reconIgPhyML - 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.