findSwitches {dowser}

R Documentation

Create a bootstrap distribution for clone sequence alignments, and estimate trees for each bootstrap replicate.

Description

findSwitches Phylogenetic bootstrap function.

Usage

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

Arguments

clones	tibble airrClone objects, the output of formatClones
permutations	number of bootstrap replicates to perform
trait	trait to use for parsimony models
igphyml	location of igphyml executible
fixtrees	keep tree topologies fixed? (bootstrapping will not be perfomed)
downsample	downsample clones to have a maximum specified tip/switch ratio?
tip_switch	maximum allowed tip/switch ratio if downsample=TRUE
nproc	number of cores to parallelize computations
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
quiet	amount of rubbish to print to console
rm_temp	remove temporary files (default=TRUE)
palette	a named vector specifying colors for each state
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
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

Details

Tree building details are the same as getTrees. If keeptrees=TRUE (default) the returned object will contain a list named "trees" which contains a list of estimated tree objects for each bootstrap replicate. The object is structured like: trees[[<replicate>]][[<tree index>]]. If igphyml is specified (as well as trait), the returned object will contain a tibble named "switches" containing switch count information. This object can be passed to testSP and other functions to perform parsimony based trait value tests.

Value

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

See Also

Uses output from formatClones with similar arguments to getTrees. Output can be visualized with plotTrees, and tested with testPS, testSC, and testSP.

Examples

## Not run: 
data(ExampleAirr)
ExampleAirr$sample_id <- sample(ExampleAirr$sample_id)
clones <- formatClones(ExampleAirr, trait="sample_id")

igphyml <- "~/apps/igphyml/src/igphyml"
btrees <- findSwitches(clones[1:2,], permutations=10, nproc=1,
   igphyml=igphyml, trait="sample_id")
plotTrees(btrees$trees[[4]])[[1]]
testPS(btrees$switches)

## End(Not run)

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