getTimeTreesIterate: 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,
  ...
)

Value

A tibble of tidytree and airrClone objects.

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

Details

For a full list of options (of which there are many more), see getTimeTrees

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