TreeSearch (version 0.2.2)

IWScore: Implied weights parsimony Score

Description

Calculate a tree's Parsimony score with a given dataset using implied weights (Goloboff 1997)

Usage

IWScore(tree, dataset, concavity = 4, ...)
IWInitMorphy(dataset)
IWDestroyMorphy(dataset)

Arguments

tree

A tree of class phylo.

dataset

Dataset of class phyDat. The dataset should have been prepared using dataset <- PrepareDataIW(dataset); if this step has not been completed, the dataset will be (time-consumingly) prepared within the function. In subsidiary functions, the dataset will have been initialized using IWInitMorphy, and must be destroyed using IWDestroyMorphy.

concavity

A numeric value to use as the concavity constant (`k`) in implied weighting.

…

unused; allows additional parameters specified within … to be received by the function without throwing an error.

Value

The 'fit', `h / h + k`, where `h` is the amount of homoplasy ('extra steps') and `k` is a constant (the 'concavity constant')

Functions

• IWInitMorphy: Initialize dataset by adding morphyObjs and min.steps.

• IWDestroyMorphy: Free memory from morphyObjs initialized by IWScoreMorphy.

References

Goloboff1997TreeSearch

Examples

# NOT RUN {
  data(referenceTree)
  data(congreveLamsdellMatrices)
  dataset <- PrepareDataIW(congreveLamsdellMatrices[[42]])
  IWScore(referenceTree, dataset)

# }