PRE_FATE.params_PFGdispersal: Create _DISPERSAL_ parameter files for a 'FATE' simulation

In leca-dev/RFate: FATE with R

Create DISPERSAL parameter files for a FATE simulation

Description

This script is designed to create parameter files containing dispersal distances for each PFG (one file for each of them) used in the dispersal module of FATE.

Usage

PRE_FATE.params_PFGdispersal(
  name.simulation,
  mat.PFG.disp,
  opt.folder.name = NULL
)

Arguments

name.simulation	a string corresponding to the main directory or simulation name of the FATE simulation
mat.PFG.disp	a data.frame with 4 columns : PFG, d50, d99, ldd
opt.folder.name	(optional) a string corresponding to the name of the folder that will be created into the name.simulation/DATA/PFGS/DISP/ directory to store the results

Details

A dispersal module is available to make the FATE model spatially explicit by dispersing seeds of each PFG with a kernel (see PRE_FATE.params_globalParameters).

Dispersal distances are needed for each PFG to quantify the amount of seeds dispersed into 3 different concentric circles :

d50

the distance at which 50% of seeds are dispersed

d99

the distance at which 99% of seeds are dispersed

ldd

the long dispersal distance at which 100% of seeds are dispersed

Value

A .txt file per PFG into the name.simulation/DATA/PFGS/DISP/ directory with the following parameters :

DISPERS_DIST

dispersal distances (3 values) (in meters)

A ‘DISP_COMPLETE_TABLE.csv’ file summarizing information for all groups into the ‘name.simulation/DATA/PFGS/’ directory.

If the opt.folder.name has been used, the files will be into the folder ‘name.simulation/DATA/PFGS/DISP/opt.folder.name/’.

Author(s)

Maya Guéguen

See Also

PRE_FATE.skeletonDirectory, PRE_FATE.params_globalParameters

Examples

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

mat.disp = data.frame(PFG = paste0('PFG', 1:6)
                      , d50 = c(10, 25, 100, 100, 500, 1000)
                      , d99 = c(500, 600, 300, 300, 1250, 1200)
                      , ldd = c(1500, 1500, 900, 900, 1500, 2000))

## Create PFG dispersal parameter files -----------------------------------------------------
PRE_FATE.params_PFGdispersal(name.simulation = 'FATE_simulation'
                             , mat.PFG.disp = mat.disp)
                                                        
                                                        
## -------------------------------------------------------------------------------------------

# ## Load example data
# Champsaur_PFG = .loadData('Champsaur_PFG', 'RData')
#
# ## Build PFG traits for dispersal
# tab.traits = Champsaur_PFG$PFG.traits
# ## Dispersal values
# ##   = Short: 0.1-2m;    Medium: 40-100m;    Long: 400-500m
# ##   = Vittoz correspondance : 1-3: Short;    4-5: Medium;   6-7:Long
# corres = data.frame(dispersal = 1:7
#                     , d50 = c(0.1, 0.5, 2, 40, 100, 400, 500)
#                     , d99 = c(1, 5, 15, 150, 500, 1500, 5000)
#                     , ldd = c(1000, 1000, 1000, 5000, 5000, 10000, 10000))
# tab.traits$d50 = corres$d50[tab.traits$dispersal]
# tab.traits$d99 = corres$d99[tab.traits$dispersal]
# tab.traits$ldd = corres$ldd[tab.traits$dispersal]
# str(tab.traits)


## Load example data
Champsaur_params = .loadData('Champsaur_params', 'RData')

## Create a skeleton folder
PRE_FATE.skeletonDirectory(name.simulation = 'FATE_Champsaur')


## PFG traits for dispersal
tab.disp = Champsaur_params$tab.DISP
str(tab.disp)

## Create PFG dispersal parameter files ------------------------------------------------------
PRE_FATE.params_PFGdispersal(name.simulation = 'FATE_Champsaur'
                             , mat.PFG.disp = Champsaur_params$tab.DISP)

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