write_clone_to_xml: 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,
  ...
)

Value

File path of the written XML file

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