write_clone_to_xml: Takes an airr clone object and template and writes a BEAST2...

In dowser: B Cell Receptor Phylogenetics Toolkit

Takes an airr clone object and template and writes a BEAST2 XML file

Description

Takes an airr clone object and template and writes a BEAST2 XML file

Usage

write_clone_to_xml(
  clone,
  file,
  id,
  time = NULL,
  trait = NULL,
  trait_data_type = NULL,
  template = NULL,
  mcmc_length = 1e+06,
  log_every = 1000,
  replacements = NULL,
  include_germline_as_root = FALSE,
  include_germline_as_tip = FALSE,
  germline_range = c(-10000, 10000),
  tree = NULL,
  trait_list = NULL,
  log_every_trait = 10,
  tree_states = FALSE,
  start_edge_length = 100,
  start_date = NULL,
  max_start_date = NULL,
  ...
)

Arguments

clone	an airrClone object
file	output file path
id	unique identifer for this analysis
time	name of column representing sample time
trait	name of column representing a trait
trait_data_type	optional data type for the trait
template	XML template
mcmc_length	number of MCMC iterations
log_every	frequency of states logged. auto will divide mcmc_length by log_target
replacements	list of additional replacements to make in the template
include_germline_as_root	include germline in analysis as root?
include_germline_as_tip	include germline in analysis as tip?
germline_range	possible date range of germline
tree	starting tree, either a phylo object or a newick string
trait_list	list of all possible trait values
log_every_trait	frequency of trait states logged relative to log_every
tree_states	use states in the starting tree?
start_edge_length	edge length to use for all branches in starting tree
start_date	starting date to use as prior, in forward time
max_start_date	max starting date to use as prior, in forward time
...	additional arguments for XML writing functions

Value

File path of the written XML file

dowser documentation built on Nov. 5, 2025, 6:36 p.m.