dartR.sim (version 0.71)

gl.sim.WF.run: Runs Wright-Fisher simulations

Description

This function simulates populations made up of diploid organisms that reproduce in non-overlapping generations. Each individual has a pair of homologous chromosomes that contains interspersed selected and neutral loci. For the initial generation, the genotype for each individual’s chromosomes is randomly drawn from distributions at linkage equilibrium and in Hardy-Weinberg equilibrium.

See documentation and tutorial for a complete description of the simulations. These documents can be accessed at https://github.com/green-striped-gecko/dartR/wiki/Simulations-tutorial

Take into account that the simulations will take a little longer the first time you use the function gl.sim.WF.run() because C++ functions must be compiled.

Usage

gl.sim.WF.run(
  file_var,
  ref_table,
  x = NULL,
  file_dispersal = NULL,
  number_iterations = 1,
  every_gen = 10,
  sample_percent = 50,
  store_phase1 = FALSE,
  interactive_vars = TRUE,
  seed = NULL,
  verbose = NULL,
  ...
)

Value

Returns genlight objects with simulated data.

Arguments

file_var

Path of the variables file 'sim_variables.csv' (see details) [required if interactive_vars = FALSE].

ref_table

Reference table created by the function gl.sim.WF.table [required].

x

Name of the genlight object containing the SNP data to extract values for some simulation variables (see details) [default NULL].

file_dispersal

Path of the file with the dispersal table created with the function gl.sim.create_dispersal [default NULL].

number_iterations

Number of iterations of the simulations [default 1].

every_gen

Generation interval at which simulations should be stored in a genlight object [default 10].

sample_percent

Percentage of individuals, from the total population, to sample and save in the genlight object every generation [default 50].

store_phase1

Whether to store simulations of phase 1 in genlight objects [default FALSE].

interactive_vars

Run a shiny app to input interactively the values of simulations variables [default TRUE].

seed

Set the seed for the simulations [default NULL].

verbose

Verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log; 3, progress and results summary; 5, full report [default 2, unless specified using gl.set.verbosity].

...

Any variable and its value can be added separately within the function, will be changed over the input value supplied by the csv file. See tutorial.

Author

Custodian: Luis Mijangos

See Also

gl.sim.WF.table

Other simulation functions: gl.sim.WF.table(), gl.sim.create_dispersal()

Examples

ref_table <- gl.sim.WF.table(file_var=system.file("extdata", 
"ref_variables.csv", package = "dartR.sim"),interactive_vars = FALSE)

res_sim <- gl.sim.WF.run(file_var = system.file("extdata",
 "sim_variables.csv", package ="dartR.sim"),ref_table=ref_table,
 interactive_vars = FALSE)