getTimeTrees: Estimate time trees by running BEAST on each clone Applies...

In dowser: B Cell Receptor Phylogenetics Toolkit

Estimate time trees by running BEAST on each clone Applies XML template to each clone

Description

getTimeTrees Tree building function.

Usage

getTimeTrees(
  clones,
  template,
  beast,
  dir,
  id,
  time,
  mcmc_length = 3e+07,
  log_every = "auto",
  burnin = 10,
  trait = NULL,
  resume_clones = NULL,
  nproc = 1,
  quiet = 0,
  rm_temp = FALSE,
  include_germline = TRUE,
  seq = "sequence",
  germline_range = c(-10000, 10000),
  java = TRUE,
  seed = NULL,
  log_target = 10000,
  tree_states = FALSE,
  trees = NULL,
  ...
)

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
mcmc_length	Number of MCMC steps
log_every	Frequency of states logged. "auto" will divide mcmc_length by log_target
burnin	Burnin percent (default 10)
trait	Trait column to be used
resume_clones	Clones to resume for mcmc_length more steps
nproc	Number of cores for parallelization. At most 1 core/tree can be used.
quiet	amount of rubbish to print to console
rm_temp	remove temporary files (default=TRUE)
include_germline	Include germline sequence in analysis?
seq	Sequence column in data
germline_range	Possible date range of germline tip
java	Use the -java flag for BEAST run
seed	Use specified seeed for the -seed option for BEAST
log_target	Target number of samples from MCMC chain
tree_states	Use states vector for starting tree
trees	optional list of starting trees, either phylo objects or newick strings
...	Additional arguments passed to tree building programs

Details

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

Value

A tibble with a column of phylo objects and parameters column

See Also

getTrees, readBEAST

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