findSwitches: 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,
  ...
)

Value

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

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: 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
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.

Trait values cannot contain values N, UCA, or NTIP. These are reserved for use by test statistic functions.

Examples

Run this code

if (FALSE) {
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)
}