getTimeTreesIterate: Iteratively resume getTimeTrees until convergence, as defined...
In dowser: B Cell Receptor Phylogenetics Toolkit

getTimeTreesIterate

R Documentation

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,
  template,
  beast,
  dir,
  id,
  time,
  iterations = 10,
  ess_cutoff = 200,
  burnin = 10,
  ignore = c("traitfrequencies"),
  continue = FALSE,
  posterior = c("none", "all", "parameters", "trees_with_traits", "trees"),
  trait = NULL,
  nproc = 1,
  quiet = 0,
  asr = FALSE,
  low_ram = TRUE,
  trim_ids = FALSE,
  ...
)

Arguments

`clones`	a tibble of `airrClone` objects, the output of formatClones
`template`	XML template
`beast`	location of beast binary directory (beast/bin)
`dir`	directory where temporary files will be placed.
`id`	unique identifer for this analysis
`time`	Name of sample time column
`iterations`	Maximum number of times to resume MCMC chain
`ess_cutoff`	Minimum number of ESS for all parameters
`burnin`	Burnin percent (default 10)
`ignore`	Vector of parameters to ignore for ESS calculation
`continue`	If TRUE, will check for iteration folder and resume from last iteration if found (default FALSE)
`posterior`	Read un full distribution of parameters and trees? Can be "none" to just have summary objects, "all" to have parameters, trees, and trees_with_traits, or a vector with the desired combination of "parameters", "trees_with_traits", and "trees".
`trait`	Trait column to be used
`nproc`	Number of cores for parallelization. At most 1 core/tree can be used.
`quiet`	quiet notifications if > 0
`asr`	Log ancestral sequences?
`low_ram`	run with less memory (slightly slower)
`trim_ids`	remove last _ group from tips?
`...`	Additional arguments for getTimeTrees