MeilaVariationOfInformation: Use variation of clustering information to compare pairs of...

In TreeDist: Calculate and Map Distances Between Phylogenetic Trees

Use variation of clustering information to compare pairs of splits

Description

Compare a pair of splits viewed as clusterings of taxa, using the variation of clustering information proposed by \insertCiteMeila2007TreeDist.

Usage

MeilaVariationOfInformation(split1, split2)

MeilaMutualInformation(split1, split2)

Arguments

split1, split2

Logical vectors listing leaves in a consistent order, identifying each leaf as a member of the ingroup (TRUE) or outgroup (FALSE) of the split in question.

Details

This is equivalent to the mutual clustering information \insertCiteVinh2010TreeDist. For the total information content, multiply the VoI by the number of leaves.

Value

MeilaVariationOfInformation() returns the variation of (clustering) information, measured in bits.

MeilaMutualInformation() returns the mutual information, measured in bits.

Author(s)

Martin R. Smith ([e-mail])

References

\insertAllCited

Examples

# Maximum variation = information content of each split separately
A <- TRUE
B <- FALSE
MeilaVariationOfInformation(c(A, A, A, B, B, B), c(A, A, A, A, A, A))
Entropy(c(3, 3) / 6) + Entropy(c(0, 6) / 6)

# Minimum variation = 0
MeilaVariationOfInformation(c(A, A, A, B, B, B), c(A, A, A, B, B, B))

# Not always possible for two evenly-sized splits to reach maximum
# variation of information
Entropy(c(3, 3) / 6) * 2  # = 2
MeilaVariationOfInformation(c(A, A, A,B ,B, B), c(A, B, A, B, A, B)) # < 2

# Phylogenetically uninformative groupings contain spliting information
Entropy(c(1, 5) / 6)
MeilaVariationOfInformation(c(B, A, A, A, A, A), c(A, A, A, A, A, B))

TreeDist documentation built on Sept. 11, 2024, 9:10 p.m.