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
)
Arguments¶
- clones
- either a tibble (getTrees) or list of
airrCloneobjects - 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