dispersal_simulation: Helper function to simulate species dispersal processes

In fmachados/grinnell: Dispersal Simulations Based on Ecological Niches

Helper function to simulate species dispersal processes

Description

dispersal_simulation generates a python script to perform a multistep simulation of species dispersal to reconstruct areas that have been accessed based on environmental suitability and user-defined dispersal parameters.

Usage

dispersal_simulation(data, suit_layers, dispersal_kernel = "normal",
                     kernel_spread = 1, max_dispersers = 4,
                     replicates = 10, dispersal_events = 25,
                     access_threshold = 5, output_directory)

Arguments

data	(character) name of the csv file with all the species occurrences, columns must be: species, longitude, latitude.
suit_layers	(character) vector of names of suitability layers to be used as distinct scenarios. If more than one, the layer names must be ordered from past to current. Layer names should include parent directory if needed.
dispersal_kernel	(character) dispersal kernel (dispersal function) used to simulate the movement of the species. Options are: "normal", "log_normal". Default = "normal".
kernel_spread	(numeric) standard deviation for the dispersal_kernel. Default = 1.
max_dispersers	(numeric) maximum number of dispersers that depart from each colonized pixel. Depending on suitability this number will automatically decrease in areas with low suitability values. Default = 4.
replicates	(numeric) number of times to repeat the simulation per scenario. Default = 10.
dispersal_events	(numeric) number of dispersal events to happen per scenario. Default = 25.
access_threshold	(numeric) percentage to be considered when excluding accessed cells with lower values. Default = 5.
output_directory	(character) name of the output directory where results should be written. If this directory does not exist, it will be created.

fmachados/grinnell documentation built on Jan. 29, 2024, 6:48 p.m.