readBEAST: Reads in a BEAST output directory

In dowser: B Cell Receptor Phylogenetics Toolkit

Reads in a BEAST output directory

Description

readBEAST Reads in data from BEAST output directory

Usage

readBEAST(
  clones,
  dir,
  id,
  beast,
  burnin = 10,
  trait = NULL,
  nproc = 1,
  quiet = 0,
  posterior = c("none", "all", "parameters", "trees_with_traits", "trees"),
  asr = FALSE,
  low_ram = TRUE,
  trim_ids = FALSE
)

Arguments

clones	either a tibble (getTrees) or list of airrClone objects
dir	directory where BEAST output files have been placed.
id	unique identifer for this analysis
beast	location of beast binary directory (beast/bin)
burnin	percent of initial tree samples to discard (default 10)
trait	Trait column used
nproc	Number of cores for parallelization. Uses at most 1 core per tree.
quiet	amount of rubbish to print to console
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".
asr	Log ancestral sequences?
low_ram	run with less memory (slightly slower)
trim_ids	remove last _ group from tips?

Value

If data is a tibble, then the input clones tibble with additional columns for trees and parameter estimates given the specified burnin. If input is just a list of airrClone objects, it will return the corresponding list of trees given the burnin

dowser documentation built on Aug. 20, 2026, 5:06 p.m.