getTrees {dowser}

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,
  ...
)

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

Value

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

See Also

formatClones, findSwitches, buildPhylo, buildPratchet, buildPML, buildIgphyml

Examples

data(ExampleClones)

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

## Not run: 
data(ExampleClones)

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

## End(Not run)