sevenTipDistances: Distances between unrooted seven-leaf trees

In ms609/TreeDistData: Analysis of Phylogenetic Tree Distance Measures

Distances between unrooted seven-leaf trees

Description

Distances between each possible pairing of the 945 unrooted seven-leaf trees (equivalent to rooted 6-leaf trees). Following Kendall and Colijn (2016).

Usage

sevenTipDistances

Format

An object of class list of length 21.

Details

Each list entry is named with the abbreviation of the corresponding tree distance method (see 'Methods tested' below).

Each item in the list contains a 945×945 matrix reporting the distance between each pair of seven-leaf trees. The first 630 trees are pectinate (tree shape 0), the final 315 are balanced (tree shape 1).

Methods tested

• pid: Phylogenetic Information Distance (Smith 2020), normalized against the phylogenetic information content of the splits in the trees being compared.

• msid: Matching Split Information Distance (Smith 2020), normalized against the phylogenetic information content of the splits in the trees being compared.

• cid: Clustering Information Distance (Smith 2020), normalized against the entropy of the splits in the trees being compared.

• qd: Quartet divergence (Smith 2019), normalized against its maximum possible value for n-leaf trees.

• nye: Nye et al. tree distance (Nye et al. 2006), normalized against the total number of splits in the trees being compared.

• jnc2, jnc4: Jaccard-Robinson-Foulds distances with k = 2, 4, conflicting pairings prohibited ('no-conflict'), normalized against the total number of splits in the trees being compared.

• jco2, jco4: Jaccard-Robinson-Foulds distances with k = 2, 4, conflicting pairings permitted ('conflict-ok'), normalized against the total number of splits in the trees being compared.

• ms: Matching Split Distance (Bogdanowicz & Giaro 2012), unnormalized.

• mast: Size of Maximum Agreement Subtree (Valiente 2009), unnormalized.

• masti: Information content of Maximum Agreement Subtree, unnormalized.

• nni_l, nni_L, nni_t, nni_U, nni_u: Lower, best lower, tight upper, best upper, and upper bounds for nearest-neighbour interchange distance (Li et al. 1996), unnormalized. 'Best' lower bounds jump sharply when mismatched regions of a tree become large enough that a tight upper bound cannot be exactly calculated, so are discontinuous and cannot readily be compared between trees.

• spr: Approximate subtree prune and regraft SPR distance, unnormalized.

• tbr_l, tbr_u: Lower and upper bound for tree bisection and reconnection (TBR) distance, calculated using TBRDist; unnormalized.

• rf: Robinson-Foulds distance (Robinson & Foulds 1981), unnormalized.

• icrf: Robinson-Foulds distance, splits weighted by phylogenetic information content (Smith 2020), unnormalized.

• path: Path distance (Steel & Penny 1993), unnormalized.

Source

Scripts used to generate data objects are housed in the data-raw directory.

References

\insertRef

Bogdanowicz2012TreeDist

\insertRef

Li1996TreeDist

\insertRef

Kendall2016TreeDistData

\insertRef

Nye2006TreeDist

\insertRef

Robinson1981TreeDist

\insertRef

Smith2019TreeDist

\insertRef

SmithDistTreeDist

\insertRef

Steel1993TreeDist

\insertRef

Valiente2009TreeDist

Examples

library('TreeTools', quietly = TRUE, warn.conflicts = FALSE)

# Pectinate unrooted tree shape:
plot(UnrootedTreeWithShape(0, 7))

# Balanced unrooted tree shape:
plot(UnrootedTreeWithShape(1, 7))

ms609/TreeDistData documentation built on June 30, 2024, 7:21 p.m.