Run genetic algorithm (GA) inference of the parameters of the given model

Runs a simulation-based GA routine of the given model, using the degree of a match between observed and simulated data as a measure of fitness.

run_ga(
  model,
  functions,
  observed,
  bounds,
  iterations,
  sequence_length,
  recombination_rate,
  mutation_rate = 0,
  engine = NULL,
  model_args = NULL,
  engine_args = NULL,
  ...
)

Arguments

model: Either a slendr model generating function (in which case engine must be either "msprime" or "slim", i.e. one of the two of slendr's simulation back ends), or a path to a custom user-defined SLiM or msprime script (in which case engine must be "custom").
functions: A named list of summary statistic functions to apply on simulated tree sequences
observed: A named list of observed summary statistics
iterations: How many simulation replicates to run?
sequence_length: Amount of sequence to simulate using slendr (in numbers of basepairs)
recombination_rate: Recombination rate to use for the simulation
mutation_rate: Mutation rate to use for the simulation
engine: Which simulation engine to use? Values "msprime" and "slim" will use one of the built-in slendr simulation back ends. Which engine will be used is determined by the nature of the model. If engine = NULL, then spatial slendr models will by default use the "slim" back end, non-spatial models will use the "msprime" back end, and custom user-defined model scripts will use the "custom" engine. Setting this argument explicitly will change the back ends (where appropriate). Setting this argument for custom simulation script has no effect.
model_args: Optional (non-prior) arguments for the slendr model generating function. Setting this argument for custom simulation script has no effect.
engine_args: Optional arguments for the slendr simulation back end. Setting this argument for custom simulation script has no effect.
...: Additional arguments passed on the ga function from the GA package
priors: A list of prior distributions to use for sampling of model parameters

Details

This function internally uses the functionga from the R package GA. All function arguments except to data are passed to the abc function, appropriately unpacking the prior sample matrix, and binding together matrices with observed statistics and simulated statistics in the format required by the inference function.

This function exists to avoid the need to manually track parameter matrices and summary statistics as inputs to the abc function but acts entirely transparently. A such, all implementation details can be found in the abc vignette and the manpage which you can access by typing ?abc::abc.