dowser (version 2.5.1)

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,
  posterior = c("none", "all", "parameters", "trees_with_traits", "trees"),
  asr = FALSE,
  low_ram = TRUE,
  trim_ids = FALSE
)

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 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?