findSwitches {dowser}

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

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.

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)