write_clones_to_xmls: Wrapper to write multiple clones to XML files

In dowser: B Cell Receptor Phylogenetics Toolkit

Wrapper to write multiple clones to XML files

Description

Wrapper to write multiple clones to XML files

Usage

write_clones_to_xmls(
  data,
  id,
  trees = NULL,
  time = NULL,
  trait = NULL,
  template = NULL,
  outfile = NULL,
  replacements = NULL,
  trait_list = NULL,
  mcmc_length = 1e+06,
  log_every = 1000,
  include_germline_as_root = FALSE,
  include_germline_as_tip = FALSE,
  germline_range = c(-10000, 10000),
  tree_states = FALSE,
  start_edge_length = 100,
  start_date = NULL,
  max_start_date = NULL,
  ...
)

Arguments

data	a list of airrClone objects
id	identifer for this analysis
trees	optional list of starting trees, either phylo objects or newick strings
time	name of column representing sample time
trait	name of column representing a trait
template	XML template
outfile	output file path prefix
replacements	list of additional replacements to make in the template
trait_list	list of all possible trait values
mcmc_length	number of MCMC iterations
log_every	frequency of states logged. auto will divide mcmc_length by log_target
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_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 paths of the written XML files

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