R/POST_FATE.temporalEvolution.R
In leca-dev/RFate: FATE with R
Defines functions
POST_FATE.temporalEvolution
Documented in
POST_FATE.temporalEvolution
### HEADER #####################################################################
##' @title Create tables of pixel temporal evolution of PFG abundances (and
##' light and soil resources if activated) for a \code{FATE} simulation
##'
##' @name POST_FATE.temporalEvolution
##'
##' @author Maya Guéguen
##'
##' @description This script is designed to produce from 1 to 3 tables
##' containing pixel temporal evolution of PFG abundances, as well as light and
##' soil resources if those modules were activated, in a \code{FATE}
##' simulation.
##'
##'
##' @param name.simulation a \code{string} corresponding to the main directory
##' or simulation name of the \code{FATE} simulation
##' @param file.simulParam default \code{NULL}. \cr A \code{string}
##' corresponding to the name of a parameter file that will be contained into
##' the \code{PARAM_SIMUL} folder of the \code{FATE} simulation
##' @param no_years an \code{integer} corresponding to the number of simulation
##' years that will be used to extract PFG abundance / light / soil maps
##' @param opt.ras_habitat (\emph{optional}) default \code{NULL}. \cr
##' A \code{string} corresponding to the file name of a raster mask, with an
##' \code{integer} value within each pixel, corresponding to a specific habitat
##' @param opt.no_CPU (\emph{optional}) default \code{1}. \cr The number of
##' resources that can be used to parallelize the \code{unzip/zip} of raster
##' files, as well as the extraction of values from raster files
##'
##'
##' @details
##'
##' This function allows to obtain, for a specific \code{FATE} simulation and
##' a specific parameter file within this simulation, \strong{one to three
##' preanalytical tables that can then be used to create graphics}. \cr \cr
##'
##' For each PFG and each selected simulation year, raster maps are retrieved
##' from the results folder \code{ABUND_perPFG_allStrata} and unzipped.
##' Informations extracted lead to the production of one table before the maps
##' are compressed again :
##'
##' \itemize{
##' \item{the value of \strong{abundance for each Plant Functional Group}
##' for each selected simulation year(s) in every pixel in which the PFG is
##' present for at least one of the selected simulation year(s) \cr \cr
##' }
##' }
##'
##' \strong{If the light module was activated} (see
##' \code{\link{PRE_FATE.params_globalParameters}}), for each height stratum
##' and each selected simulation year, raster maps are retrieved from the
##' results folder \code{LIGHT} and unzipped.
##' Informations extracted lead to the production of one table before the maps
##' are compressed again :
##'
##' \itemize{
##' \item{the value of \strong{light resources for each height stratum} for
##' each selected simulation year(s) in every pixel \cr \cr
##' }
##' }
##'
##' \strong{If the soil module was activated} (see
##' \code{\link{PRE_FATE.params_globalParameters}}), for each selected
##' simulation year, raster maps are retrieved from the results folder
##' \code{SOIL} and unzipped.
##' Informations extracted lead to the production of one table before the maps
##' are compressed again :
##'
##' \itemize{
##' \item{the value of \strong{soil resources} for each selected simulation
##' year(s) in every pixel \cr \cr
##' }
##' }
##'
##' \strong{If a raster mask for habitat has been provided}, the tables will
##' also contain information about the pixel habitat. \cr \cr
##'
##'
##' \strong{These \code{.csv} files can then be used by other functions} :
##'
##' \itemize{
##' \item to produce graphics of temporal evolution of modelled abundances
##' and space occupancy at the \emph{whole area level} \cr (see
##' \code{\link{POST_FATE.graphic_evolutionCoverage}})
##' \item to produce graphics of temporal evolution of modelled abundances
##' and / or resources at the \emph{pixel level} \cr (see
##' \code{\link{POST_FATE.graphic_evolutionPixels}})
##' \item to produce graphics of temporal evolution of community composition
##' at the \emph{habitat level} \cr (see
##' \code{\link{POST_FATE.graphic_evolutionStability}})
##' }
##'
##'
##'
##' @return A \code{list} containing three \code{data.frame} objects with the
##' following columns :
##' \describe{
##' \item{\code{PFG}}{concerned plant functional group (for abundance)}
##' \item{\code{STRATUM}}{concerned height stratum (for LIGHT)}
##' \item{\code{ID.pixel}}{number of the concerned pixel}
##' \item{\code{X, Y}}{coordinates of the concerned pixel}
##' \item{\code{HAB}}{habitat of the concerned pixel}
##' \item{\emph{years}}{values of the corresponding object (abundance / LIGHT
##' / SOIL) for each selected simulation year(s) \cr \cr}
##' }
##'
##' One to three \file{POST_FATE_TABLE_PIXEL_evolution_[...].csv} files are created :
##' \describe{
##' \item{\file{abundance}}{always}
##' \item{\file{light}}{\emph{if light module was activated}}
##' \item{\file{soil}}{\emph{if soil module was activated}}
##' }
##'
##'
##' @keywords FATE, outputs, temporal evolution
##'
##' @seealso \code{\link{PRE_FATE.params_globalParameters}},
##' \code{\link{POST_FATE.graphic_evolutionCoverage}},
##' \code{\link{POST_FATE.graphic_evolutionPixels}},
##' \code{\link{POST_FATE.graphic_evolutionStability}}
##'
##'
##' @export
##'
##' @importFrom foreach foreach %do% %dopar%
##' @importFrom data.table rbindlist fwrite
##' @importFrom raster raster stack
##' rasterToPoints as.data.frame extract cellFromXY
## @importFrom doParallel registerDoParallel
##'
##'
## END OF HEADER ###############################################################
POST_FATE.temporalEvolution = function(
name.simulation
, file.simulParam = NULL
, no_years
, opt.ras_habitat = NULL
, opt.no_CPU = 1
){
#############################################################################
## CHECK parameter name.simulation
.testParam_existFolder(name.simulation, "PARAM_SIMUL/")
.testParam_existFolder(name.simulation, "RESULTS/")
.testParam_existFolder(name.simulation, "DATA/")
name.simulation = sub("/", "", name.simulation)
## CHECK parameter file.simulParam
abs.simulParams = .getParam_abs.simulParams(file.simulParam, name.simulation)
## CHECK parameter no_years
.testParam_notInteger.m("no_years", no_years)
## CHECK parameter opt.ras_habitat
if (!.testParam_notDef(opt.ras_habitat))
{
.testParam_notChar.m("opt.ras_habitat", opt.ras_habitat)
.testParam_existFile(opt.ras_habitat)
ras.habitat = raster(opt.ras_habitat)
}
cat("\n\n #------------------------------------------------------------#")
cat("\n # POST_FATE.temporalEvolution")
cat("\n #------------------------------------------------------------# \n")
#############################################################################
res = foreach (abs.simulParam = abs.simulParams) %do%
{
cat("\n+++++++\n")
cat("\n Simulation name : ", name.simulation)
cat("\n Simulation file : ", abs.simulParam)
cat("\n")
## Get results directories ------------------------------------------------
GLOB_DIR = .getGraphics_results(name.simulation = name.simulation
, abs.simulParam = abs.simulParam)
## Get number of PFGs -----------------------------------------------------
## Get PFG names ----------------------------------------------------------
GLOB_SIM = .getGraphics_PFG(name.simulation = name.simulation
, abs.simulParam = abs.simulParam)
## Get raster mask --------------------------------------------------------
GLOB_MASK = .getGraphics_mask(name.simulation = name.simulation
, abs.simulParam = abs.simulParam)
## Get habitat information ----------------------------------------------
if (exists("ras.habitat"))
{
ras.habitat = ras.habitat * GLOB_MASK$ras.mask
}
## Get list of arrays and extract years of simulation -------------------
raster.perPFG.allStrata = .getRasterNames(years = NULL, "allStrata", "ABUND", GLOB_DIR)
years = sapply(sub("Abund_YEAR_", "", raster.perPFG.allStrata)
, function(x) strsplit(as.character(x), "_")[[1]][1])
years = sort(unique(as.numeric(years)))
years = years[round(seq(1, length(years)
, length.out = min(no_years, length(years))))]
no_years = length(years)
cat("\n Selected years : ", years)
cat("\n Number of years : ", no_years)
cat("\n")
## UNZIP the raster saved -----------------------------------------------
raster.perPFG.allStrata = .getRasterNames(years, "allStrata", "ABUND", GLOB_DIR)
.unzip(folder_name = GLOB_DIR$dir.output.perPFG.allStrata
, list_files = raster.perPFG.allStrata
, no_cores = opt.no_CPU)
if (GLOB_SIM$doLight){
.unzip(folder_name = GLOB_DIR$dir.output.light
, list_files = list.files(path = GLOB_DIR$dir.output.light
, pattern = paste0("YEAR_", years, "_", collapse = "|"))
, no_cores = opt.no_CPU)
}
if (GLOB_SIM$doSoil){
.unzip(folder_name = GLOB_DIR$dir.output.soil
, list_files = list.files(path = GLOB_DIR$dir.output.soil
, pattern = paste0("YEAR_", years, collapse = "|"))
, no_cores = opt.no_CPU)
}
doWriting.abund = TRUE
doWriting.light = ifelse(GLOB_SIM$doLight, TRUE, FALSE)
doWriting.soil = ifelse(GLOB_SIM$doSoil, TRUE, FALSE)
## get the data inside the rasters --------------------------------------
cat("\n ---------- GETTING ABUNDANCE for pfg")
if (opt.no_CPU > 1)
{
if (.getOS() != "windows")
{
if (!isNamespaceLoaded("doParallel")) {
if(!requireNamespace('doParallel', quietly = TRUE)) stop("Package 'doParallel' not found")
}
doParallel::registerDoParallel(cores = opt.no_CPU)
} else
{
warning("Parallelisation with `foreach` is not available for Windows. Sorry.")
}
}
tabAbund.list = foreach (pfg = GLOB_SIM$PFG) %dopar%
{
cat(" ", pfg)
file_name = paste0(GLOB_DIR$dir.output.perPFG.allStrata,
"Abund_YEAR_",
years,
"_",
pfg,
"_STRATA_all")
if (length(which(file.exists(paste0(file_name, ".tif")))) > 0)
{
file_name = paste0(file_name, ".tif")
} else if (length(which(file.exists(paste0(file_name, ".img")))) > 0)
{
file_name = paste0(file_name, ".img")
} else if (length(which(file.exists(paste0(file_name, ".asc")))) > 0)
{
file_name = paste0(file_name, ".asc")
}
ye = years[which(file.exists(file_name))]
file_name = file_name[which(file.exists(file_name))]
if (length(file_name) > 0)
{
ras = stack(file_name) * GLOB_MASK$ras.mask
ras.df = rasterToPoints(ras)
ras.df = as.data.frame(ras.df)
colnames(ras.df) = c("X", "Y", ye)
ID.abund = rowSums(ras.df[, 3:ncol(ras.df), drop = FALSE])
ras.df = ras.df[which(ID.abund > 0), , drop = FALSE]
if (nrow(ras.df) > 0)
{
ras.df$ID.pixel = cellFromXY(GLOB_MASK$ras.mask, ras.df[, c("X", "Y")])
ras.df$PFG = pfg
if (exists("ras.habitat"))
{
ras.df$HAB = extract(ras.habitat, ras.df[, c("X", "Y")])
} else
{
ras.df$HAB = "ALL"
}
ras.df = ras.df[, c("PFG", "ID.pixel", "X", "Y", "HAB", ye)]
return(ras.df)
}
}
} ## END loop on PFG
cat("\n")
tabAbund = rbindlist(tabAbund.list, fill = TRUE)
tabAbund = as.data.frame(tabAbund, stringsAsFactors = FALSE)
if (nrow(tabAbund) > 0 && ncol(tabAbund) > 0)
{
fwrite(tabAbund
, file = paste0(name.simulation
, "/RESULTS/POST_FATE_TABLE_PIXEL_evolution_abundance_"
, basename(GLOB_DIR$dir.save)
, ".csv")
, row.names = FALSE)
} else
{
tabAbund = NA
doWriting.abund = FALSE
warning("No abundance values were found! Please check.")
}
## get the data inside the rasters --------------------------------------
if (GLOB_SIM$doLight)
{
cat("\n ---------- GETTING LIGHT for stratum")
tabLight.list = foreach (stra = c(1:GLOB_SIM$no_STRATA)-1) %dopar%
{
cat(" ", stra)
file_name = paste0(GLOB_DIR$dir.output.light
, "Light_Resources_YEAR_"
, years
, "_STRATA_"
, stra)
if (length(which(file.exists(paste0(file_name, ".tif")))) > 0)
{
file_name = paste0(file_name, ".tif")
} else if (length(which(file.exists(paste0(file_name, ".img")))) > 0)
{
file_name = paste0(file_name, ".img")
} else if (length(which(file.exists(paste0(file_name, ".asc")))) > 0)
{
file_name = paste0(file_name, ".asc")
}
ye = years[which(file.exists(file_name))]
file_name = file_name[which(file.exists(file_name))]
if (length(file_name) > 0)
{
ras = stack(file_name) * GLOB_MASK$ras.mask
ras.df = rasterToPoints(ras)
ras.df = as.data.frame(ras.df)
colnames(ras.df) = c("X", "Y", ye)
ras.df$ID.pixel = cellFromXY(GLOB_MASK$ras.mask, ras.df[, c("X", "Y")])
ras.df$STRATUM = stra
if (exists("ras.habitat"))
{
ras.df$HAB = extract(ras.habitat, ras.df[, c("X", "Y")])
} else
{
ras.df$HAB = "ALL"
}
ras.df = ras.df[, c("STRATUM", "ID.pixel", "X", "Y", "HAB", ye)]
return(ras.df)
}
} ## END loop on STRATUM
cat("\n")
tabLight = rbindlist(tabLight.list, fill = TRUE)
tabLight = as.data.frame(tabLight, stringsAsFactors = FALSE)
if (nrow(tabLight) > 0 && ncol(tabLight) > 0)
{
fwrite(tabLight
, file = paste0(name.simulation
, "/RESULTS/POST_FATE_TABLE_PIXEL_evolution_light_"
, basename(GLOB_DIR$dir.save)
, ".csv")
, row.names = FALSE)
} else
{
tabLight = NA
doWriting.light = FALSE
warning("No light values were found! Please check.")
}
} else
{
tabLight = NA
} ## END loop for light
## get the data inside the rasters --------------------------------------
if (GLOB_SIM$doSoil)
{
cat("\n ---------- GETTING SOIL")
file_name = paste0(GLOB_DIR$dir.output.soil,
"Soil_Resources_YEAR_",
years)
if (length(which(file.exists(paste0(file_name, ".tif")))) > 0)
{
file_name = paste0(file_name, ".tif")
} else if (length(which(file.exists(paste0(file_name, ".img")))) > 0)
{
file_name = paste0(file_name, ".img")
} else if (length(which(file.exists(paste0(file_name, ".asc")))) > 0)
{
file_name = paste0(file_name, ".asc")
}
ye = years[which(file.exists(file_name))]
file_name = file_name[which(file.exists(file_name))]
if (length(file_name) > 0)
{
ras = stack(file_name) * GLOB_MASK$ras.mask
ras.df = rasterToPoints(ras)
ras.df = as.data.frame(ras.df)
colnames(ras.df) = c("X", "Y", ye)
ras.df$ID.pixel = cellFromXY(GLOB_MASK$ras.mask, ras.df[, c("X", "Y")])
if (exists("ras.habitat"))
{
ras.df$HAB = extract(ras.habitat, ras.df[, c("X", "Y")])
} else
{
ras.df$HAB = "ALL"
}
tabSoil = ras.df[, c("ID.pixel", "X", "Y", "HAB", ye)]
} else
{
tabSoil = data.frame()
}
if (nrow(tabSoil) > 0 && ncol(tabSoil) > 0)
{
fwrite(tabSoil
, file = paste0(name.simulation
, "/RESULTS/POST_FATE_TABLE_PIXEL_evolution_soil_"
, basename(GLOB_DIR$dir.save)
, ".csv")
, row.names = FALSE)
} else
{
tabSoil = NA
doWriting.soil = FALSE
warning("No soil values were found! Please check.")
}
} else
{
tabSoil = NA
} ## END loop for soil
cat("\n")
## ZIP the raster saved -------------------------------------------------
.zip_ALL(folder_name = GLOB_DIR$dir.output.perPFG.allStrata, no_cores= opt.no_CPU)
if (GLOB_SIM$doLight) .zip_ALL(folder_name = GLOB_DIR$dir.output.light, no_cores = opt.no_CPU)
if (GLOB_SIM$doSoil) .zip_ALL(folder_name = GLOB_DIR$dir.output.soil, no_cores = opt.no_CPU)
cat("\n> Done!\n")
if(doWriting.abund || doWriting.light || doWriting.soil)
{
message(paste0("\n The output files \n"
, ifelse(doWriting.abund
, paste0(" > POST_FATE_TABLE_PIXEL_evolution_abundance_"
, basename(GLOB_DIR$dir.save)
, ".csv \n")
, "")
, ifelse(doWriting.light
, paste0(" > POST_FATE_TABLE_PIXEL_evolution_light_"
, basename(GLOB_DIR$dir.save)
, ".csv \n")
, "")
, ifelse(doWriting.soil
, paste0(" > POST_FATE_TABLE_PIXEL_evolution_soil_"
, basename(GLOB_DIR$dir.save)
, ".csv \n")
, "")
, "have been successfully created !\n"))
return(list(tab.abundance = tabAbund
, tab.light = tabLight
, tab.soil = tabSoil))
}
} ## END loop on abs.simulParams
names(res) = abs.simulParams
return(res)
}
leca-dev/RFate documentation built on Sept. 19, 2024, 6:09 a.m.
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Defines functions POST_FATE.temporalEvolution
Documented in POST_FATE.temporalEvolution
### HEADER #####################################################################
##' @title Create tables of pixel temporal evolution of PFG abundances (and
##' light and soil resources if activated) for a \code{FATE} simulation
##'
##' @name POST_FATE.temporalEvolution
##'
##' @author Maya Guéguen
##'
##' @description This script is designed to produce from 1 to 3 tables
##' containing pixel temporal evolution of PFG abundances, as well as light and
##' soil resources if those modules were activated, in a \code{FATE}
##' simulation.
##'
##'
##' @param name.simulation a \code{string} corresponding to the main directory
##' or simulation name of the \code{FATE} simulation
##' @param file.simulParam default \code{NULL}. \cr A \code{string}
##' corresponding to the name of a parameter file that will be contained into
##' the \code{PARAM_SIMUL} folder of the \code{FATE} simulation
##' @param no_years an \code{integer} corresponding to the number of simulation
##' years that will be used to extract PFG abundance / light / soil maps
##' @param opt.ras_habitat (\emph{optional}) default \code{NULL}. \cr
##' A \code{string} corresponding to the file name of a raster mask, with an
##' \code{integer} value within each pixel, corresponding to a specific habitat
##' @param opt.no_CPU (\emph{optional}) default \code{1}. \cr The number of
##' resources that can be used to parallelize the \code{unzip/zip} of raster
##' files, as well as the extraction of values from raster files
##'
##'
##' @details
##'
##' This function allows to obtain, for a specific \code{FATE} simulation and
##' a specific parameter file within this simulation, \strong{one to three
##' preanalytical tables that can then be used to create graphics}. \cr \cr
##'
##' For each PFG and each selected simulation year, raster maps are retrieved
##' from the results folder \code{ABUND_perPFG_allStrata} and unzipped.
##' Informations extracted lead to the production of one table before the maps
##' are compressed again :
##'
##' \itemize{
##' \item{the value of \strong{abundance for each Plant Functional Group}
##' for each selected simulation year(s) in every pixel in which the PFG is
##' present for at least one of the selected simulation year(s) \cr \cr
##' }
##' }
##'
##' \strong{If the light module was activated} (see
##' \code{\link{PRE_FATE.params_globalParameters}}), for each height stratum
##' and each selected simulation year, raster maps are retrieved from the
##' results folder \code{LIGHT} and unzipped.
##' Informations extracted lead to the production of one table before the maps
##' are compressed again :
##'
##' \itemize{
##' \item{the value of \strong{light resources for each height stratum} for
##' each selected simulation year(s) in every pixel \cr \cr
##' }
##' }
##'
##' \strong{If the soil module was activated} (see
##' \code{\link{PRE_FATE.params_globalParameters}}), for each selected
##' simulation year, raster maps are retrieved from the results folder
##' \code{SOIL} and unzipped.
##' Informations extracted lead to the production of one table before the maps
##' are compressed again :
##'
##' \itemize{
##' \item{the value of \strong{soil resources} for each selected simulation
##' year(s) in every pixel \cr \cr
##' }
##' }
##'
##' \strong{If a raster mask for habitat has been provided}, the tables will
##' also contain information about the pixel habitat. \cr \cr
##'
##'
##' \strong{These \code{.csv} files can then be used by other functions} :
##'
##' \itemize{
##' \item to produce graphics of temporal evolution of modelled abundances
##' and space occupancy at the \emph{whole area level} \cr (see
##' \code{\link{POST_FATE.graphic_evolutionCoverage}})
##' \item to produce graphics of temporal evolution of modelled abundances
##' and / or resources at the \emph{pixel level} \cr (see
##' \code{\link{POST_FATE.graphic_evolutionPixels}})
##' \item to produce graphics of temporal evolution of community composition
##' at the \emph{habitat level} \cr (see
##' \code{\link{POST_FATE.graphic_evolutionStability}})
##' }
##'
##'
##'
##' @return A \code{list} containing three \code{data.frame} objects with the
##' following columns :
##' \describe{
##' \item{\code{PFG}}{concerned plant functional group (for abundance)}
##' \item{\code{STRATUM}}{concerned height stratum (for LIGHT)}
##' \item{\code{ID.pixel}}{number of the concerned pixel}
##' \item{\code{X, Y}}{coordinates of the concerned pixel}
##' \item{\code{HAB}}{habitat of the concerned pixel}
##' \item{\emph{years}}{values of the corresponding object (abundance / LIGHT
##' / SOIL) for each selected simulation year(s) \cr \cr}
##' }
##'
##' One to three \file{POST_FATE_TABLE_PIXEL_evolution_[...].csv} files are created :
##' \describe{
##' \item{\file{abundance}}{always}
##' \item{\file{light}}{\emph{if light module was activated}}
##' \item{\file{soil}}{\emph{if soil module was activated}}
##' }
##'
##'
##' @keywords FATE, outputs, temporal evolution
##'
##' @seealso \code{\link{PRE_FATE.params_globalParameters}},
##' \code{\link{POST_FATE.graphic_evolutionCoverage}},
##' \code{\link{POST_FATE.graphic_evolutionPixels}},
##' \code{\link{POST_FATE.graphic_evolutionStability}}
##'
##'
##' @export
##'
##' @importFrom foreach foreach %do% %dopar%
##' @importFrom data.table rbindlist fwrite
##' @importFrom raster raster stack
##' rasterToPoints as.data.frame extract cellFromXY
## @importFrom doParallel registerDoParallel
##'
##'
## END OF HEADER ###############################################################
POST_FATE.temporalEvolution = function(
name.simulation
, file.simulParam = NULL
, no_years
, opt.ras_habitat = NULL
, opt.no_CPU = 1
){
#############################################################################
## CHECK parameter name.simulation
.testParam_existFolder(name.simulation, "PARAM_SIMUL/")
.testParam_existFolder(name.simulation, "RESULTS/")
.testParam_existFolder(name.simulation, "DATA/")
name.simulation = sub("/", "", name.simulation)
## CHECK parameter file.simulParam
abs.simulParams = .getParam_abs.simulParams(file.simulParam, name.simulation)
## CHECK parameter no_years
.testParam_notInteger.m("no_years", no_years)
## CHECK parameter opt.ras_habitat
if (!.testParam_notDef(opt.ras_habitat))
{
.testParam_notChar.m("opt.ras_habitat", opt.ras_habitat)
.testParam_existFile(opt.ras_habitat)
ras.habitat = raster(opt.ras_habitat)
}
cat("\n\n #------------------------------------------------------------#")
cat("\n # POST_FATE.temporalEvolution")
cat("\n #------------------------------------------------------------# \n")
#############################################################################
res = foreach (abs.simulParam = abs.simulParams) %do%
{
cat("\n+++++++\n")
cat("\n Simulation name : ", name.simulation)
cat("\n Simulation file : ", abs.simulParam)
cat("\n")
## Get results directories ------------------------------------------------
GLOB_DIR = .getGraphics_results(name.simulation = name.simulation
, abs.simulParam = abs.simulParam)
## Get number of PFGs -----------------------------------------------------
## Get PFG names ----------------------------------------------------------
GLOB_SIM = .getGraphics_PFG(name.simulation = name.simulation
, abs.simulParam = abs.simulParam)
## Get raster mask --------------------------------------------------------
GLOB_MASK = .getGraphics_mask(name.simulation = name.simulation
, abs.simulParam = abs.simulParam)
## Get habitat information ----------------------------------------------
if (exists("ras.habitat"))
{
ras.habitat = ras.habitat * GLOB_MASK$ras.mask
}
## Get list of arrays and extract years of simulation -------------------
raster.perPFG.allStrata = .getRasterNames(years = NULL, "allStrata", "ABUND", GLOB_DIR)
years = sapply(sub("Abund_YEAR_", "", raster.perPFG.allStrata)
, function(x) strsplit(as.character(x), "_")[[1]][1])
years = sort(unique(as.numeric(years)))
years = years[round(seq(1, length(years)
, length.out = min(no_years, length(years))))]
no_years = length(years)
cat("\n Selected years : ", years)
cat("\n Number of years : ", no_years)
cat("\n")
## UNZIP the raster saved -----------------------------------------------
raster.perPFG.allStrata = .getRasterNames(years, "allStrata", "ABUND", GLOB_DIR)
.unzip(folder_name = GLOB_DIR$dir.output.perPFG.allStrata
, list_files = raster.perPFG.allStrata
, no_cores = opt.no_CPU)
if (GLOB_SIM$doLight){
.unzip(folder_name = GLOB_DIR$dir.output.light
, list_files = list.files(path = GLOB_DIR$dir.output.light
, pattern = paste0("YEAR_", years, "_", collapse = "|"))
, no_cores = opt.no_CPU)
}
if (GLOB_SIM$doSoil){
.unzip(folder_name = GLOB_DIR$dir.output.soil
, list_files = list.files(path = GLOB_DIR$dir.output.soil
, pattern = paste0("YEAR_", years, collapse = "|"))
, no_cores = opt.no_CPU)
}
doWriting.abund = TRUE
doWriting.light = ifelse(GLOB_SIM$doLight, TRUE, FALSE)
doWriting.soil = ifelse(GLOB_SIM$doSoil, TRUE, FALSE)
## get the data inside the rasters --------------------------------------
cat("\n ---------- GETTING ABUNDANCE for pfg")
if (opt.no_CPU > 1)
{
if (.getOS() != "windows")
{
if (!isNamespaceLoaded("doParallel")) {
if(!requireNamespace('doParallel', quietly = TRUE)) stop("Package 'doParallel' not found")
}
doParallel::registerDoParallel(cores = opt.no_CPU)
} else
{
warning("Parallelisation with `foreach` is not available for Windows. Sorry.")
}
}
tabAbund.list = foreach (pfg = GLOB_SIM$PFG) %dopar%
{
cat(" ", pfg)
file_name = paste0(GLOB_DIR$dir.output.perPFG.allStrata,
"Abund_YEAR_",
years,
"_",
pfg,
"_STRATA_all")
if (length(which(file.exists(paste0(file_name, ".tif")))) > 0)
{
file_name = paste0(file_name, ".tif")
} else if (length(which(file.exists(paste0(file_name, ".img")))) > 0)
{
file_name = paste0(file_name, ".img")
} else if (length(which(file.exists(paste0(file_name, ".asc")))) > 0)
{
file_name = paste0(file_name, ".asc")
}
ye = years[which(file.exists(file_name))]
file_name = file_name[which(file.exists(file_name))]
if (length(file_name) > 0)
{
ras = stack(file_name) * GLOB_MASK$ras.mask
ras.df = rasterToPoints(ras)
ras.df = as.data.frame(ras.df)
colnames(ras.df) = c("X", "Y", ye)
ID.abund = rowSums(ras.df[, 3:ncol(ras.df), drop = FALSE])
ras.df = ras.df[which(ID.abund > 0), , drop = FALSE]
if (nrow(ras.df) > 0)
{
ras.df$ID.pixel = cellFromXY(GLOB_MASK$ras.mask, ras.df[, c("X", "Y")])
ras.df$PFG = pfg
if (exists("ras.habitat"))
{
ras.df$HAB = extract(ras.habitat, ras.df[, c("X", "Y")])
} else
{
ras.df$HAB = "ALL"
}
ras.df = ras.df[, c("PFG", "ID.pixel", "X", "Y", "HAB", ye)]
return(ras.df)
}
}
} ## END loop on PFG
cat("\n")
tabAbund = rbindlist(tabAbund.list, fill = TRUE)
tabAbund = as.data.frame(tabAbund, stringsAsFactors = FALSE)
if (nrow(tabAbund) > 0 && ncol(tabAbund) > 0)
{
fwrite(tabAbund
, file = paste0(name.simulation
, "/RESULTS/POST_FATE_TABLE_PIXEL_evolution_abundance_"
, basename(GLOB_DIR$dir.save)
, ".csv")
, row.names = FALSE)
} else
{
tabAbund = NA
doWriting.abund = FALSE
warning("No abundance values were found! Please check.")
}
## get the data inside the rasters --------------------------------------
if (GLOB_SIM$doLight)
{
cat("\n ---------- GETTING LIGHT for stratum")
tabLight.list = foreach (stra = c(1:GLOB_SIM$no_STRATA)-1) %dopar%
{
cat(" ", stra)
file_name = paste0(GLOB_DIR$dir.output.light
, "Light_Resources_YEAR_"
, years
, "_STRATA_"
, stra)
if (length(which(file.exists(paste0(file_name, ".tif")))) > 0)
{
file_name = paste0(file_name, ".tif")
} else if (length(which(file.exists(paste0(file_name, ".img")))) > 0)
{
file_name = paste0(file_name, ".img")
} else if (length(which(file.exists(paste0(file_name, ".asc")))) > 0)
{
file_name = paste0(file_name, ".asc")
}
ye = years[which(file.exists(file_name))]
file_name = file_name[which(file.exists(file_name))]
if (length(file_name) > 0)
{
ras = stack(file_name) * GLOB_MASK$ras.mask
ras.df = rasterToPoints(ras)
ras.df = as.data.frame(ras.df)
colnames(ras.df) = c("X", "Y", ye)
ras.df$ID.pixel = cellFromXY(GLOB_MASK$ras.mask, ras.df[, c("X", "Y")])
ras.df$STRATUM = stra
if (exists("ras.habitat"))
{
ras.df$HAB = extract(ras.habitat, ras.df[, c("X", "Y")])
} else
{
ras.df$HAB = "ALL"
}
ras.df = ras.df[, c("STRATUM", "ID.pixel", "X", "Y", "HAB", ye)]
return(ras.df)
}
} ## END loop on STRATUM
cat("\n")
tabLight = rbindlist(tabLight.list, fill = TRUE)
tabLight = as.data.frame(tabLight, stringsAsFactors = FALSE)
if (nrow(tabLight) > 0 && ncol(tabLight) > 0)
{
fwrite(tabLight
, file = paste0(name.simulation
, "/RESULTS/POST_FATE_TABLE_PIXEL_evolution_light_"
, basename(GLOB_DIR$dir.save)
, ".csv")
, row.names = FALSE)
} else
{
tabLight = NA
doWriting.light = FALSE
warning("No light values were found! Please check.")
}
} else
{
tabLight = NA
} ## END loop for light
## get the data inside the rasters --------------------------------------
if (GLOB_SIM$doSoil)
{
cat("\n ---------- GETTING SOIL")
file_name = paste0(GLOB_DIR$dir.output.soil,
"Soil_Resources_YEAR_",
years)
if (length(which(file.exists(paste0(file_name, ".tif")))) > 0)
{
file_name = paste0(file_name, ".tif")
} else if (length(which(file.exists(paste0(file_name, ".img")))) > 0)
{
file_name = paste0(file_name, ".img")
} else if (length(which(file.exists(paste0(file_name, ".asc")))) > 0)
{
file_name = paste0(file_name, ".asc")
}
ye = years[which(file.exists(file_name))]
file_name = file_name[which(file.exists(file_name))]
if (length(file_name) > 0)
{
ras = stack(file_name) * GLOB_MASK$ras.mask
ras.df = rasterToPoints(ras)
ras.df = as.data.frame(ras.df)
colnames(ras.df) = c("X", "Y", ye)
ras.df$ID.pixel = cellFromXY(GLOB_MASK$ras.mask, ras.df[, c("X", "Y")])
if (exists("ras.habitat"))
{
ras.df$HAB = extract(ras.habitat, ras.df[, c("X", "Y")])
} else
{
ras.df$HAB = "ALL"
}
tabSoil = ras.df[, c("ID.pixel", "X", "Y", "HAB", ye)]
} else
{
tabSoil = data.frame()
}
if (nrow(tabSoil) > 0 && ncol(tabSoil) > 0)
{
fwrite(tabSoil
, file = paste0(name.simulation
, "/RESULTS/POST_FATE_TABLE_PIXEL_evolution_soil_"
, basename(GLOB_DIR$dir.save)
, ".csv")
, row.names = FALSE)
} else
{
tabSoil = NA
doWriting.soil = FALSE
warning("No soil values were found! Please check.")
}
} else
{
tabSoil = NA
} ## END loop for soil
cat("\n")
## ZIP the raster saved -------------------------------------------------
.zip_ALL(folder_name = GLOB_DIR$dir.output.perPFG.allStrata, no_cores= opt.no_CPU)
if (GLOB_SIM$doLight) .zip_ALL(folder_name = GLOB_DIR$dir.output.light, no_cores = opt.no_CPU)
if (GLOB_SIM$doSoil) .zip_ALL(folder_name = GLOB_DIR$dir.output.soil, no_cores = opt.no_CPU)
cat("\n> Done!\n")
if(doWriting.abund || doWriting.light || doWriting.soil)
{
message(paste0("\n The output files \n"
, ifelse(doWriting.abund
, paste0(" > POST_FATE_TABLE_PIXEL_evolution_abundance_"
, basename(GLOB_DIR$dir.save)
, ".csv \n")
, "")
, ifelse(doWriting.light
, paste0(" > POST_FATE_TABLE_PIXEL_evolution_light_"
, basename(GLOB_DIR$dir.save)
, ".csv \n")
, "")
, ifelse(doWriting.soil
, paste0(" > POST_FATE_TABLE_PIXEL_evolution_soil_"
, basename(GLOB_DIR$dir.save)
, ".csv \n")
, "")
, "have been successfully created !\n"))
return(list(tab.abundance = tabAbund
, tab.light = tabLight
, tab.soil = tabSoil))
}
} ## END loop on abs.simulParams
names(res) = abs.simulParams
return(res)
}
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