 }

man/mecoCrossTable.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/MECO.R
+% Please edit documentation in R/MECO.R, R/MECO_sav.R
 \name{mecoCrossTable}
 \alias{mecoCrossTable}
 \title{Create modified MECO data for crosstable}
 \usage{
+mecoCrossTable(dataFileIn, dataFileOut, biome_classes_in, pickCells = NULL)
+
 mecoCrossTable(dataFileIn, dataFileOut, biome_classes_in, pickCells = NULL)
 }
 \arguments{
@@ -17,6 +19,12 @@ mecoCrossTable(dataFileIn, dataFileOut, biome_classes_in, pickCells = NULL)
 instead of computing the average state}
 }
 \description{
+Function to create a modified MECO data file where for each biome
+the average scenario cell is compared to the average scenario 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)
+
 Function to create a modified MECO data file where for each biome
 the average scenario cell is compared to the average scenario cell of all 
 other biomes. This can then be used to compute a crosstable with the average 
@@ -26,4 +34,6 @@ difference between each of them as in the SI of Ostberg et al. 2013
 \examples{
 \dontrun{
 }
+\dontrun{
+}
 }

man/mecoWrapper.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/MECO.R, R/MECO_sav.R
+\name{mecoWrapper}
+\alias{mecoWrapper}
+\title{Wrapper for calculating the ecosystem change metric MECO}
+\usage{
+mecoWrapper(
+  folderRef,
+  folderRef2 = NULL,
+  folderScen,
+  readPreviouslySavedData = FALSE,
+  saveFileData = NULL,
+  saveFileMECO = NULL,
+  combined = FALSE,
+  nitrogen = FALSE,
+  weighting = "equal",
+  varnames = NULL,
+  headerout = 0,
+  timespan_full_ref,
+  timespan_full_scen,
+  timespan_focus_ref,
+  timespan_focus_ref2 = NULL,
+  timespan_focus_scen,
+  npfts,
+  ncfts,
+  nbfts,
+  ncells,
+  soillayers = 6,
+  dimensionsOnlyLocal = F,
+  overtime = F,
+  window = 30
+)
+
+mecoWrapper(
+  folderRef,
+  folderRef2 = NULL,
+  folderScen,
+  readPreviouslySavedData = FALSE,
+  saveFileData = NULL,
+  saveFileMECO = NULL,
+  combined = FALSE,
+  nitrogen = FALSE,
+  weighting = "equal",
+  varnames = NULL,
+  headerout = 0,
+  timespan_full_ref,
+  timespan_full_scen,
+  timespan_focus_ref,
+  timespan_focus_ref2 = NULL,
+  timespan_focus_scen,
+  npfts,
+  ncfts,
+  nbfts,
+  ncells,
+  soillayers = 6,
+  dimensionsOnlyLocal = F,
+  overtime = F,
+  window = 30
+)
+}
+\arguments{
+\item{folderRef}{folder of reference run}
+
+\item{folderRef2}{optional 2nd reference run folder (default NULL - no split)}
+
+\item{folderScen}{folder of scenario run}
+
+\item{readPreviouslySavedData}{whether to read in previously saved data
+(default: FALSE)}
+
+\item{saveFileData}{file to save read in data to (default NULL)}
+
+\item{saveFileMECO}{file to save MECO 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 MECO
+calculation (default F)}
+
+\item{weighting}{apply "old" (Ostberg-like), "new", or "equal" weighting of
+deltaV weights (default "equal")}
+
+\item{varnames}{data.frame with names of output files (outname) and time res.
+(timestep) -- can be specified to account for variable file names
+(default NULL -- standard names as below)
+varnames <- data.frame(row.names = c("grid",    "fpc",    "fpc_bft",    "cftfrac",    "firec",    "rh_harvest",    "npp",    "evapinterc",    "runoff",    "transp",    "soillitc",    "vegc",    "swcsum",    "firef",    "rh",    "harvestc",    "evap",    "interc",    "soilc",    "litc",    "swc",    "vegn",    "soilnh4",    "soilno3",    "leaching",    "n2o_denit",    "n2o_nit",    "n2o_denit",    "n2_emis",    "bnf",    "n_volatilization"),
+outname = c("grid.bin","fpc.bin","fpc_bft.bin","cftfrac.bin","firec.bin","rh_harvest.bin","npp.bin","evapinterc.bin","runoff.bin","transp.bin","soillitc.bin","vegc.bin","swcsum.bin","firef.bin","rh.bin","harvestc.bin","evap.bin","interc.bin","soilc.bin","litc.bin","swc.bin","vegn.bin","soilnh4.bin","soilno3.bin","leaching.bin","n2o_denit.bin","n2o_nit.bin","n2o_denit.bin","n2_emis.bin","bnf.bin","n_volatilization.bin"),
+timestep = c("Y",       "Y",      "Y",          "Y",          "Y",        "Y",             "Y",      "Y",             "Y",         "Y",         "Y",           "Y",       "Y",         "Y",        "Y",     "Y",           "Y",       "Y",         "Y",        "Y",       "Y",      ,"Y",      "Y",          "Y",          "Y",           "Y",            "Y",          "Y",            "Y",          "Y",      "Y"))}
+
+\item{headerout}{headersize of the output files (default: 0 bytes)}
+
+\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 bands (rainfed+irrigated)}
+
+\item{nbfts}{number of bands in fpc_bft (bioenergy functional types)}
+
+\item{ncells}{number of cells in lpjml grid}
+
+\item{soillayers}{number of soil layers (default: 6)}
+
+\item{dimensionsOnlyLocal}{flag whether to use only local change component
+for water/carbon/nitrogen fluxes and pools, or use an average of
+local change, global change and ecosystem balance (default F)}
+}
+\value{
+list data object containing arrays of meco_total, deltaV, local_change,
+        global_change, ecosystem_balance, carbon_stocks, carbon_fluxes,
+        water_fluxes (+ nitrogen_stocks and nitrogen_fluxes)
+
+list data object containing arrays of meco_total, deltaV, local_change,
+        global_change, ecosystem_balance, carbon_stocks, carbon_fluxes,
+        water_fluxes (+ nitrogen_stocks and nitrogen_fluxes)
+}
+\description{
+Function to read in data for meco, and call the calculation function once,
+if overtime is F, or for each timeslice of length window years, if 
+overtime is T
+
+Function to read in data for meco, and call the calculation function once,
+if overtime is F, or for each timeslice of length window years, if 
+overtime is T
+}
+\examples{
+\dontrun{
+}
+\dontrun{
+}
+}

man/plotBiomeAverages.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/MECO.R
+% Please edit documentation in R/MECO.R, R/MECO_sav.R
 \name{plotBiomeAverages}
 \alias{plotBiomeAverages}
 \title{Plot radial MECO plot to file with 4/16 biomes}
 \usage{
+plotBiomeAverages(
+  data,
+  file,
+  biome_class_names,
+  title = "",
+  titleSize = 2,
+  leg_scale = 1,
+  eps = FALSE
+)
+
 plotBiomeAverages(
   data,
   file,
@@ -30,14 +40,22 @@ plotBiomeAverages(
 \item{eps}{write as eps, replacing png in filename (default: True)}
 }
 \value{
+None
+
 None
 }
 \description{
+Function to plot an aggregated radial status of MECO values [0-1]
+for the different sub-categories to file
+
 Function to plot an aggregated radial status of MECO values [0-1]
 for the different sub-categories to file
 }
 \examples{
 \dontrun{
 
+}
+\dontrun{
+
 }
 }

man/plotBiomeAveragesToScreen.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/MECO.R
+% Please edit documentation in R/MECO.R, R/MECO_sav.R
 \name{plotBiomeAveragesToScreen}
 \alias{plotBiomeAveragesToScreen}
 \title{Plot radial MECO plot to file with 4/16 biomes}
 \usage{
+plotBiomeAveragesToScreen(
+  data,
+  biome_class_names,
+  title = "",
+  titleSize = 2,
+  leg_scale = 0.5
+)
+
 plotBiomeAveragesToScreen(
   data,
   biome_class_names,
@@ -24,14 +32,22 @@ plotBiomeAveragesToScreen(
 \item{leg_scale}{character string title for plot}
 }
 \value{
+None
+
 None
 }
 \description{
+Function to plot an aggregated radial status of MECO values [0-1]
+for the different sub-categories to file
+
 Function to plot an aggregated radial status of MECO values [0-1]
 for the different sub-categories to file
 }
 \examples{
 \dontrun{
 
+}
+\dontrun{
+
 }
 }

man/plotBiomeInternalDistribution.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/MECO.R, R/MECO_sav.R
+\name{plotBiomeInternalDistribution}
+\alias{plotBiomeInternalDistribution}
+\title{Plot to file distribution of similarity within biomes}
+\usage{
+plotBiomeInternalDistribution(
+  data,
+  file,
+  biomes_abbrv,
+  scale,
+  title = "",
+  legendtitle = "",
+  eps = FALSE
+)
+
+plotBiomeInternalDistribution(
+  data,
+  file,
+  biomes_abbrv,
+  scale,
+  title = "",
+  legendtitle = "",
+  eps = FALSE
+)
+}
+\arguments{
+\item{data}{data object with distibution - as returned by 
+calculateWithInBiomeDiffs. dim: c(biomes,bins)}
+
+\item{file}{to write into}
+
+\item{biomes_abbrv}{to mask the focusBiome from}
+
+\item{scale}{scaling factor for distribution. defaults to 1}
+
+\item{title}{character string title for plot, default empty}
+
+\item{legendtitle}{character string legend title, default empty}
+
+\item{eps}{write as eps or png (default: F -> png)}
+}
+\value{
+None
+
+None
+}
+\description{
+Function to plot to file the distribution of similarity within biomes
+
+Function to plot to file the distribution of similarity within biomes
+}
+\examples{
+\dontrun{
+
+}
+\dontrun{
+
+}
+}

man/plotBiomeInternalDistributionToScreen.Rd

+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/MECO.R, R/MECO_sav.R
+\name{plotBiomeInternalDistributionToScreen}
+\alias{plotBiomeInternalDistributionToScreen}
+\title{Plot distribution of similarity within biomes}
+\usage{
+plotBiomeInternalDistributionToScreen(
+  data,
+  biomes_abbrv,
+  title = "",
+  legendtitle = "",
+  scale = 1
+)
+
+plotBiomeInternalDistributionToScreen(
+  data,
+  biomes_abbrv,
+  title = "",
+  legendtitle = "",
+  scale = 1
+)
+}
+\arguments{
+\item{data}{data object with distibution - as returned by 
+calculateWithInBiomeDiffs for each subcategory of meco.
+dim: c(biomes,bins)}
+
+\item{biomes_abbrv}{to mask the focusBiome from}
+
+\item{title}{character string title for plot, default empty}
+
+\item{legendtitle}{character string legend title, default empty}
+
+\item{scale}{scaling factor for distribution. defaults to 1}
+}
+\value{
+None
+
+None
+}
+\description{
+Function to plot the distribution of similarity within biomes
+
+Function to plot the distribution of similarity within biomes
+}
+\examples{
+\dontrun{
+
+}
+\dontrun{
+
+}
+}

man/plotBiomes.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/MECO.R
+% Please edit documentation in R/MECO.R, R/MECO_sav.R
 \name{plotBiomes}
 \alias{plotBiomes}
 \title{Plot biomes to file}
 \usage{
+plotBiomes(
+  biome_ids,
+  biomeNameLength = 1,
+  orderLegend = "plants",
+  file,
+  title = "",
+  titleSize = 2,
+  legYes = T,
+  leg_scale = 1,
+  eps = FALSE
+)
+
 plotBiomes(
   biome_ids,
   biomeNameLength = 1,
@@ -39,13 +51,20 @@ grasslands, then tundra ..., or "zones" to go from north to south
 \item{eps}{write as eps, replacing png in filename (default: True)}
 }
 \value{
+None
+
 None
 }
 \description{
+Function to plot biome classification to file
+
 Function to plot biome classification to file
 }
 \examples{
 \dontrun{
 
+}
+\dontrun{
+
 }
 }

man/plotBiomesToScreen.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/MECO.R
+% Please edit documentation in R/MECO.R, R/MECO_sav.R
 \name{plotBiomesToScreen}
 \alias{plotBiomesToScreen}
 \title{Plot biomes}
 \usage{
+plotBiomesToScreen(
+  biome_ids,
+  biomeNameLength = 1,
+  orderLegend = "plants",
+  title = "",
+  titleSize = 2,
+  legYes = T,
+  leg_scale = 0.5
+)
+
 plotBiomesToScreen(
   biome_ids,
   biomeNameLength = 1,
@@ -33,13 +43,20 @@ grasslands, then tundra ..., or "zones" to go from north to south
 (default: "plants")}
 }
 \value{
+None
+
 None
 }
 \description{
+Function to plot biome classification
+
 Function to plot biome classification
 }
 \examples{
 \dontrun{
 
+}
+\dontrun{
+
 }
 }

man/plotMCOL.Rd

 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/MCOL.R
+% Please edit documentation in R/MCOL.R, R/MCOL_sav.R
 \name{plotMCOL}
 \alias{plotMCOL}
 \title{Plot absolute MCOL, overtime, maps, and npp into given folder}
 \usage{
+plotMCOL(
+  mcolData,
+  outFol,
+  plotyears,
+  minVal,
+  maxVal,
+  legendpos,
+  startyr,
+  mapyear,
+  mapyear_buffer = 5,
+  highlightyear,
+  eps = FALSE
+)
+
 plotMCOL(
   mcolData,
   outFol,
@@ -22,7 +36,8 @@ plotMCOL(
 \item{mcolData}{mcol data list object (returned from calcMCOL) containing
 mcol, npp_eco_overtime, npp_act_overtime, npp_pot_overtime,
 npp_bioenergy_overtime, mcol_overtime, npp_harv_overtime,
-mcol_overtime_perc_piref, mcol_perc, mcol_perc_piref, ynpp}
+mcol_overtime_perc_piref, mcol_perc, mcol_perc_piref, ynpp
+all in GtC}
 
 \item{outFol}{folder to write into}
 
@@ -46,12 +61,18 @@ mcol_overtime_perc_piref, mcol_perc, mcol_perc_piref, ynpp}
 \item{eps}{write plots as eps, instead of png (default = FALSE)}
 }
 \value{
+none
+
 none
 }
 \description{
+Wrapper function to plot absolute mcol, overtime, maps, and npp into given folder
+
 Wrapper function to plot absolute mcol, overtime, maps, and npp into given folder
 }
 \examples{
 \dontrun{
 }
+\dontrun{
+}
 }