Create DISPERSAL parameter files for a FATE simulation

Source: R/PRE_FATE.params_PFGdispersal.R

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.

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

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/.

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

Author

Maya Guéguen

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)