PRE_FATE.params_changingYears: Create _SCENARIO_ parameter files for a 'FATE' simulation
In leca-dev/RFate: FATE with R

View source: R/PRE_FATE.params_changingYears.R

PRE_FATE.params_changingYears

R Documentation

Create SCENARIO parameter files for a `FATE` simulation

Description

This script is designed to create several parameter files to manage the update of simulation maps : 1) simulation years at which the maps should be changed ; 2) filenames corresponding to the new simulation maps to be used.

Usage

PRE_FATE.params_changingYears(
  name.simulation,
  type.changing,
  mat.changing,
  opt.folder.name = NULL
)

Arguments

`name.simulation`	a `string` corresponding to the main directory or simulation name of the `FATE` simulation
`type.changing`	a `string` to choose the concerned module : `MASK` (succession), `HABSUIT` (habitat suitability), `DIST` (disturbances), `DROUGHT` (drought disturbance), `ALIENS` or `ALIENS_F` (aliens introduction, masks or frequencies) `FIRE` or `FIRE_F` (fire disturbance, masks or frequencies)
`mat.changing`	a `data.frame` with 3 columns : `year`, `order`, `new.value`
`opt.folder.name`	(optional) a `string` corresponding to the name of the folder that will be created into the `name.simulation/DATA/SCENARIO/` directory to store the results

Details

Several modules of the FATE software allow the user to simulate changes over time :

succession: the core module is based on a raster mask given within the Simul_parameters file with the MASK flag (see PRE_FATE.params_simulParameters), with either 0 or 1 within each pixel, 1 corresponding to the cells in which the PFG can try to colonize. The available pixels can change through time, to simulate habitat loss (e.g. urbanization) or gain (e.g. glacial retreat).
habitat suitability: if this module is activated (see PRE_FATE.params_globalParameters), PFG colonization depends on maps given for each PFG within the Simul_parameters file with the PFG_HAB_MASK flag (see PRE_FATE.params_simulParameters).
These maps must contain values between 0 and 1 corresponding to the probability of presence of the PFG in each pixel. These probabilities can change through time, as they often come from Species Distribution Models (SDM) that can be based for example on climatic variables (e.g. simulating regional warming).
disturbances: if this module is activated (see PRE_FATE.params_globalParameters), each disturbance relies on a raster given within the Simul_parameters file with the DIST_MASK flag (see PRE_FATE.params_simulParameters).
As for succession, this mask is filled with either 0 or 1 to define where the perturbation occurs. The impacted pixels can also change through time (e.g. change in forestry practices, expansion of grazing areas, etc).
drought disturbance: if this module is activated (see PRE_FATE.params_globalParameters), drought disturbance relies on a raster given within the Simul_parameters file with the DROUGHT_MASK flag (see PRE_FATE.params_simulParameters).
This map contains values defining the drought intensity experienced by the area. This intensity can change through time and space (e.g. regional warming, extreme years, change in agriculture practices that can leave a place more exposed, etc).
aliens introduction: if this module is activated (see PRE_FATE.params_globalParameters), aliens introduction depends on maps given for each alien within the Simul_parameters file with the PFG_ALIENS_MASK flag (see PRE_FATE.params_simulParameters).
As for succession, these masks are filled with either 0 or 1 to define where the introductions occur. The impacted pixels can also change through time (e.g. colonization, eradication campaign, etc), as well as the frequencies of introduction (see ALIENS_FREQ flag in PRE_FATE.params_globalParameters).
fire disturbance: if this module is activated (see PRE_FATE.params_globalParameters), fire disturbance can rely on a raster given within the Simul_parameters file with the FIRE_MASK flag (see PRE_FATE.params_simulParameters).
As for succession, this mask is filled with either 0 or 1 to define where the perturbation occurs. The impacted pixels can also change through time (e.g. change in forestry practices, expansion of drought events, etc), as well as the frequencies of perturbations (see FIRE_FREQ flag in PRE_FATE.params_globalParameters).

Several parameters, given within mat.changing, are required to set up these temporal changes :

year: all simulation years at which the raster files of a specific module (succession MASK, habitat suitability HABSUIT, disturbance DIST, drought DROUGHT, aliens introduction ALIENS or ALIENS_F, fire FIRE or FIRE_F) will be changed
new.value: the names of the new raster files for each year of change. It can be either .img or .tif.
There is an exception if ALIENS_F or FIRE_F is selected : the values should be integer representing the frequencies of aliens introduction or fire perturbations.
order: an integer associated to each new map in order to always give the raster maps in the same order throughout the years

Value

Several ‘.txt’ files into the name.simulation/DATA/SCENARIO/ :

..type.changing..‘.changingmask_years.txt’ : one line for each simulation year
..type.changing..‘.changingmask_files_t’..year..‘.txt’ : one line for each new raster file

..type.changing..‘.changingfreq_years.txt’ : one line for each simulation year
..type.changing..‘.changingfreq_files_t’..year..‘.txt’ : one line for each new frequency

If the opt.folder.name has been used, the files will be into the folder name.simulation/DATA/SCENARIO/opt.folder.name/.

Author(s)

Maya Guéguen

Examples


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

tab.changing = data.frame(year = c(50,50,80,80)
                          , order = c(1,2,1,2)
                          , new.value = c('FATE_simulation/DATA/MASK/MASK_DIST1_50.tif'
                                          , 'FATE_simulation/DATA/MASK/MASK_DIST2_50.tif'
                                          , 'FATE_simulation/DATA/MASK/MASK_DIST1_80.tif'
                                          , 'FATE_simulation/DATA/MASK/MASK_DIST2_80.tif'))

## Create a Changing_times parameter file ----------------------------------------------------
PRE_FATE.params_changingYears(name.simulation = 'FATE_simulation'
                              , type.changing = 'DIST'
                              , mat.changing = tab.changing)

leca-dev/RFate documentation built on Sept. 19, 2024, 6:09 a.m.