Validate individual components of an ABC model

Validates the ABC setup by checking that all priors can be correctly sampled from, that a slendr model resulting from those priors can simulate a tree sequence, and that the user-defined summary functions produce output compatible with the provided empirical summary statistics.

validate_abc(
  model,
  priors,
  functions,
  observed,
  sequence_length,
  recombination_rate,
  mutation_rate = 0,
  format = c("ts", "files"),
  data = NULL,
  engine = NULL,
  model_args = NULL,
  engine_args = NULL,
  quiet = FALSE,
  attempts = 1000
)

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").

priors

A list of prior distributions to use for sampling of model parameters

functions

A named list of summary statistic functions to apply on different simulated results (tree sequences or custom files)

observed

A named list of observed summary statistics

sequence_length

Amount of sequence to simulate using slendr (in base pairs). Ignored when custom simulations scripts are provided.

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.

quiet

Should the log output of the validation be printed to the console? (Default is TRUE.)

attempts

Maximum number of attempts to generate prior values for a valid demographic model (default is 1000)

Value

No return value. The function is ran for its terminal output.