dowser (version 2.4.0)

readBEAST: 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
)

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

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)