R/PRE_FATE.params_simulParameters.R
In MayaGueguen/RFate: Vegetation modelling with the FATE model
Defines functions
PRE_FATE.params_simulParameters
Documented in
PRE_FATE.params_simulParameters
### HEADER #####################################################################
##' @title Create \emph{Simul_parameters} parameter file for a \code{FATE}
##' simulation
##'
##' @name PRE_FATE.params_simulParameters
##'
##' @author Maya Guéguen
##'
##' @description This script is designed to create one (or several) parameter
##' file containing \code{PARAMETER FILENAMES} used in \code{FATE} model.
##'
##' @param name.simulation a \code{string} corresponding to the main directory
##' or simulation name of the \code{FATE} simulation
##' @param name.MASK a \code{string} corresponding to the file name of a raster
##' mask, with either \code{0} or \code{1} within each pixel, \code{1}
##' corresponding to the cells of the studied area in which the succession
##' (core) module of the \code{FATE} simulation will take place (see
##' \href{PRE_FATE.params_globalParameters.html#details}{\code{PRE_FATE.params_globalParameters}})
##' @param name.SAVED_STATE (\emph{optional}) \cr a \code{string} corresponding
##' to the file name of a \code{FATE} object, obtained from a previous
##' simulation and from which to restart this new simulation
##' @param name.DIST (\emph{optional}) \cr a \code{string} corresponding to the
##' file name of a raster mask, with either \code{0} or \code{1} within each
##' pixel, \code{1} corresponding to the cells of the studied area in which the
##' disturbance module of the \code{FATE} simulation will take place (see
##' \href{PRE_FATE.params_globalParameters.html#details}{\code{PRE_FATE.params_globalParameters}})
##' @param name.DROUGHT (\emph{optional}) \cr a \code{string} corresponding to
##' the name of a raster file, with a \code{numeric} value within each pixel
##' corresponding to the drought intensity experienced by this pixel through
##' the drought (or fire) disturbance module of the \code{FATE} simulation (see
##' \href{PRE_FATE.params_globalParameters.html#details}{\code{PRE_FATE.params_globalParameters}})
##' @param name.FIRE (\emph{optional}) \cr a \code{string} corresponding to the
##' file name of a raster mask, with either \code{0} or \code{1} within each
##' pixel, \code{1} corresponding to the cells of the studied area in which the
##' fire disturbance module of the \code{FATE} simulation will take place (see
##' \href{PRE_FATE.params_globalParameters.html#details}{\code{PRE_FATE.params_globalParameters}})
##' @param name.ELEVATION (\emph{optional}) \cr a \code{string} corresponding to
##' the name of a raster file, with a \code{numeric} value within each pixel
##' corresponding to the elevation of this pixel and used by the fire
##' disturbance module of the \code{FATE} simulation (see
##' \href{PRE_FATE.params_globalParameters.html#details}{\code{PRE_FATE.params_globalParameters}})
##' @param name.SLOPE (\emph{optional}) \cr a \code{string} corresponding to
##' the name of a raster file, with a \code{numeric} value within each pixel
##' corresponding to the slope of this pixel and used by the fire
##' disturbance module of the \code{FATE} simulation (see
##' \href{PRE_FATE.params_globalParameters.html#details}{\code{PRE_FATE.params_globalParameters}})
##' @param opt.global.name (\emph{optional}) \cr a \code{string} corresponding
##' to the name of the global parameter file in the folder
##' \code{name.simulation/DATA/GLOBAL_PARAMETERS/} that will be used to build
##' the simulation parameter file
##' @param opt.folder.name (\emph{optional}) \cr a \code{string} corresponding
##' to the name of the folder in each \code{name.simulation/DATA/PFGS/module/}
##' from which PFG file names will be extracted to build the simulation
##' parameter file
##'
##'
##'
##' @details
##'
##' The \code{FATE} software takes only one input parameter : a file
##' containing links to other files containing all the parameters and data
##' needed by the program to run.
##'
##'
##' \describe{
##' \item{GLOBAL_PARAMS}{file where parameters related to the simulation
##' definition are referred (e.g. number of PFG involved, number of height
##' strata, simulation duration, computer resources, modules loaded, etc) \cr
##' (see \code{\link{PRE_FATE.params_globalParameters}}) \cr \cr
##' }
##' \item{SAVING_DIR}{directory where simulation outputs will be stored}
##' \item{SAVED_STATE (\emph{optional})}{file containing the results of a
##' previous \code{FATE} simulation from which to restart this new simulation
##' \cr }
##' \item{SAVING_YEARS_ \cr ARRAYS (\emph{optional})}{file containing the
##' years for which simulation maps will be saved \cr
##' (see \code{\link{PRE_FATE.params_savingYears}})
##' }
##' \item{SAVING_YEARS_ \cr OBJECTS (\emph{optional})}{file containing the
##' years for which simulation outputs will be saved \cr
##' (see \code{\link{PRE_FATE.params_savingYears}}) \cr \cr
##' }
##' \item{MASK}{raster mask that will define the study area}
##' \item{MASK_CHANGEMASK_YEARS \cr (\emph{optional})}{file containing the years
##' to change rasters for the succession module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})
##' }
##' \item{MASK_CHANGEMASK_FILES \cr (\emph{optional})}{file containing the files
##' to change rasters for the succession module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}}) \cr \cr
##' }
##' \item{PFG_PARAMS_ \cr LIFE_HISTORY}{PFG life history related parameters
##' (one by PFG) \cr
##' (see \code{\link{PRE_FATE.params_PFGsuccession}}) \cr \cr
##' }
##' \item{PFG_PARAMS_ \cr LIGHT (\emph{optional})}{PFG light preferences and
##' tolerance related parameters (one by PFG) \cr
##' (see \code{\link{PRE_FATE.params_PFGlight}}) \cr \cr
##' }
##' \item{PFG_PARAMS_ \cr SOIL (\emph{optional})}{PFG soil contribution and
##' tolerance related parameters (one by PFG) \cr
##' (see \code{\link{PRE_FATE.params_PFGsoil}}) \cr \cr
##' }
##' \item{PFG_PARAMS_ \cr DISPERSAL (\emph{optional})}{PFG dispersal
##' capacity related parameters (one by PFG) \cr
##' (see \code{\link{PRE_FATE.params_PFGdispersal}}) \cr \cr
##' }
##' \item{PFG_MASK_HABSUIT \cr (\emph{optional})}{raster masks (one by PFG)
##' containing PFG habitat suitability for the study area}
##' \item{HABSUIT_CHANGEMASK_YEARS \cr (\emph{optional})}{file containing the years
##' to change rasters for the habitat suitability module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})
##' }
##' \item{HABSUIT_CHANGEMASK_FILES \cr (\emph{optional})}{file containing the files
##' to change rasters for the habitat suitability module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}}) \cr \cr
##' }
##' \item{PFG_PARAMS_ \cr DISTURBANCES (\emph{optional})}{PFG disturbance
##' related parameters in terms of resprouting and mortality (one by PFG) \cr
##' (see \code{\link{PRE_FATE.params_PFGdisturbance}})
##' }
##' \item{DIST_MASK \cr (\emph{optional})}{raster masks that will define the
##' disturbance areas}
##' \item{DIST_CHANGEMASK_YEARS \cr (\emph{optional})}{file containing the years
##' to change rasters for the disturbance module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})
##' }
##' \item{DIST_CHANGEMASK_FILES \cr (\emph{optional})}{file containing the files
##' to change rasters for the disturbance module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}}) \cr \cr
##' }
##' \item{PFG_PARAMS_DROUGHT \cr (\emph{optional})}{PFG drought disturbance
##' related parameters in terms of resprouting and mortality (one by PFG) \cr
##' (see \code{\link{PRE_FATE.params_PFGdrought}})}
##' \item{DROUGHT_MASK \cr (\emph{optional})}{raster mask that will define the
##' drought intensity of the area}
##' \item{DROUGHT_CHANGEMASK_YEARS \cr (\emph{optional})}{file containing the
##' years to change rasters for the drought disturbances module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})}
##' \item{DROUGHT_CHANGEMASK_FILES \cr (\emph{optional})}{file containing the
##' files to change rasters for the drought disturbances module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}}) \cr \cr}
##' \item{PFG_MASK_ALIENS \cr (\emph{optional})}{raster masks (one by alien)
##' containing alien introduction zones for the study area}
##' \item{ALIENS_CHANGEMASK_YEARS \cr (\emph{optional})}{file containing the
##' years to change rasters for the aliens introduction module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})}
##' \item{ALIENS_CHANGEMASK_FILES \cr (\emph{optional})}{file containing the
##' files to change rasters for the aliens introduction module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})}
##' \item{ALIENS_CHANGEFREQ_YEARS \cr (\emph{optional})}{file containing the
##' years to change frequencies for the aliens introduction module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})}
##' \item{ALIENS_CHANGEFREQ_FILES \cr (\emph{optional})}{file containing the
##' files to change frequencies for the aliens introduction module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}}) \cr \cr}
##' \item{PFG_PARAMS_FIRE \cr (\emph{optional})}{PFG fire disturbance
##' related parameters in terms of resprouting and mortality (one by PFG) \cr
##' (see \code{\link{PRE_FATE.params_PFGdisturbance}})}
##' \item{FIRE_MASK \cr (\emph{optional})}{raster mask that will define the
##' fire disturbance areas}
##' \item{FIRE_CHANGEMASK_YEARS \cr (\emph{optional})}{file containing the
##' years to change rasters for the fire disturbances module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})}
##' \item{FIRE_CHANGEMASK_FILES \cr (\emph{optional})}{file containing the
##' files to change rasters for the fire disturbances module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})}
##' \item{FIRE_CHANGEFREQ_YEARS \cr (\emph{optional})}{file containing the
##' years to change frequencies for the fire disturbances module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})}
##' \item{FIRE_CHANGEFREQ_FILES \cr (\emph{optional})}{file containing the
##' files to change frequencies for the fire disturbances module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})}
##' \item{ELEVATION_MASK \cr (\emph{optional})}{raster mask that will define
##' the elevation of the area}
##' \item{SLOPE_MASK \cr (\emph{optional})}{raster mask that will define the
##' slope of the area}
##' }
##'
##'
##'
##' @note
##'
##' \itemize{
##' \item The function produces links to files that are \strong{NOT absolute
##' paths BUT relative ones}. \cr
##' \emph{When relative paths are used}, the user should be careful of the
##' folder from which the simulation is launched. \cr
##' \emph{A function allows to transform these relative paths into absolute
##' ones. (see examples of \code{\link{.setPattern}})}.
##' \item \strong{The order of files matters!} \cr
##' For instance the first link below \code{--PFG_PARAMS_LIFE_HISTORY--} flag
##' (e.g. \emph{PFG Albert}) has to match with the first item below the
##' \code{--PFG_PARAMS_DISPERSAL--} flag (must be \emph{PFG Albert} too).
##' }
##'
##'
##'
##'
##' @return A \code{.txt} file into the \code{name.simulation/PARAM_SIMUL/}
##' directory with the following parameters :
##'
##' \itemize{
##' \item \strong{--GLOBAL_PARAMS--}
##' \item \strong{--SAVING_DIR--}
##' \itemize{
##' \item --SAVED_STATE-- (\emph{optional})
##' \item --SAVING_YEARS_MAPS-- (\emph{optional})
##' \item --SAVING_YEARS_OBJECTS-- (\emph{optional})
##' }
##' \item \strong{--MASK--}
##' \itemize{
##' \item --MASK_CHANGEMASK_YEARS-- (\emph{optional})
##' \item --MASK_CHANGEMASK_FILES-- (\emph{optional})
##' }
##' \item \strong{--PFG_PARAMS_LIFE_HISTORY--}
##' \itemize{
##' \item --PFG_PARAMS_LIGHT-- (\emph{optional})
##' \item --PFG_PARAMS_SOIL-- (\emph{optional})
##' \item --PFG_PARAMS_DISPERSAL-- (\emph{optional})
##' \item --PFG_MASK_HABSUIT-- (\emph{optional})
##' \item --HABSUIT_CHANGEMASK_YEARS-- (\emph{optional})
##' \item --HABSUIT_CHANGEMASK_FILES-- (\emph{optional})
##' \item --PFG_PARAMS_DISTURBANCES-- (\emph{optional})
##' \item --DIST_MASK-- (\emph{optional})
##' \item --DIST_CHANGEMASK_YEARS-- (\emph{optional})
##' \item --DIST_CHANGEMASK_FILES-- (\emph{optional})
##' \item --PFG_PARAMS_DROUGHT-- (\emph{optional})
##' \item --DROUGHT_MASK-- (\emph{optional})
##' \item --DROUGHT_CHANGEMASK_YEARS-- (\emph{optional})
##' \item --DROUGHT_CHANGEMASK_FILES-- (\emph{optional})
##' \item --PFG_MASK_ALIENS-- (\emph{optional})
##' \item --ALIENS_CHANGEMASK_YEARS-- (\emph{optional})
##' \item --ALIENS_CHANGEMASK_FILES-- (\emph{optional})
##' \item --ALIENS_CHANGEFREQ_YEARS-- (\emph{optional})
##' \item --ALIENS_CHANGEFREQ_FILES-- (\emph{optional})
##' \item --PFG_PARAMS_FIRE-- (\emph{optional})
##' \item --FIRE_MASK-- (\emph{optional})
##' \item --FIRE_CHANGEMASK_YEARS-- (\emph{optional})
##' \item --FIRE_CHANGEMASK_FILES-- (\emph{optional})
##' \item --FIRE_CHANGEFREQ_YEARS-- (\emph{optional})
##' \item --FIRE_CHANGEFREQ_FILES-- (\emph{optional})
##' \item --ELEVATION_MASK-- (\emph{optional})
##' \item --SLOPE_MASK-- (\emph{optional})
##' }
##' \item \strong{--END_OF_FILE--}
##' }
##'
##'
##' @keywords FATE, simulation
##'
##' @seealso \code{\link{PRE_FATE.skeletonDirectory}},
##' \code{\link{PRE_FATE.params_globalParameters}},
##' \code{\link{PRE_FATE.params_PFGsuccession}},
##' \code{\link{PRE_FATE.params_PFGlight}},
##' \code{\link{PRE_FATE.params_PFGsoil}},
##' \code{\link{PRE_FATE.params_PFGdispersal}},
##' \code{\link{PRE_FATE.params_PFGdisturbance}},
##' \code{\link{PRE_FATE.params_PFGdrought}},
##' \code{\link{PRE_FATE.params_savingYears}},
##' \code{\link{PRE_FATE.params_changingYears}},
##' \code{\link{.setPattern}}
##'
##' @examples
##'
##'
##' ## ----------------------------------------------------------------------------------------- ##
##'
##' ## Load example data
##'
##' @export
##'
##' @importFrom foreach foreach %do%
##'
## END OF HEADER ###############################################################
PRE_FATE.params_simulParameters = function(
name.simulation
, name.MASK
, name.SAVED_STATE = NULL
, name.DIST = NULL
, name.DROUGHT = NULL
, name.FIRE = NULL
, name.ELEVATION = NULL
, name.SLOPE = NULL
, opt.global.name = NULL
, opt.folder.name = NULL
){
#############################################################################
.testParam_existFolder(name.simulation, "PARAM_SIMUL/")
.testParam_existFolder(name.simulation, "DATA/GLOBAL_PARAMETERS/")
.testParam_existFolder(name.simulation, "DATA/SAVE/")
.testParam_existFolder(name.simulation, "DATA/SCENARIO/")
.testParam_existFolder(name.simulation, "DATA/MASK/")
.testParam_existFolder(name.simulation, "DATA/PFGS/SUCC/")
.testParam_existFolder(name.simulation, "RESULTS/")
.testParam_notChar.m("name.MASK", name.MASK)
.testParam_existFile(paste0(name.simulation, "/DATA/MASK/", name.MASK))
## CHECK parameter opt.global.name
opt.global.name = .getParam_opt.folder.name(opt.global.name
, basename(opt.global.name)
, create.dir = FALSE)
opt.global.name = sub("/$", "", opt.global.name)
## CHECK parameter opt.folder.name
opt.folder.name = .getParam_opt.folder.name(opt.folder.name
, paste0(opt.folder.name, "/")
, create.dir = FALSE)
type.changing1 = c("MASK", "HABSUIT", "DIST", "DROUGHT", "ALIENS", "FIRE") #, "ALIENS_F")
type.changing2 = c("HABSUIT", "ALIENS")
#############################################################################
## Get the name(s) of global parameter file(s) that will
## be used to create the simulation parameter file(s)
if (opt.global.name == "")
{
files.GLOBAL = list.files(path = paste0(name.simulation
, "/DATA/GLOBAL_PARAMETERS")
, pattern = "^Global_parameters.*.txt"
, full.names = TRUE)
} else
{
files.GLOBAL = paste0(name.simulation
, "/DATA/GLOBAL_PARAMETERS/"
, opt.global.name)
}
if (length(files.GLOBAL) == 0)
{
stop(paste0("Wrong number of files!\n There is no adequate file "
, "(`.txt` file starting with `Global_parameters`) "
, "into the DATA/GLOBAL_PARAMETERS/ folder"))
}
#############################################################################
## Get the name(s) of SAVE directory
dirs.SAVE = list.dirs(path = paste0(name.simulation, "/DATA/SAVE")
, full.names = FALSE
, recursive = FALSE)
if (length(dirs.SAVE) > 0)
{
dirs.SAVE = paste0(name.simulation, "/DATA/SAVE/", dirs.SAVE)
} else
{
dirs.SAVE = paste0(name.simulation, "/DATA/SAVE")
}
#############################################################################
## Get the name(s) of SCENARIO directory
dirs.SCENARIO = list.dirs(path = paste0(name.simulation, "/DATA/SCENARIO")
, full.names = FALSE
, recursive = FALSE)
if (length(dirs.SCENARIO) > 0)
{
dirs.SCENARIO = paste0(name.simulation, "/DATA/SCENARIO/", dirs.SCENARIO)
} else
{
dirs.SCENARIO = paste0(name.simulation, "/DATA/SCENARIO")
}
warn.messages = list()
for (ty in type.changing1)
{
assign(x = paste0("dirs.SCENARIO.", ty), value = vector())
for (di in dirs.SCENARIO)
{
files.ty = list.files(path = di
, pattern = paste0("^", ty, "_changingmask_years")
, full.names = TRUE)
if (length(files.ty) > 0)
{
eval(parse(text = paste0("dirs.SCENARIO.", ty
, " = c(dirs.SCENARIO.", ty
, ", di)")))
} else
{
warn.messages[[length(warn.messages) +1]] = c(ty, di)
# warning(paste0("There is no adequate file (`.txt` file starting with `"
# , ty, "_changingmask_years`) "
# , "into the folder ", di))
}
}
}
if (length(warn.messages) > 0)
{
warning(paste0("There is no adequate file(s) into some folder(s) : \n"
, paste0(" > ", sapply(warn.messages, function(x) x[1])
, "_changingmask_years[...].txt (folder "
, sapply(warn.messages, function(x) x[2]), ") \n"
, collapse = "")))
}
#############################################################################
## Get the name(s) of HABSUIT / ALIENS directory
for (ty in type.changing2)
{
name.dir = paste0(name.simulation, "/DATA/PFGS/", ty)
dirs.SCE = list.dirs(path = name.dir
, full.names = FALSE
, recursive = FALSE)
if (length(dirs.SCE) > 0)
{
dirs.SCE = paste0(name.dir, "/", dirs.SCE)
} else
{
dirs.SCE = name.dir
}
assign(x = paste0("dirs.", ty), value = vector())
for (di in dirs.SCE)
{
files.di = list.files(path = di, full.names = TRUE)
if (length(files.di) > 0)
{
eval(parse(text = paste0("dirs.", ty, " = c(dirs.", ty, ", di)")))
}
}
}
#############################################################################
#############################################################################
## Combine the names found (global parameters, SAVE directory,
## SCENARIO directory, HABSUIT directory)
sce.mask = sce.habsuit = sce.dist = sce.drought = sce.aliens = sce.fire = 0
ras.habsuit = ras.aliens = 0
if (length(dirs.SCENARIO.MASK) > 0) sce.mask = 1:length(dirs.SCENARIO.MASK)
if (length(dirs.SCENARIO.HABSUIT) > 0) sce.habsuit = 1:length(dirs.SCENARIO.HABSUIT)
if (length(dirs.SCENARIO.DIST) > 0) sce.dist = 1:length(dirs.SCENARIO.DIST)
if (length(dirs.SCENARIO.DROUGHT) > 0) sce.drought = 1:length(dirs.SCENARIO.DROUGHT)
if (length(dirs.SCENARIO.ALIENS) > 0) sce.aliens = 1:length(dirs.SCENARIO.ALIENS)
if (length(dirs.SCENARIO.FIRE) > 0) sce.fire = 1:length(dirs.SCENARIO.FIRE)
if (length(dirs.HABSUIT) > 0) ras.habsuit = 1:length(dirs.HABSUIT)
if (length(dirs.ALIENS) > 0) ras.aliens = 1:length(dirs.ALIENS)
PARAMS.combi = expand.grid(GLOBAL = 1:length(files.GLOBAL)
, SAVE = 1:length(dirs.SAVE)
, SCENARIO.MASK = sce.mask
, SCENARIO.HABSUIT = sce.habsuit
, SCENARIO.DIST = sce.dist
, SCENARIO.DROUGHT = sce.drought
, SCENARIO.ALIENS = sce.aliens
, SCENARIO.FIRE = sce.fire
, PFG.HABSUIT = ras.habsuit
, PFG.ALIENS = ras.aliens)
#############################################################################
#############################################################################
## Build a simulation parameter file for each combination found
for (i in 1:nrow(PARAMS.combi))
{
params.combi = data.frame(GLOBAL = files.GLOBAL[PARAMS.combi$GLOBAL[i]]
, MASK = paste0(name.simulation
, "/DATA/MASK/"
, name.MASK)
, stringsAsFactors = FALSE)
names.params.combi = c("--GLOBAL_PARAMS--", "--MASK--")
if (!is.null(name.SAVED_STATE) && nchar(name.SAVED_STATE) > 0)
{
.testParam_existFile(name.SAVED_STATE)
params.combi[["SAVED_STATE"]] = name.SAVED_STATE
names.params.combi = c(names.params.combi, "--SAVED_STATE--")
}
#############################################################################
di = dirs.SAVE[PARAMS.combi$SAVE[i]]
di.opt = data.frame(pat = c("SAVE_YEARS_maps", "SAVE_YEARS_objects")
, nam = c("SAVE.maps", "SAVE.obj")
, param = c("SAVING_YEARS_MAPS", "SAVING_YEARS_OBJECTS")
, stringsAsFactors = FALSE)
warn.messages = list()
for (ii in 1:nrow(di.opt))
{
files.found = list.files(path = di
, pattern = paste0("^", di.opt$pat[ii])
, full.names = TRUE)
if (length(files.found) == 0)
{
warn.messages[[length(warn.messages) +1]] = c(di.opt$pat[ii], di)
# warning(paste0("There is no adequate file (`.txt` file starting with `"
# , di.opt$pat[ii], "`) "
# , "into the folder ", di))
} else if (length(files.found) == 1)
{
params.combi[[di.opt$nam[ii]]] = files.found
names.params.combi = c(names.params.combi
, paste0("--", di.opt$param[ii], "--"))
} else
{
stop(paste0("There is too many adequate files (`.txt` file starting with `"
, di.opt$pat[ii], "`) "
, "into the folder ", di))
}
}
if (length(warn.messages) > 0)
{
warning(paste0("There is no adequate file(s) into some folder(s) : \n"
, paste0(" > ", sapply(warn.messages, function(x) x[1])
, "[...].txt (folder "
, sapply(warn.messages, function(x) x[2]), ") \n"
, collapse = "")))
}
#############################################################################
warn.messages = list()
for (ty in type.changing1)
{
if (PARAMS.combi[, paste0("SCENARIO.", ty)][i] > 0)
{
eval(parse(text = paste0("di = dirs.SCENARIO.", ty
, "[PARAMS.combi$SCENARIO.", ty, "[i]]")))
## Changing years
files.SCE.years = list.files(path = di
, pattern = paste0("^", ty, "_changingmask_years")
, full.names = TRUE)
if (length(files.SCE.years) == 1)
{
params.combi[[paste0("SCENARIO.", ty)]] = files.SCE.years
names.params.combi = c(names.params.combi
, paste0("--", ty, "_CHANGEMASK_YEARS--"))
} else
{
stop(paste0("There is too many adequate files (`.txt` file starting with `"
, ty, "_changingmask_years`) "
, "into the folder ", di))
}
## Changing files
files.SCE.masks = list.files(path = di
, pattern = paste0("^", ty, "_changingmask_files")
, full.names = TRUE)
if (length(files.SCE.masks) == 0)
{
warn.messages[[length(warn.messages) +1]] = c(ty, di)
# warning(paste0("There is no adequate file (`.txt` file starting with `"
# , ty, "_changingmask_files`) "
# , "into the folder ", di))
} else if (length(files.SCE.masks) > 0)
{
assign(x = paste0("SCENARIO.", ty), value = files.SCE.masks)
}
}
}
if (length(warn.messages) > 0)
{
warning(paste0("There is no adequate file(s) into some folder(s) : \n"
, paste0(" > ", sapply(warn.messages, function(x) x[1])
, "_changingmask_files[...].txt (folder "
, sapply(warn.messages, function(x) x[2]), ") \n"
, collapse = "")))
}
#############################################################################
globi = as.character(files.GLOBAL[PARAMS.combi$GLOBAL[i]])
### -------------------------------------------------------------------- ###
no_PFG = .getParam(params.lines = globi
, flag = "NO_PFG"
, flag.split = " "
, is.num = TRUE)
no_PFG = as.numeric(no_PFG)
do.SUCC = 1
do.LIGHT = .getParam(params.lines = globi
, flag = "DO_LIGHT_COMPETITION"
, flag.split = " "
, is.num = TRUE)
do.SOIL = .getParam(params.lines = globi
, flag = "DO_SOIL_COMPETITION"
, flag.split = " "
, is.num = TRUE)
do.DISP = .getParam(params.lines = globi
, flag = "DO_DISPERSAL"
, flag.split = " "
, is.num = TRUE)
do.HABSUIT = .getParam(params.lines = globi
, flag = "DO_HAB_SUITABILITY"
, flag.split = " "
, is.num = TRUE)
do.DIST = .getParam(params.lines = globi
, flag = "DO_DISTURBANCES"
, flag.split = " "
, is.num = TRUE)
do.DROUGHT = .getParam(params.lines = globi
, flag = "DO_DROUGHT_DISTURBANCE"
, flag.split = " "
, is.num = TRUE)
do.ALIENS = .getParam(params.lines = globi
, flag = "DO_ALIENS_INTRODUCTION"
, flag.split = " "
, is.num = TRUE)
do.FIRE = .getParam(params.lines = globi
, flag = "DO_FIRE_DISTURBANCE"
, flag.split = " "
, is.num = TRUE)
### -------------------------------------------------------------------- ###
MODULES = c("SUCC", "LIGHT", "SOIL", "DISP", "DIST", "DROUGHT", "FIRE")
for (mod in MODULES)
{
if (get(paste0("do.", mod)))
{
.testParam_existFolder(name.simulation, paste0("DATA/PFGS/", mod, "/"))
name.dir = paste0(name.simulation, "/DATA/PFGS/", mod)
## Get folders
if (opt.folder.name != "")
{
dirs.mod = paste0(name.dir, "/", opt.folder.name)
}
if (opt.folder.name == "" || !dir.exists(dirs.mod))
{
dirs.mod = list.dirs(path = name.dir
, full.names = FALSE
, recursive = FALSE)
if (length(dirs.mod) > 0)
{
dirs.mod = paste0(name.dir, "/", dirs.mod)
} else
{
dirs.mod = name.dir
}
}
## Get files
files.PFG = foreach (di.mod = dirs.mod, .combine = "cbind") %do%
{
files.PFG = list.files(path = di.mod
, pattern = paste0("^", mod)
, full.names = TRUE)
if (length(files.PFG) != no_PFG)
{
stop(paste0("There is not the same number of files "
, "(`.txt` file starting with `", mod, "`) "
, "into the ", di.mod, "/ folder as the number of PFG "
, "indicated into the file "
, globi))
}
return(data.frame(files.PFG, stringsAsFactors = FALSE))
}
assign(x = paste0("files.PFG.", mod), value = files.PFG)
assign(x = paste0("no_files.PFG.", mod)
, value = ncol(get(paste0("files.PFG.", mod))))
} else
{
assign(x = paste0("files.PFG.", mod), value = "")
assign(x = paste0("no_files.PFG.", mod), value = 0)
}
}
no_files.PFG = sapply(MODULES, function(x) get(paste0("no_files.PFG.", x)))
no_files.PFG = no_files.PFG[which(no_files.PFG > 0)]
if (length(unique(no_files.PFG)) > 1)
{
PFG.combi = expand.grid(sapply(no_files.PFG, function(x) 1:x))
} else
{
PFG.combi = matrix(rep(0, length(no_files.PFG) * unique(no_files.PFG))
, ncol = length(no_files.PFG))
PFG.combi = as.data.frame(PFG.combi)
colnames(PFG.combi) = names(no_files.PFG)
for (mod in 1:length(no_files.PFG))
{
PFG.combi[[names(no_files.PFG)[mod]]] = 1:no_files.PFG[mod]
}
}
### -------------------------------------------------------------------- ###
MODULES = c("DIST", "DROUGHT", "FIRE")
for (mod in MODULES)
{
if (get(paste0("do.", mod)))
{
.testParam_notChar.m(paste0("name.", mod), get(paste0("name.", mod)))
.testParam_existFile(paste0(name.simulation
, "/DATA/MASK/"
, get(paste0("name.", mod))))
assign(x = paste0("no.", mod)
, value = .getParam(params.lines = globi
, flag = paste0(mod, "_NO")
, flag.split = " "
, is.num = TRUE))
} else
{
assign(x = paste0("no.", mod), value = 0)
}
}
### -------------------------------------------------------------------- ###
MODULES = c("HABSUIT", "ALIENS")
for (mod in MODULES)
{
if (get(paste0("do.", mod)))
{
.testParam_existFolder(name.simulation, paste0("DATA/PFGS/", mod, "/"))
if (PARAMS.combi[[paste0("PFG.", mod)]][i] > 0)
{
eval(parse(text = paste0("di = dirs.", mod
, "[PARAMS.combi$PFG.", mod, "[i]]")))
assign(x = paste0("files.PFG.", mod)
, value = list.files(path = di, full.names = TRUE))
if (length(get(paste0("files.PFG.", mod))) != no_PFG)
{
warning(paste0("There is not the same number of files into the "
, "DATA/PFGS/", mod, "/ folder as the number of PFG "
, "indicated into the file "
, globi))
}
} else
{
assign(x = paste0("files.PFG.", mod), value = "")
}
} else
{
assign(x = paste0("files.PFG.", mod), value = "")
}
}
#############################################################################
FILE_NUMBER = 0
if (nrow(PARAMS.combi) == 1 && nrow(PFG.combi) == 1)
{
FILE_NUMBER = length(list.files(path = paste0(name.simulation, "/PARAM_SIMUL/")
, pattern = "^Simul_parameters_V"
, recursive = FALSE
, include.dirs = FALSE)) + 1
}
#############################################################################
#############################################################################
for (ii in 1:nrow(PFG.combi))
{
params.list = lapply(1:ncol(params.combi)
, function(x) { as.character(params.combi[, x]) })
names.params.list = names.params.combi
if (FILE_NUMBER == 0)
{
params.list = c(params.list, list(paste0(name.simulation
, "/RESULTS/SIMUL_V"
, i, ".", ii)))
} else
{
params.list = c(params.list, list(paste0(name.simulation
, "/RESULTS/SIMUL_V"
, FILE_NUMBER)))
}
names.params.list = c(names.params.list, "--SAVING_DIR--")
params.list = c(params.list, list(files.PFG.SUCC[, PFG.combi$SUCC[ii]]))
names.params.list = c(names.params.list, "--PFG_PARAMS_LIFE_HISTORY--")
if (exists("SCENARIO.MASK"))
{
params.list = c(params.list, list(SCENARIO.MASK))
names.params.list = c(names.params.list, "--MASK_CHANGEMASK_FILES--")
}
if (do.LIGHT)
{
params.list = c(params.list, list(files.PFG.LIGHT[, PFG.combi$LIGHT[ii]]))
names.params.list = c(names.params.list, "--PFG_PARAMS_LIGHT--")
}
if (do.SOIL)
{
params.list = c(params.list, list(files.PFG.SOIL[, PFG.combi$SOIL[ii]]))
names.params.list = c(names.params.list, "--PFG_PARAMS_SOIL--")
}
if (do.DISP)
{
params.list = c(params.list, list(files.PFG.DISP[, PFG.combi$DISP[ii]]))
names.params.list = c(names.params.list, "--PFG_PARAMS_DISPERSAL--")
}
if (do.HABSUIT)
{
params.list = c(params.list, list(files.PFG.HABSUIT))
names.params.list = c(names.params.list, "--PFG_MASK_HABSUIT--")
if (exists("SCENARIO.HABSUIT"))
{
params.list = c(params.list, list(SCENARIO.HABSUIT))
names.params.list = c(names.params.list, "--HABSUIT_CHANGEMASK_FILES--")
}
}
if (do.DIST)
{
params.list = c(params.list
, list(files.PFG.DIST[, PFG.combi$DIST[ii]])
, list(rep(paste0(name.simulation
, "/DATA/MASK/"
, name.DIST)
, no.DIST)))
names.params.list = c(names.params.list
, "--PFG_PARAMS_DISTURBANCES--"
, "--DIST_MASK--")
if (exists("SCENARIO.DIST"))
{
params.list = c(params.list, list(SCENARIO.DIST))
names.params.list = c(names.params.list, "--DIST_CHANGEMASK_FILES--")
}
}
if (do.DROUGHT)
{
params.list = c(params.list
, list(files.PFG.DROUGHT[, PFG.combi$DROUGHT[ii]])
, list(paste0(name.simulation
, "/DATA/MASK/"
, name.DROUGHT)))
names.params.list = c(names.params.list
, "--PFG_PARAMS_DROUGHT--"
, "--DROUGHT_MASK--")
if (exists("SCENARIO.DROUGHT"))
{
params.list = c(params.list, list(SCENARIO.DROUGHT))
names.params.list = c(names.params.list, "--DROUGHT_CHANGEMASK_FILES--")
}
}
if (do.ALIENS)
{
params.list = c(params.list, list(files.PFG.ALIENS))
names.params.list = c(names.params.list, "--PFG_MASK_ALIENS--")
if (exists("SCENARIO.ALIENS"))
{
params.list = c(params.list, list(SCENARIO.ALIENS))
names.params.list = c(names.params.list, "--ALIENS_CHANGEMASK_FILES--")
}
}
if (do.FIRE)
{
params.list = c(params.list
, list(files.PFG.FIRE[, PFG.combi$FIRE[ii]])
, list(rep(paste0(name.simulation
, "/DATA/MASK/"
, name.FIRE)
, no.FIRE)))
names.params.list = c(names.params.list
, "--PFG_PARAMS_FIRE--"
, "--FIRE_MASK--")
if (exists("SCENARIO.FIRE"))
{
params.list = c(params.list, list(SCENARIO.FIRE))
names.params.list = c(names.params.list, "--FIRE_CHANGEMASK_FILES--")
}
}
### -------------------------------------------------------------------- ###
params = c(params.list, list(""))
names(params) = c(names.params.list, "--END_OF_FILE--")
.createParams(params.file = paste0(name.simulation
, "/PARAM_SIMUL/Simul_parameters_V"
, ifelse(FILE_NUMBER == 0
, paste0(i, ".", ii)
, FILE_NUMBER)
, ".txt")
, params.list = params
, separator = "\n")
}
}
}
MayaGueguen/RFate documentation built on Oct. 17, 2020, 8:06 a.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Defines functions PRE_FATE.params_simulParameters
Documented in PRE_FATE.params_simulParameters
### HEADER #####################################################################
##' @title Create \emph{Simul_parameters} parameter file for a \code{FATE}
##' simulation
##'
##' @name PRE_FATE.params_simulParameters
##'
##' @author Maya Guéguen
##'
##' @description This script is designed to create one (or several) parameter
##' file containing \code{PARAMETER FILENAMES} used in \code{FATE} model.
##'
##' @param name.simulation a \code{string} corresponding to the main directory
##' or simulation name of the \code{FATE} simulation
##' @param name.MASK a \code{string} corresponding to the file name of a raster
##' mask, with either \code{0} or \code{1} within each pixel, \code{1}
##' corresponding to the cells of the studied area in which the succession
##' (core) module of the \code{FATE} simulation will take place (see
##' \href{PRE_FATE.params_globalParameters.html#details}{\code{PRE_FATE.params_globalParameters}})
##' @param name.SAVED_STATE (\emph{optional}) \cr a \code{string} corresponding
##' to the file name of a \code{FATE} object, obtained from a previous
##' simulation and from which to restart this new simulation
##' @param name.DIST (\emph{optional}) \cr a \code{string} corresponding to the
##' file name of a raster mask, with either \code{0} or \code{1} within each
##' pixel, \code{1} corresponding to the cells of the studied area in which the
##' disturbance module of the \code{FATE} simulation will take place (see
##' \href{PRE_FATE.params_globalParameters.html#details}{\code{PRE_FATE.params_globalParameters}})
##' @param name.DROUGHT (\emph{optional}) \cr a \code{string} corresponding to
##' the name of a raster file, with a \code{numeric} value within each pixel
##' corresponding to the drought intensity experienced by this pixel through
##' the drought (or fire) disturbance module of the \code{FATE} simulation (see
##' \href{PRE_FATE.params_globalParameters.html#details}{\code{PRE_FATE.params_globalParameters}})
##' @param name.FIRE (\emph{optional}) \cr a \code{string} corresponding to the
##' file name of a raster mask, with either \code{0} or \code{1} within each
##' pixel, \code{1} corresponding to the cells of the studied area in which the
##' fire disturbance module of the \code{FATE} simulation will take place (see
##' \href{PRE_FATE.params_globalParameters.html#details}{\code{PRE_FATE.params_globalParameters}})
##' @param name.ELEVATION (\emph{optional}) \cr a \code{string} corresponding to
##' the name of a raster file, with a \code{numeric} value within each pixel
##' corresponding to the elevation of this pixel and used by the fire
##' disturbance module of the \code{FATE} simulation (see
##' \href{PRE_FATE.params_globalParameters.html#details}{\code{PRE_FATE.params_globalParameters}})
##' @param name.SLOPE (\emph{optional}) \cr a \code{string} corresponding to
##' the name of a raster file, with a \code{numeric} value within each pixel
##' corresponding to the slope of this pixel and used by the fire
##' disturbance module of the \code{FATE} simulation (see
##' \href{PRE_FATE.params_globalParameters.html#details}{\code{PRE_FATE.params_globalParameters}})
##' @param opt.global.name (\emph{optional}) \cr a \code{string} corresponding
##' to the name of the global parameter file in the folder
##' \code{name.simulation/DATA/GLOBAL_PARAMETERS/} that will be used to build
##' the simulation parameter file
##' @param opt.folder.name (\emph{optional}) \cr a \code{string} corresponding
##' to the name of the folder in each \code{name.simulation/DATA/PFGS/module/}
##' from which PFG file names will be extracted to build the simulation
##' parameter file
##'
##'
##'
##' @details
##'
##' The \code{FATE} software takes only one input parameter : a file
##' containing links to other files containing all the parameters and data
##' needed by the program to run.
##'
##'
##' \describe{
##' \item{GLOBAL_PARAMS}{file where parameters related to the simulation
##' definition are referred (e.g. number of PFG involved, number of height
##' strata, simulation duration, computer resources, modules loaded, etc) \cr
##' (see \code{\link{PRE_FATE.params_globalParameters}}) \cr \cr
##' }
##' \item{SAVING_DIR}{directory where simulation outputs will be stored}
##' \item{SAVED_STATE (\emph{optional})}{file containing the results of a
##' previous \code{FATE} simulation from which to restart this new simulation
##' \cr }
##' \item{SAVING_YEARS_ \cr ARRAYS (\emph{optional})}{file containing the
##' years for which simulation maps will be saved \cr
##' (see \code{\link{PRE_FATE.params_savingYears}})
##' }
##' \item{SAVING_YEARS_ \cr OBJECTS (\emph{optional})}{file containing the
##' years for which simulation outputs will be saved \cr
##' (see \code{\link{PRE_FATE.params_savingYears}}) \cr \cr
##' }
##' \item{MASK}{raster mask that will define the study area}
##' \item{MASK_CHANGEMASK_YEARS \cr (\emph{optional})}{file containing the years
##' to change rasters for the succession module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})
##' }
##' \item{MASK_CHANGEMASK_FILES \cr (\emph{optional})}{file containing the files
##' to change rasters for the succession module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}}) \cr \cr
##' }
##' \item{PFG_PARAMS_ \cr LIFE_HISTORY}{PFG life history related parameters
##' (one by PFG) \cr
##' (see \code{\link{PRE_FATE.params_PFGsuccession}}) \cr \cr
##' }
##' \item{PFG_PARAMS_ \cr LIGHT (\emph{optional})}{PFG light preferences and
##' tolerance related parameters (one by PFG) \cr
##' (see \code{\link{PRE_FATE.params_PFGlight}}) \cr \cr
##' }
##' \item{PFG_PARAMS_ \cr SOIL (\emph{optional})}{PFG soil contribution and
##' tolerance related parameters (one by PFG) \cr
##' (see \code{\link{PRE_FATE.params_PFGsoil}}) \cr \cr
##' }
##' \item{PFG_PARAMS_ \cr DISPERSAL (\emph{optional})}{PFG dispersal
##' capacity related parameters (one by PFG) \cr
##' (see \code{\link{PRE_FATE.params_PFGdispersal}}) \cr \cr
##' }
##' \item{PFG_MASK_HABSUIT \cr (\emph{optional})}{raster masks (one by PFG)
##' containing PFG habitat suitability for the study area}
##' \item{HABSUIT_CHANGEMASK_YEARS \cr (\emph{optional})}{file containing the years
##' to change rasters for the habitat suitability module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})
##' }
##' \item{HABSUIT_CHANGEMASK_FILES \cr (\emph{optional})}{file containing the files
##' to change rasters for the habitat suitability module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}}) \cr \cr
##' }
##' \item{PFG_PARAMS_ \cr DISTURBANCES (\emph{optional})}{PFG disturbance
##' related parameters in terms of resprouting and mortality (one by PFG) \cr
##' (see \code{\link{PRE_FATE.params_PFGdisturbance}})
##' }
##' \item{DIST_MASK \cr (\emph{optional})}{raster masks that will define the
##' disturbance areas}
##' \item{DIST_CHANGEMASK_YEARS \cr (\emph{optional})}{file containing the years
##' to change rasters for the disturbance module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})
##' }
##' \item{DIST_CHANGEMASK_FILES \cr (\emph{optional})}{file containing the files
##' to change rasters for the disturbance module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}}) \cr \cr
##' }
##' \item{PFG_PARAMS_DROUGHT \cr (\emph{optional})}{PFG drought disturbance
##' related parameters in terms of resprouting and mortality (one by PFG) \cr
##' (see \code{\link{PRE_FATE.params_PFGdrought}})}
##' \item{DROUGHT_MASK \cr (\emph{optional})}{raster mask that will define the
##' drought intensity of the area}
##' \item{DROUGHT_CHANGEMASK_YEARS \cr (\emph{optional})}{file containing the
##' years to change rasters for the drought disturbances module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})}
##' \item{DROUGHT_CHANGEMASK_FILES \cr (\emph{optional})}{file containing the
##' files to change rasters for the drought disturbances module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}}) \cr \cr}
##' \item{PFG_MASK_ALIENS \cr (\emph{optional})}{raster masks (one by alien)
##' containing alien introduction zones for the study area}
##' \item{ALIENS_CHANGEMASK_YEARS \cr (\emph{optional})}{file containing the
##' years to change rasters for the aliens introduction module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})}
##' \item{ALIENS_CHANGEMASK_FILES \cr (\emph{optional})}{file containing the
##' files to change rasters for the aliens introduction module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})}
##' \item{ALIENS_CHANGEFREQ_YEARS \cr (\emph{optional})}{file containing the
##' years to change frequencies for the aliens introduction module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})}
##' \item{ALIENS_CHANGEFREQ_FILES \cr (\emph{optional})}{file containing the
##' files to change frequencies for the aliens introduction module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}}) \cr \cr}
##' \item{PFG_PARAMS_FIRE \cr (\emph{optional})}{PFG fire disturbance
##' related parameters in terms of resprouting and mortality (one by PFG) \cr
##' (see \code{\link{PRE_FATE.params_PFGdisturbance}})}
##' \item{FIRE_MASK \cr (\emph{optional})}{raster mask that will define the
##' fire disturbance areas}
##' \item{FIRE_CHANGEMASK_YEARS \cr (\emph{optional})}{file containing the
##' years to change rasters for the fire disturbances module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})}
##' \item{FIRE_CHANGEMASK_FILES \cr (\emph{optional})}{file containing the
##' files to change rasters for the fire disturbances module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})}
##' \item{FIRE_CHANGEFREQ_YEARS \cr (\emph{optional})}{file containing the
##' years to change frequencies for the fire disturbances module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})}
##' \item{FIRE_CHANGEFREQ_FILES \cr (\emph{optional})}{file containing the
##' files to change frequencies for the fire disturbances module \cr
##' (see \code{\link{PRE_FATE.params_changingYears}})}
##' \item{ELEVATION_MASK \cr (\emph{optional})}{raster mask that will define
##' the elevation of the area}
##' \item{SLOPE_MASK \cr (\emph{optional})}{raster mask that will define the
##' slope of the area}
##' }
##'
##'
##'
##' @note
##'
##' \itemize{
##' \item The function produces links to files that are \strong{NOT absolute
##' paths BUT relative ones}. \cr
##' \emph{When relative paths are used}, the user should be careful of the
##' folder from which the simulation is launched. \cr
##' \emph{A function allows to transform these relative paths into absolute
##' ones. (see examples of \code{\link{.setPattern}})}.
##' \item \strong{The order of files matters!} \cr
##' For instance the first link below \code{--PFG_PARAMS_LIFE_HISTORY--} flag
##' (e.g. \emph{PFG Albert}) has to match with the first item below the
##' \code{--PFG_PARAMS_DISPERSAL--} flag (must be \emph{PFG Albert} too).
##' }
##'
##'
##'
##'
##' @return A \code{.txt} file into the \code{name.simulation/PARAM_SIMUL/}
##' directory with the following parameters :
##'
##' \itemize{
##' \item \strong{--GLOBAL_PARAMS--}
##' \item \strong{--SAVING_DIR--}
##' \itemize{
##' \item --SAVED_STATE-- (\emph{optional})
##' \item --SAVING_YEARS_MAPS-- (\emph{optional})
##' \item --SAVING_YEARS_OBJECTS-- (\emph{optional})
##' }
##' \item \strong{--MASK--}
##' \itemize{
##' \item --MASK_CHANGEMASK_YEARS-- (\emph{optional})
##' \item --MASK_CHANGEMASK_FILES-- (\emph{optional})
##' }
##' \item \strong{--PFG_PARAMS_LIFE_HISTORY--}
##' \itemize{
##' \item --PFG_PARAMS_LIGHT-- (\emph{optional})
##' \item --PFG_PARAMS_SOIL-- (\emph{optional})
##' \item --PFG_PARAMS_DISPERSAL-- (\emph{optional})
##' \item --PFG_MASK_HABSUIT-- (\emph{optional})
##' \item --HABSUIT_CHANGEMASK_YEARS-- (\emph{optional})
##' \item --HABSUIT_CHANGEMASK_FILES-- (\emph{optional})
##' \item --PFG_PARAMS_DISTURBANCES-- (\emph{optional})
##' \item --DIST_MASK-- (\emph{optional})
##' \item --DIST_CHANGEMASK_YEARS-- (\emph{optional})
##' \item --DIST_CHANGEMASK_FILES-- (\emph{optional})
##' \item --PFG_PARAMS_DROUGHT-- (\emph{optional})
##' \item --DROUGHT_MASK-- (\emph{optional})
##' \item --DROUGHT_CHANGEMASK_YEARS-- (\emph{optional})
##' \item --DROUGHT_CHANGEMASK_FILES-- (\emph{optional})
##' \item --PFG_MASK_ALIENS-- (\emph{optional})
##' \item --ALIENS_CHANGEMASK_YEARS-- (\emph{optional})
##' \item --ALIENS_CHANGEMASK_FILES-- (\emph{optional})
##' \item --ALIENS_CHANGEFREQ_YEARS-- (\emph{optional})
##' \item --ALIENS_CHANGEFREQ_FILES-- (\emph{optional})
##' \item --PFG_PARAMS_FIRE-- (\emph{optional})
##' \item --FIRE_MASK-- (\emph{optional})
##' \item --FIRE_CHANGEMASK_YEARS-- (\emph{optional})
##' \item --FIRE_CHANGEMASK_FILES-- (\emph{optional})
##' \item --FIRE_CHANGEFREQ_YEARS-- (\emph{optional})
##' \item --FIRE_CHANGEFREQ_FILES-- (\emph{optional})
##' \item --ELEVATION_MASK-- (\emph{optional})
##' \item --SLOPE_MASK-- (\emph{optional})
##' }
##' \item \strong{--END_OF_FILE--}
##' }
##'
##'
##' @keywords FATE, simulation
##'
##' @seealso \code{\link{PRE_FATE.skeletonDirectory}},
##' \code{\link{PRE_FATE.params_globalParameters}},
##' \code{\link{PRE_FATE.params_PFGsuccession}},
##' \code{\link{PRE_FATE.params_PFGlight}},
##' \code{\link{PRE_FATE.params_PFGsoil}},
##' \code{\link{PRE_FATE.params_PFGdispersal}},
##' \code{\link{PRE_FATE.params_PFGdisturbance}},
##' \code{\link{PRE_FATE.params_PFGdrought}},
##' \code{\link{PRE_FATE.params_savingYears}},
##' \code{\link{PRE_FATE.params_changingYears}},
##' \code{\link{.setPattern}}
##'
##' @examples
##'
##'
##' ## ----------------------------------------------------------------------------------------- ##
##'
##' ## Load example data
##'
##' @export
##'
##' @importFrom foreach foreach %do%
##'
## END OF HEADER ###############################################################
PRE_FATE.params_simulParameters = function(
name.simulation
, name.MASK
, name.SAVED_STATE = NULL
, name.DIST = NULL
, name.DROUGHT = NULL
, name.FIRE = NULL
, name.ELEVATION = NULL
, name.SLOPE = NULL
, opt.global.name = NULL
, opt.folder.name = NULL
){
#############################################################################
.testParam_existFolder(name.simulation, "PARAM_SIMUL/")
.testParam_existFolder(name.simulation, "DATA/GLOBAL_PARAMETERS/")
.testParam_existFolder(name.simulation, "DATA/SAVE/")
.testParam_existFolder(name.simulation, "DATA/SCENARIO/")
.testParam_existFolder(name.simulation, "DATA/MASK/")
.testParam_existFolder(name.simulation, "DATA/PFGS/SUCC/")
.testParam_existFolder(name.simulation, "RESULTS/")
.testParam_notChar.m("name.MASK", name.MASK)
.testParam_existFile(paste0(name.simulation, "/DATA/MASK/", name.MASK))
## CHECK parameter opt.global.name
opt.global.name = .getParam_opt.folder.name(opt.global.name
, basename(opt.global.name)
, create.dir = FALSE)
opt.global.name = sub("/$", "", opt.global.name)
## CHECK parameter opt.folder.name
opt.folder.name = .getParam_opt.folder.name(opt.folder.name
, paste0(opt.folder.name, "/")
, create.dir = FALSE)
type.changing1 = c("MASK", "HABSUIT", "DIST", "DROUGHT", "ALIENS", "FIRE") #, "ALIENS_F")
type.changing2 = c("HABSUIT", "ALIENS")
#############################################################################
## Get the name(s) of global parameter file(s) that will
## be used to create the simulation parameter file(s)
if (opt.global.name == "")
{
files.GLOBAL = list.files(path = paste0(name.simulation
, "/DATA/GLOBAL_PARAMETERS")
, pattern = "^Global_parameters.*.txt"
, full.names = TRUE)
} else
{
files.GLOBAL = paste0(name.simulation
, "/DATA/GLOBAL_PARAMETERS/"
, opt.global.name)
}
if (length(files.GLOBAL) == 0)
{
stop(paste0("Wrong number of files!\n There is no adequate file "
, "(`.txt` file starting with `Global_parameters`) "
, "into the DATA/GLOBAL_PARAMETERS/ folder"))
}
#############################################################################
## Get the name(s) of SAVE directory
dirs.SAVE = list.dirs(path = paste0(name.simulation, "/DATA/SAVE")
, full.names = FALSE
, recursive = FALSE)
if (length(dirs.SAVE) > 0)
{
dirs.SAVE = paste0(name.simulation, "/DATA/SAVE/", dirs.SAVE)
} else
{
dirs.SAVE = paste0(name.simulation, "/DATA/SAVE")
}
#############################################################################
## Get the name(s) of SCENARIO directory
dirs.SCENARIO = list.dirs(path = paste0(name.simulation, "/DATA/SCENARIO")
, full.names = FALSE
, recursive = FALSE)
if (length(dirs.SCENARIO) > 0)
{
dirs.SCENARIO = paste0(name.simulation, "/DATA/SCENARIO/", dirs.SCENARIO)
} else
{
dirs.SCENARIO = paste0(name.simulation, "/DATA/SCENARIO")
}
warn.messages = list()
for (ty in type.changing1)
{
assign(x = paste0("dirs.SCENARIO.", ty), value = vector())
for (di in dirs.SCENARIO)
{
files.ty = list.files(path = di
, pattern = paste0("^", ty, "_changingmask_years")
, full.names = TRUE)
if (length(files.ty) > 0)
{
eval(parse(text = paste0("dirs.SCENARIO.", ty
, " = c(dirs.SCENARIO.", ty
, ", di)")))
} else
{
warn.messages[[length(warn.messages) +1]] = c(ty, di)
# warning(paste0("There is no adequate file (`.txt` file starting with `"
# , ty, "_changingmask_years`) "
# , "into the folder ", di))
}
}
}
if (length(warn.messages) > 0)
{
warning(paste0("There is no adequate file(s) into some folder(s) : \n"
, paste0(" > ", sapply(warn.messages, function(x) x[1])
, "_changingmask_years[...].txt (folder "
, sapply(warn.messages, function(x) x[2]), ") \n"
, collapse = "")))
}
#############################################################################
## Get the name(s) of HABSUIT / ALIENS directory
for (ty in type.changing2)
{
name.dir = paste0(name.simulation, "/DATA/PFGS/", ty)
dirs.SCE = list.dirs(path = name.dir
, full.names = FALSE
, recursive = FALSE)
if (length(dirs.SCE) > 0)
{
dirs.SCE = paste0(name.dir, "/", dirs.SCE)
} else
{
dirs.SCE = name.dir
}
assign(x = paste0("dirs.", ty), value = vector())
for (di in dirs.SCE)
{
files.di = list.files(path = di, full.names = TRUE)
if (length(files.di) > 0)
{
eval(parse(text = paste0("dirs.", ty, " = c(dirs.", ty, ", di)")))
}
}
}
#############################################################################
#############################################################################
## Combine the names found (global parameters, SAVE directory,
## SCENARIO directory, HABSUIT directory)
sce.mask = sce.habsuit = sce.dist = sce.drought = sce.aliens = sce.fire = 0
ras.habsuit = ras.aliens = 0
if (length(dirs.SCENARIO.MASK) > 0) sce.mask = 1:length(dirs.SCENARIO.MASK)
if (length(dirs.SCENARIO.HABSUIT) > 0) sce.habsuit = 1:length(dirs.SCENARIO.HABSUIT)
if (length(dirs.SCENARIO.DIST) > 0) sce.dist = 1:length(dirs.SCENARIO.DIST)
if (length(dirs.SCENARIO.DROUGHT) > 0) sce.drought = 1:length(dirs.SCENARIO.DROUGHT)
if (length(dirs.SCENARIO.ALIENS) > 0) sce.aliens = 1:length(dirs.SCENARIO.ALIENS)
if (length(dirs.SCENARIO.FIRE) > 0) sce.fire = 1:length(dirs.SCENARIO.FIRE)
if (length(dirs.HABSUIT) > 0) ras.habsuit = 1:length(dirs.HABSUIT)
if (length(dirs.ALIENS) > 0) ras.aliens = 1:length(dirs.ALIENS)
PARAMS.combi = expand.grid(GLOBAL = 1:length(files.GLOBAL)
, SAVE = 1:length(dirs.SAVE)
, SCENARIO.MASK = sce.mask
, SCENARIO.HABSUIT = sce.habsuit
, SCENARIO.DIST = sce.dist
, SCENARIO.DROUGHT = sce.drought
, SCENARIO.ALIENS = sce.aliens
, SCENARIO.FIRE = sce.fire
, PFG.HABSUIT = ras.habsuit
, PFG.ALIENS = ras.aliens)
#############################################################################
#############################################################################
## Build a simulation parameter file for each combination found
for (i in 1:nrow(PARAMS.combi))
{
params.combi = data.frame(GLOBAL = files.GLOBAL[PARAMS.combi$GLOBAL[i]]
, MASK = paste0(name.simulation
, "/DATA/MASK/"
, name.MASK)
, stringsAsFactors = FALSE)
names.params.combi = c("--GLOBAL_PARAMS--", "--MASK--")
if (!is.null(name.SAVED_STATE) && nchar(name.SAVED_STATE) > 0)
{
.testParam_existFile(name.SAVED_STATE)
params.combi[["SAVED_STATE"]] = name.SAVED_STATE
names.params.combi = c(names.params.combi, "--SAVED_STATE--")
}
#############################################################################
di = dirs.SAVE[PARAMS.combi$SAVE[i]]
di.opt = data.frame(pat = c("SAVE_YEARS_maps", "SAVE_YEARS_objects")
, nam = c("SAVE.maps", "SAVE.obj")
, param = c("SAVING_YEARS_MAPS", "SAVING_YEARS_OBJECTS")
, stringsAsFactors = FALSE)
warn.messages = list()
for (ii in 1:nrow(di.opt))
{
files.found = list.files(path = di
, pattern = paste0("^", di.opt$pat[ii])
, full.names = TRUE)
if (length(files.found) == 0)
{
warn.messages[[length(warn.messages) +1]] = c(di.opt$pat[ii], di)
# warning(paste0("There is no adequate file (`.txt` file starting with `"
# , di.opt$pat[ii], "`) "
# , "into the folder ", di))
} else if (length(files.found) == 1)
{
params.combi[[di.opt$nam[ii]]] = files.found
names.params.combi = c(names.params.combi
, paste0("--", di.opt$param[ii], "--"))
} else
{
stop(paste0("There is too many adequate files (`.txt` file starting with `"
, di.opt$pat[ii], "`) "
, "into the folder ", di))
}
}
if (length(warn.messages) > 0)
{
warning(paste0("There is no adequate file(s) into some folder(s) : \n"
, paste0(" > ", sapply(warn.messages, function(x) x[1])
, "[...].txt (folder "
, sapply(warn.messages, function(x) x[2]), ") \n"
, collapse = "")))
}
#############################################################################
warn.messages = list()
for (ty in type.changing1)
{
if (PARAMS.combi[, paste0("SCENARIO.", ty)][i] > 0)
{
eval(parse(text = paste0("di = dirs.SCENARIO.", ty
, "[PARAMS.combi$SCENARIO.", ty, "[i]]")))
## Changing years
files.SCE.years = list.files(path = di
, pattern = paste0("^", ty, "_changingmask_years")
, full.names = TRUE)
if (length(files.SCE.years) == 1)
{
params.combi[[paste0("SCENARIO.", ty)]] = files.SCE.years
names.params.combi = c(names.params.combi
, paste0("--", ty, "_CHANGEMASK_YEARS--"))
} else
{
stop(paste0("There is too many adequate files (`.txt` file starting with `"
, ty, "_changingmask_years`) "
, "into the folder ", di))
}
## Changing files
files.SCE.masks = list.files(path = di
, pattern = paste0("^", ty, "_changingmask_files")
, full.names = TRUE)
if (length(files.SCE.masks) == 0)
{
warn.messages[[length(warn.messages) +1]] = c(ty, di)
# warning(paste0("There is no adequate file (`.txt` file starting with `"
# , ty, "_changingmask_files`) "
# , "into the folder ", di))
} else if (length(files.SCE.masks) > 0)
{
assign(x = paste0("SCENARIO.", ty), value = files.SCE.masks)
}
}
}
if (length(warn.messages) > 0)
{
warning(paste0("There is no adequate file(s) into some folder(s) : \n"
, paste0(" > ", sapply(warn.messages, function(x) x[1])
, "_changingmask_files[...].txt (folder "
, sapply(warn.messages, function(x) x[2]), ") \n"
, collapse = "")))
}
#############################################################################
globi = as.character(files.GLOBAL[PARAMS.combi$GLOBAL[i]])
### -------------------------------------------------------------------- ###
no_PFG = .getParam(params.lines = globi
, flag = "NO_PFG"
, flag.split = " "
, is.num = TRUE)
no_PFG = as.numeric(no_PFG)
do.SUCC = 1
do.LIGHT = .getParam(params.lines = globi
, flag = "DO_LIGHT_COMPETITION"
, flag.split = " "
, is.num = TRUE)
do.SOIL = .getParam(params.lines = globi
, flag = "DO_SOIL_COMPETITION"
, flag.split = " "
, is.num = TRUE)
do.DISP = .getParam(params.lines = globi
, flag = "DO_DISPERSAL"
, flag.split = " "
, is.num = TRUE)
do.HABSUIT = .getParam(params.lines = globi
, flag = "DO_HAB_SUITABILITY"
, flag.split = " "
, is.num = TRUE)
do.DIST = .getParam(params.lines = globi
, flag = "DO_DISTURBANCES"
, flag.split = " "
, is.num = TRUE)
do.DROUGHT = .getParam(params.lines = globi
, flag = "DO_DROUGHT_DISTURBANCE"
, flag.split = " "
, is.num = TRUE)
do.ALIENS = .getParam(params.lines = globi
, flag = "DO_ALIENS_INTRODUCTION"
, flag.split = " "
, is.num = TRUE)
do.FIRE = .getParam(params.lines = globi
, flag = "DO_FIRE_DISTURBANCE"
, flag.split = " "
, is.num = TRUE)
### -------------------------------------------------------------------- ###
MODULES = c("SUCC", "LIGHT", "SOIL", "DISP", "DIST", "DROUGHT", "FIRE")
for (mod in MODULES)
{
if (get(paste0("do.", mod)))
{
.testParam_existFolder(name.simulation, paste0("DATA/PFGS/", mod, "/"))
name.dir = paste0(name.simulation, "/DATA/PFGS/", mod)
## Get folders
if (opt.folder.name != "")
{
dirs.mod = paste0(name.dir, "/", opt.folder.name)
}
if (opt.folder.name == "" || !dir.exists(dirs.mod))
{
dirs.mod = list.dirs(path = name.dir
, full.names = FALSE
, recursive = FALSE)
if (length(dirs.mod) > 0)
{
dirs.mod = paste0(name.dir, "/", dirs.mod)
} else
{
dirs.mod = name.dir
}
}
## Get files
files.PFG = foreach (di.mod = dirs.mod, .combine = "cbind") %do%
{
files.PFG = list.files(path = di.mod
, pattern = paste0("^", mod)
, full.names = TRUE)
if (length(files.PFG) != no_PFG)
{
stop(paste0("There is not the same number of files "
, "(`.txt` file starting with `", mod, "`) "
, "into the ", di.mod, "/ folder as the number of PFG "
, "indicated into the file "
, globi))
}
return(data.frame(files.PFG, stringsAsFactors = FALSE))
}
assign(x = paste0("files.PFG.", mod), value = files.PFG)
assign(x = paste0("no_files.PFG.", mod)
, value = ncol(get(paste0("files.PFG.", mod))))
} else
{
assign(x = paste0("files.PFG.", mod), value = "")
assign(x = paste0("no_files.PFG.", mod), value = 0)
}
}
no_files.PFG = sapply(MODULES, function(x) get(paste0("no_files.PFG.", x)))
no_files.PFG = no_files.PFG[which(no_files.PFG > 0)]
if (length(unique(no_files.PFG)) > 1)
{
PFG.combi = expand.grid(sapply(no_files.PFG, function(x) 1:x))
} else
{
PFG.combi = matrix(rep(0, length(no_files.PFG) * unique(no_files.PFG))
, ncol = length(no_files.PFG))
PFG.combi = as.data.frame(PFG.combi)
colnames(PFG.combi) = names(no_files.PFG)
for (mod in 1:length(no_files.PFG))
{
PFG.combi[[names(no_files.PFG)[mod]]] = 1:no_files.PFG[mod]
}
}
### -------------------------------------------------------------------- ###
MODULES = c("DIST", "DROUGHT", "FIRE")
for (mod in MODULES)
{
if (get(paste0("do.", mod)))
{
.testParam_notChar.m(paste0("name.", mod), get(paste0("name.", mod)))
.testParam_existFile(paste0(name.simulation
, "/DATA/MASK/"
, get(paste0("name.", mod))))
assign(x = paste0("no.", mod)
, value = .getParam(params.lines = globi
, flag = paste0(mod, "_NO")
, flag.split = " "
, is.num = TRUE))
} else
{
assign(x = paste0("no.", mod), value = 0)
}
}
### -------------------------------------------------------------------- ###
MODULES = c("HABSUIT", "ALIENS")
for (mod in MODULES)
{
if (get(paste0("do.", mod)))
{
.testParam_existFolder(name.simulation, paste0("DATA/PFGS/", mod, "/"))
if (PARAMS.combi[[paste0("PFG.", mod)]][i] > 0)
{
eval(parse(text = paste0("di = dirs.", mod
, "[PARAMS.combi$PFG.", mod, "[i]]")))
assign(x = paste0("files.PFG.", mod)
, value = list.files(path = di, full.names = TRUE))
if (length(get(paste0("files.PFG.", mod))) != no_PFG)
{
warning(paste0("There is not the same number of files into the "
, "DATA/PFGS/", mod, "/ folder as the number of PFG "
, "indicated into the file "
, globi))
}
} else
{
assign(x = paste0("files.PFG.", mod), value = "")
}
} else
{
assign(x = paste0("files.PFG.", mod), value = "")
}
}
#############################################################################
FILE_NUMBER = 0
if (nrow(PARAMS.combi) == 1 && nrow(PFG.combi) == 1)
{
FILE_NUMBER = length(list.files(path = paste0(name.simulation, "/PARAM_SIMUL/")
, pattern = "^Simul_parameters_V"
, recursive = FALSE
, include.dirs = FALSE)) + 1
}
#############################################################################
#############################################################################
for (ii in 1:nrow(PFG.combi))
{
params.list = lapply(1:ncol(params.combi)
, function(x) { as.character(params.combi[, x]) })
names.params.list = names.params.combi
if (FILE_NUMBER == 0)
{
params.list = c(params.list, list(paste0(name.simulation
, "/RESULTS/SIMUL_V"
, i, ".", ii)))
} else
{
params.list = c(params.list, list(paste0(name.simulation
, "/RESULTS/SIMUL_V"
, FILE_NUMBER)))
}
names.params.list = c(names.params.list, "--SAVING_DIR--")
params.list = c(params.list, list(files.PFG.SUCC[, PFG.combi$SUCC[ii]]))
names.params.list = c(names.params.list, "--PFG_PARAMS_LIFE_HISTORY--")
if (exists("SCENARIO.MASK"))
{
params.list = c(params.list, list(SCENARIO.MASK))
names.params.list = c(names.params.list, "--MASK_CHANGEMASK_FILES--")
}
if (do.LIGHT)
{
params.list = c(params.list, list(files.PFG.LIGHT[, PFG.combi$LIGHT[ii]]))
names.params.list = c(names.params.list, "--PFG_PARAMS_LIGHT--")
}
if (do.SOIL)
{
params.list = c(params.list, list(files.PFG.SOIL[, PFG.combi$SOIL[ii]]))
names.params.list = c(names.params.list, "--PFG_PARAMS_SOIL--")
}
if (do.DISP)
{
params.list = c(params.list, list(files.PFG.DISP[, PFG.combi$DISP[ii]]))
names.params.list = c(names.params.list, "--PFG_PARAMS_DISPERSAL--")
}
if (do.HABSUIT)
{
params.list = c(params.list, list(files.PFG.HABSUIT))
names.params.list = c(names.params.list, "--PFG_MASK_HABSUIT--")
if (exists("SCENARIO.HABSUIT"))
{
params.list = c(params.list, list(SCENARIO.HABSUIT))
names.params.list = c(names.params.list, "--HABSUIT_CHANGEMASK_FILES--")
}
}
if (do.DIST)
{
params.list = c(params.list
, list(files.PFG.DIST[, PFG.combi$DIST[ii]])
, list(rep(paste0(name.simulation
, "/DATA/MASK/"
, name.DIST)
, no.DIST)))
names.params.list = c(names.params.list
, "--PFG_PARAMS_DISTURBANCES--"
, "--DIST_MASK--")
if (exists("SCENARIO.DIST"))
{
params.list = c(params.list, list(SCENARIO.DIST))
names.params.list = c(names.params.list, "--DIST_CHANGEMASK_FILES--")
}
}
if (do.DROUGHT)
{
params.list = c(params.list
, list(files.PFG.DROUGHT[, PFG.combi$DROUGHT[ii]])
, list(paste0(name.simulation
, "/DATA/MASK/"
, name.DROUGHT)))
names.params.list = c(names.params.list
, "--PFG_PARAMS_DROUGHT--"
, "--DROUGHT_MASK--")
if (exists("SCENARIO.DROUGHT"))
{
params.list = c(params.list, list(SCENARIO.DROUGHT))
names.params.list = c(names.params.list, "--DROUGHT_CHANGEMASK_FILES--")
}
}
if (do.ALIENS)
{
params.list = c(params.list, list(files.PFG.ALIENS))
names.params.list = c(names.params.list, "--PFG_MASK_ALIENS--")
if (exists("SCENARIO.ALIENS"))
{
params.list = c(params.list, list(SCENARIO.ALIENS))
names.params.list = c(names.params.list, "--ALIENS_CHANGEMASK_FILES--")
}
}
if (do.FIRE)
{
params.list = c(params.list
, list(files.PFG.FIRE[, PFG.combi$FIRE[ii]])
, list(rep(paste0(name.simulation
, "/DATA/MASK/"
, name.FIRE)
, no.FIRE)))
names.params.list = c(names.params.list
, "--PFG_PARAMS_FIRE--"
, "--FIRE_MASK--")
if (exists("SCENARIO.FIRE"))
{
params.list = c(params.list, list(SCENARIO.FIRE))
names.params.list = c(names.params.list, "--FIRE_CHANGEMASK_FILES--")
}
}
### -------------------------------------------------------------------- ###
params = c(params.list, list(""))
names(params) = c(names.params.list, "--END_OF_FILE--")
.createParams(params.file = paste0(name.simulation
, "/PARAM_SIMUL/Simul_parameters_V"
, ifelse(FILE_NUMBER == 0
, paste0(i, ".", ii)
, FILE_NUMBER)
, ".txt")
, params.list = params
, separator = "\n")
}
}
}
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
Embedding an R snippet on your website
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.