ProfileScore: Profile Parsimony Score
In ms609/ProfileParsimony: Phylogenetic Inference by Profile Parsimony

Description Usage Arguments Value Author(s) References Examples

Calculate a tree's Profile Parsimony score with a given dataset, after Faith and Trueman (2001)

1	ProfileScore(tree, dataset)

`tree`	A tree of class `phylo`
`dataset`	Dataset of class `profileDat` (see `PrepareDataProfile`) Alternatively, a dataset of class `phyDat` can be provided, and will be (time-consumingly) converted within the function.

Zero minus the profile score (because the optimization algorithm assumes that smaller numbers are better)

Martin R. Smith

Faith, D. P. & Trueman, J. W. H. (2001). Towards an inclusive philosophy for phylogenetic inference. Systematic Biology 50:3, 331-350, doi: 10.1080/10635150118627

  data(referenceTree)
  data(congreveLamsdellMatrices)
  # In actual use, the dataset should be prepared with a much higher precision: try 1e+06?
  # Of course, gaining higher precision takes substantially longer.
  dataset <- PrepareDataProfile(congreveLamsdellMatrices[[42]], precision=1e+03)
  ProfileScore(referenceTree, dataset)