exclude.warmup: Exclude warmup in a fitted evolving rates model

In bstaggmartin/evorates: Evolving Rate Models of Continuous Trait Evolution

Exclude warmup in a fitted evolving rates model

Description

This function gets rid of an arbitrary number of iterations at the beginning of all chains from the output of the function fit.evorates.

Usage

exclude.warmup(
  fit,
  warmup = fit$sampler.control$warmup,
  sampler = TRUE,
  simplify = TRUE
)

Arguments

fit	An object of class "evorates_fit", the output of a call to fit.evorates.
warmup	the number of iterations to be excluded, counting from the 1st iteration, even if it isn't stored in fit.
sampler	TRUE or FALSE value: should the iterations be excluded from the sampler.params element too?

Details

Keep in mind warmup counts form the first iteration. For example, if fit has 2000 iterations with the first 1000 as warmup, you would set warmup to 1500 to keep the last 500 iterations.

Value

an object of class "evorates_fit". All previously-existing elements in fit will be included.

See Also

Other chain management: combine.chains(), select.chains(), thin.chains()

Examples

#requires example fitted model object
#exclude warmup iterations from sampler
exclude.warmup(example.fit)
#exclude some non-warmup iterations
exclude.warmup(example.fit,1100)
#exclude some non-warmup iterations, but keep in sampler.params
exclude.warmup(example.fit,1100,F)

bstaggmartin/evorates documentation built on May 31, 2024, 5:56 a.m.