Generates a SLiM script from a built-in slendr 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.
slim( model, seq_length, recomb_rate, output_dir = model$path, output_prefix = "output", save_locations = FALSE, track_ancestry = FALSE, ts_recording = FALSE, sampling = NULL, method, verbose = TRUE, include = NULL, burnin = 0, seed = NULL, slim_path = NULL, overwrite = FALSE )
Model object created by the
Total length of the simulated sequence (in base-pairs)
Recombination rate of the simulated sequence (in recombinations per basepair per generation)
A directory where to put simulation outputs (by default, all output files are placed in a model directory)
A common prefix of output files (by default, all files
will share a prefix
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" - run on the command-line, "script" - simply return the script)
Write the SLiM output log to the console (default
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)
Random seed (if missing, SLiM's own seed will be used)
Optional way to specify path to an appropriate SLiM binary
Overwrite the contents of the output directory (default
A data frame of times at which a given number of individuals
should be remembered in the tree-sequence (see