write_clones_to_xmls: 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,
  ...
)

Value

File paths of the written XML files

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