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 = 10, ...)
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. Defaults to 10; TNT sets a default of 3, but this is too low in some circumstances (Smith, 2019).

…

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.length properties.
IWDestroyMorphy: Free memory from morphyObjs initialized by IWScoreMorphy().

References

Goloboff1997TreeSearch
SmithTernTreeSearch

Examples

Run this code

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

# }

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