reconIgPhyML {dowser}

Do IgPhyML maximum parsimony reconstruction

Description

reconIgPhyML IgPhyML parsimony reconstruction function

Usage

reconIgPhyML(
  file,
  modelfile,
  id,
  igphyml = "igphyml",
  mode = "switches",
  type = "recon",
  nproc = 1,
  quiet = 0,
  rm_files = FALSE,
  rm_dir = NULL,
  states = NULL,
  palette = NULL,
  resolve = 2,
  rseed = NULL,
  force_resolve = FALSE,
  ...
)

Arguments

file

IgPhyML lineage file (see writeLineageFile)

modelfile

File specifying parsimony model

id

id for IgPhyML run

igphyml

location of igphyml executable

mode

return trees or count switches? (switches or trees)

type

get observed switches or permuted switches?

nproc

cores to use for parallelization

quiet

amount of rubbish to print

rm_files

remove temporary files?

rm_dir

remove temporary directory?

states

states in parsimony model

palette

deprecated

resolve

level of polytomy resolution. 0=none, 1=maximum parsimony, 2=maximum ambiguity

rseed

random number seed if desired

force_resolve

continue even if polytomy resolution fails?

...

additional arguments

Value

Either a tibble of switch counts or a list of trees with internal nodes predicted by parsimony.