CIDist_NullDist: Simulated Null Distributions for CI Distance

In npcooley/SynExtend: Tools for Working With Synteny Objects

Simulated Null Distributions for CI Distance

Description

Simulated values of Clustering Information Distance for random trees with 4 to 200 shared leaves.

Usage

data("CIDist_NullDist")

Format

A matrix CI_DISTANCE_INTERNAL with 197 columns and 13 rows.

Details

Each column of the matrix corresponds to the distribution of distances between random trees with the given number of leaves. This begins at CI_DISTANCE_INTERNAL[,1] corresponding to 4 leaves, and ends at CI_DISTANCE_INTERNAL[,197] corresponding to 200 leaves. Distances begin at 4 leaves since there is only one unrooted tree with 1, 2, or 3 leaves (so the distance between any given tree with less than 4 leaves is always 0).

Each row of the matrix corresponds to statistics for the given simulation set. The first row gives the minimum value, the next 9 give quantiles in c(1%, 5%, 10%, 25%, 50%, 75%, 90%, 95%, 99%), and the last three rows give the max, mean, and sd (resp.).

Source

Datafiles obtained from the TreeDistData package, published as part of Smith (2020).

References

Smith, Martin R. Information theoretic generalized Robinson–Foulds metrics for comparing phylogenetic trees. Bioinformatics, 2020. 36(20):5007-5013.

Examples

data(CIDist_NullDist)

npcooley/SynExtend documentation built on Dec. 20, 2024, 4:03 p.m.