Create the skeleton folder for a FATE simulation

This script is designed to create a user-friendly directory tree to run a FATE simulation.

PRE_FATE.skeletonDirectory(name.simulation = "FATE_simulation")

Arguments

name.simulation

a string that will be used as the main directory and simulation name

Value

A directory tree with folders to contain the parameter files, the simulation files and the results.

Details

FATE requires only one input parameter (see PRE_FATE.params_simulParameters),

• which is a file containing the names of parameter files,

• which may themselves contain

  • parameters (e.g. succession, dispersal files...)

  • or other file names (e.g. disturbance or environmental change masks).

The user could give names of files stored everywhere on a machine, and does not have to put them all in one same place.
But as this is more practical, this function proposes a way to organize all those files or parameter files that will or could be used by a FATE simulation.

The tree structure is detailed below :

DATA

this folder will contain all the data or parameters that are needed by the model

GLOBAL_PARAMETERS

files containing global parameters for the simulation
(see PRE_FATE.params_globalParameters)

MASK

raster maps used in the model

SCENARIO

files containing information about changes in raster maps input
(see PRE_FATE.params_changingYears)

SAVE

files containing information about simulation times to save outputs
(see PRE_FATE.params_savingYears)

PFGS

SUCC

life history parameter files
(see PRE_FATE.params_PFGsuccession)

LIGHT

response to light interaction parameter files
(see PRE_FATE.params_PFGlight)

SOIL

response to soil interaction parameter files
(see PRE_FATE.params_PFGsoil)

DISP

dispersal parameter files
(see PRE_FATE.params_PFGdispersal)

HABSUIT

habitat suitability maps

DIST

response to disturbances parameter files
(see PRE_FATE.params_PFGdisturbance)

DROUGHT

response to drought disturbance parameter files
(see PRE_FATE.params_PFGdrought)

ALIENS

aliens introduction maps

PARAM_SIMUL

this folder will contain simulation files that can be given as input to the software
(see PRE_FATE.params_simulParameters)

RESULTS

this folder will collect all the results produced by the software with a folder for each simulation

NB :
All the functions of the RFate package are based on this folder structure.

See also

PRE_FATE.params_globalParameters, PRE_FATE.params_PFGsuccession, PRE_FATE.params_PFGlight, PRE_FATE.params_PFGsoil, PRE_FATE.params_PFGdispersal, PRE_FATE.params_PFGdisturbance, PRE_FATE.params_PFGdrought, PRE_FATE.params_changingYears, PRE_FATE.params_savingYears, PRE_FATE.params_simulParameters

Author

Maya Guéguen

Examples

## Create a skeleton folder with the default name ('FATE_simulation') ------------------------
PRE_FATE.skeletonDirectory()

## Create a skeleton folder with a specific name ---------------------------------------------
PRE_FATE.skeletonDirectory(name.simulation = 'FATE_AlpineForest')