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,
  germline_trait_value = "?",
  root_trait = 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
germline_trait_value	trait value for germline, default '?' for ambiguous
root_trait	trait value of the root, if a fixed root state desired
...	additional arguments for XML writing functions

Value

File path of the written XML file

dowser documentation built on Aug. 20, 2026, 5:06 p.m.