getTrees: Estimate lineage tree topologies, branch lengths, and internal node states if desired

Description

getTrees Tree building function.

Usage

getTrees(
  clones,
  trait = NULL,
  id = NULL,
  dir = NULL,
  modelfile = NULL,
  build = "pratchet",
  exec = NULL,
  igphyml = NULL,
  fixtrees = FALSE,
  nproc = 1,
  quiet = 0,
  rm_temp = TRUE,
  palette = NULL,
  seq = NULL,
  collapse = FALSE,
  ...
)

Value

A list of phylo objects in the same order as data.

Arguments

clones: a tibble of airrClone objects, the output of formatClones
trait: trait to use for parsimony models (required if igphyml specified)
id: unique identifer for this analysis (required if igphyml or dnapars specified)
dir: directory where temporary files will be placed.
modelfile: file specifying parsimony model to use
build: program to use for tree building (pratchet, pml, dnapars, dnaml, igphyml)
exec: location of desired phylogenetic executable
igphyml: optional location of igphyml executible for parsimony
fixtrees: if TRUE, use supplied tree topologies
nproc: number of cores to parallelize computations
quiet: amount of rubbish to print to console
rm_temp: remove temporary files (default=TRUE)
palette: deprecated
seq: column name containing sequence information
collapse: Collapse internal nodes with identical sequences?
...: Additional arguments passed to tree building programs

Details

Estimates phylogenetic tree topologies and branch lengths for a list of airrClone objects. By default, it will use phangnorn::pratchet to estimate maximum parsimony tree topologies, and ape::acctran to estimate branch lengths. If igpyhml is specified, internal node trait values will be predicted by maximum parsimony. In this case, dir will need to be specified as a temporary directory to place all the intermediate files (will be created if not available). Further, id will need to specified to serve as a unique identifier for the temporary files. This should be chosen to ensure that multiple getTrees calls using the same dir do not overwrite each others files.

modelfile is written automatically if not specified, but doesn't include any constraints. Intermediate files are deleted by default. This can be toggled using (rm_files).

For examples and vignettes, see https://dowser.readthedocs.io

Examples

Run this code

data(ExampleClones)

trees <- getTrees(ExampleClones[10,])
plotTrees(trees)[[1]]

if (FALSE) {
data(ExampleClones)

trees <- getTrees(ExampleClones[10,],igphyml="/path/to/igphyml",
         id="temp",dir="temp", trait="sample_id")
plotTrees(trees)[[1]]
}