bootstrapTrees: Deprecated! Please use findSwitches instead.

Description

bootstrapTrees Phylogenetic bootstrap function.

Usage

bootstrapTrees(
  clones,
  bootstraps,
  nproc = 1,
  trait = NULL,
  dir = NULL,
  id = NULL,
  modelfile = NULL,
  build = "pratchet",
  exec = NULL,
  igphyml = NULL,
  fixtrees = FALSE,
  quiet = 0,
  rm_temp = TRUE,
  palette = NULL,
  resolve = 2,
  rep = NULL,
  keeptrees = TRUE,
  lfile = NULL,
  seq = NULL,
  downsample = FALSE,
  tip_switch = 20,
  boot_part = "locus",
  force_resolve = FALSE,
  ...
)

Value

A list of trees and/or switch counts for each bootstrap replicate.

Arguments

clones: tibble airrClone objects, the output of formatClones
bootstraps: number of bootstrap replicates to perform
nproc: number of cores to parallelize computations
trait: trait to use for parsimony models (required if igphyml specified)
dir: directory where temporary files will be placed (required if igphyml or dnapars specified)
id: unique identifer for this analysis (required if igphyml or dnapars specified)
modelfile: file specifying parsimony model to use
build: program to use for tree building (phangorn, dnapars)
exec: location of desired phylogenetic executable
igphyml: location of igphyml executible if trait models desired
fixtrees: keep tree topologies fixed? (bootstrapping will not be perfomed)
quiet: amount of rubbish to print to console
rm_temp: remove temporary files (default=TRUE)
palette: deprecated
resolve: how should polytomies be resolved? 0=none, 1=max parsminy, 2=max ambiguity + polytomy skipping, 3=max ambiguity
rep: current bootstrap replicate (experimental)
keeptrees: keep trees estimated from bootstrap replicates? (TRUE)
lfile: lineage file input to igphyml if desired (experimental)
seq: column name containing sequence information
downsample: downsample clones to have a maximum specified tip/switch ratio?
tip_switch: maximum allowed tip/switch ratio if downsample=TRUE
boot_part: is "locus" bootstrap columns for each locus separately
force_resolve: continue even if polytomy resolution fails?
...: additional arguments to be passed to tree building program