getTimeTreesIterate: Iteratively resume getTimeTrees until convergence, as defined...

In dowser: B Cell Receptor Phylogenetics Toolkit

Iteratively resume getTimeTrees until convergence, as defined by all parameters (except those in ignore vector) having ESS greater than or equal to the specified ess_cutoff

Description

getTimeTreesIterate Iteratively resume getTimeTrees til convergence.

Usage

getTimeTreesIterate(
  clones,
  iterations = 10,
  ess_cutoff = 200,
  ignore = c("traitfrequencies"),
  quiet = 0,
  ...
)

Arguments

clones	a tibble of airrClone objects, the output of formatClones
iterations	Maximum number of times to resume MCMC chain
ess_cutoff	Minimum number of ESS for all parameters
ignore	Vector of parameters to ignore for ESS calculation
quiet	quiet notifications if > 0
...	Additional arguments for getTimeTrees

Details

For examples and vignettes, see https://dowser.readthedocs.io

Value

A tibble of tidytree and airrClone objects.

dowser documentation built on Nov. 5, 2025, 6:36 p.m.