Generates a SLiM script from a built-in spannr template, substituting all required parameters by values specified by the user. The user has an option to either run the script in batch mode, open it in SLiMgui, or simply save the generated SLiM script to a given location for later use.
run( model, sim_length, seq_length, recomb_rate, max_interaction, spread, save_locations = FALSE, track_ancestry = FALSE, keep_pedigrees = FALSE, ts_recording = FALSE, how = "gui", verbose = FALSE, include = NULL, burnin = NULL, script_path = file.path(model$config$directory, "script.slim"), output_prefix = file.path(model$config$directory, "output") )
Model object created by the
Total length of the simulation (in model time units, i.e. years)
Total length of the simulated sequence (in base-pairs)
Recombination rate of the simulated sequence (in recombinations per basepair per generation)
Maximum spatial interaction and mating choice distance
Standard deviation of the normal distribution for a distance from of an offspring from one of its parents (randomly determined by SLiM)
Save location of each individual throughout the simulation?
Track ancestry proportion dynamics in all populations throughout the simulations (default FALSE)? If a non-zero integer is provided, ancestry will be tracked using the number number of neutral ancestry markers equal to this number.
Turn on tree sequence recording during SLiM initialization?
How to run the script? ("gui" - open in SLiMgui, "batch"
Vector of paths to custom SLiM scripts which should be combined with the backend SLiM code
Length of the burnin (in model's time units, i.e. years)
Name of the compiled output script
Common prefix (including path) for all output files
Generation time (in model's time units, i.e. years)