Expected length

For a given dataset and tree topology, ExpectedLength() estimates the length expected if the states of each character are shuffled randomly across the leaves.

Usage

ExpectedLength(dataset, tree, nRelabel = 1000, compress = FALSE)

Arguments

dataset

A phylogenetic data matrix of phangorn class phyDat, whose names correspond to the labels of any accompanying tree. Perhaps load into R using ReadAsPhyDat(). Additive (ordered) characters can be handled using Decompose().

tree

A tree of class phylo.

nRelabel

Integer specifying how many times to relabel leaves when estimating null tree length for RHI calculation. Steell et al. (2025) recommend 1000, but suggest that 100 may suffice. If zero (the default), the RHI is not calculated.

compress

Logical specifying whether to retain the compression of a phyDat object or to return a vector specifying to each individual character, decompressed using the dataset's index attribute.

Value

ExpectedLength() returns a numeric vector stating the median length of each character in dataset on tree after nRelabel random relabelling of leaves.

References

Steell EM, Hsiang AY, Field DJ (2025). “Revealing Patterns of Homoplasy in Discrete Phylogenetic Datasets with a Cross-Comparable Index.” Zoological Journal of the Linnean Society, 204(1), zlaf024. doi:10.1093/zoolinnean/zlaf024 .

See also

Other tree scoring: CharacterLength(), IWScore(), LengthAdded(), MinimumLength(), MorphyTreeLength(), TaxonInfluence()

Author

Martin R. Smith (martin.smith@durham.ac.uk)