R/simulate_ts.R
simulate_ts.RdSimulates a tree sequence object from a model with parameters as specified either by sampling from priors or by a given list of fixed parameter values
simulate_ts(
model,
parameters,
sequence_length = 1e+06,
recombination_rate = 0,
mutation_rate = 0,
attempts = 1000,
engine = NULL,
model_args = NULL,
engine_args = NULL
)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").
A list of prior distributions to use for sampling of model parameters
Amount of sequence to simulate using slendr (in numbers of basepairs)
Recombination rate to use for the simulation
Mutation rate to use for the simulation
Maximum number of attempts to generate prior values for a valid demographic model (default is 1000)
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.
Optional (non-prior) arguments for the slendr model generating function. Setting this argument for custom simulation script has no effect.
Optional arguments for the slendr simulation back end. Setting this argument for custom simulation script has no effect.
A tree-sequence object of the class slendr_ts
This function is useful to generate a small tree sequence to be used when developing summary statistic functions inference using demografr.