bootstrapTrees {dowser}R Documentation

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,
  ...
)

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

Value

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


[Package dowser version 2.1.0 Index]