buildBeast: Read in a directory from a BEAST run. Runs treeannotator and...
In dowser: B Cell Receptor Phylogenetics Toolkit

buildBeast

R Documentation

Read in a directory from a BEAST run. Runs treeannotator and loganalyser.

Description

Read in a directory from a BEAST run. Runs treeannotator and loganalyser.

Usage

buildBeast(
  data,
  beast,
  time,
  template,
  dir,
  id,
  mcmc_length = 1e+06,
  resume_clones = NULL,
  trait = NULL,
  asr = FALSE,
  full_posterior = FALSE,
  log_every = "auto",
  include_germline = TRUE,
  nproc = 1,
  quiet = 0,
  burnin = 10,
  low_ram = TRUE,
  germline_range = c(-10000, 10000),
  java = TRUE,
  seed = NULL,
  log_target = 10000,
  trees = NULL,
  tree_states = FALSE,
  start_edge_length = 100,
  start_date = NULL,
  max_start_date = NULL,
  ...
)

Arguments

`data`	a list of `airrClone` objects
`beast`	location of beast binary directory (beast/bin)
`time`	Name of sample time column
`template`	XML template
`dir`	directory where temporary files will be placed.
`id`	unique identifer for this analysis
`mcmc_length`	Number of MCMC steps
`resume_clones`	Clones to resume for `mcmc_length` more steps
`trait`	Trait column used
`asr`	Log ancestral sequences?
`full_posterior`	Read un full distribution of parameters and trees?
`log_every`	Frequency of states logged. `auto` will divide mcmc_length by log_target
`include_germline`	Include germline in analysis?
`nproc`	Number of cores for parallelization. Uses at most 1 core per tree.
`quiet`	Amount of rubbish to print to console
`burnin`	Burnin percent (default 10)
`low_ram`	run with less memory (slightly slower)
`germline_range`	Possible date range of germline tip
`java`	Use the -java flag for BEAST run
`seed`	Use specified seeed for the -seed option for BEAST
`log_target`	Target number of samples over `mcmc_length`
`trees`	optional list of starting trees, either phylo objects or newick strings
`tree_states`	Use `states` vector for starting tree
`start_edge_length`	edge length to use for all branches in starting tree
`start_date`	Starting date of time tree if desired
`max_start_date`	Maximum starting date of time tree if desired
`...`	Additional arguments for XML writing functions