randomTreeDistances: Mean distances between random pairs of trees

In ms609/TreeDistData: Analysis of Phylogenetic Tree Distance Measures

Description

A three-dimensional array listing the distances between 1 000 random pairs of trees drawn from the uniform distribution using RandomTree(nTip, root = TRUE).

Usage

randomTreeDistances

Format

An object of class array of dimension 24 x 13 x 197.

Details

Distances were calculated using AllDists(); see the documentation at there for details of methods and their normalization.

Rows are named with abbreviations of the tree comparison metrics tested (see 'Methods tested' below).

Columns list the summary statistics of calculated tree distances: the minimum (min), 1%, 5%, 10%, 25%, 50% (i.e. median), 75%, 90%, 95%, 99% percentiles, maximum (max), mean (mean) and standard deviation (sd).

The third dimension lists the number of leaves in the trees compared.

For analysis of this data, see the accompanying vignette.

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_U, nni_u: Lower, best lower, 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

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Bogdanowicz2012TreeDist

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Li1996TreeDist

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Kendall2016TreeDistData

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Nye2006TreeDist

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Robinson1981TreeDist

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Smith2019TreeDist

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SmithDistTreeDist

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Steel1993TreeDist

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Valiente2009TreeDist

ms609/TreeDistData documentation built on May 21, 2021, 6:53 a.m.