This function will execute a SLiM script generated by the compile function during the compilation of a slendr demographic model.

slim(
  model,
  sequence_length,
  recombination_rate,
  output = file.path(model$path, "output"),
  spatial = !is.null(model$world),
  sampling = NULL,
  max_attempts = 1,
  save_locations = FALSE,
  method = c("batch", "gui"),
  verbose = TRUE,
  burnin = 0,
  seed = NULL,
  slim_path = NULL,
  save_sampling = FALSE
)

Arguments

model

Model object created by the compile function

sequence_length

Total length of the simulated sequence (in base-pairs)

recombination_rate

Recombination rate of the simulated sequence (in recombinations per basepair per generation)

output

A shared prefix path of output files that will be generated by the model (by default, all files will share a prefix "output" and will be placed in the model directory)

spatial

Should the model be executed in spatial mode? By default, if a world map was specified during model definition, simulation will proceed in a spatial mode.

sampling

A data frame of times at which a given number of individuals should be remembered in the tree-sequence (see sampling for a function that can generate the sampling schedule in the correct format). If missing, only individuals present at the end of the simulation will be recorded in the tree-sequence output file.

max_attempts

How many attempts should be made to place an offspring near one of its parents? Serves to prevent infinite loops on the SLiM backend. Default value is 100.

save_locations

Save location of each individual throughout the simulation?

method

How to run the script? ("gui" - open in SLiMgui, "batch" - run on the command-line)

verbose

Write the SLiM output log to the console (default FALSE)?

burnin

Length of the burnin (in model's time units, i.e. years)

seed

Random seed (if missing, SLiM's own seed will be used)

slim_path

Optional way to specify path to an appropriate SLiM binary

save_sampling

Save the sampling schedule table together with other output files? If FALSE (default), the sampling table will be saved to a temporary directory.