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,
  full_posterior = FALSE,
  asr = FALSE,
  low_ram = TRUE
)

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 coolumn used
nproc	Number of cores for parallelization. Uses at most 1 core per tree.
quiet	amount of rubbish to print to console
full_posterior	Read un full distribution of parameters and trees?
asr	Log ancestral sequences?
low_ram	run with less memory (slightly slower)

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 Nov. 5, 2025, 6:36 p.m.