sprDistances: Tree distance and SPR moves

In ms609/TreeDistData: Analysis of Phylogenetic Tree Distance Measures

Tree distance and SPR moves

Description

Datasets testing whether separating trees by increasingly many moves results in a corresponding increase in their distance.

Usage

sprDistances

Format

A list of length 21. Each entry is named according to the corresponding tree distance method; see 'Methods tested' below.

Each member of the list is a 100 × 100 matrix listing the distance between each pair of trees in the SPR chain (see 'Details'), numbered from 1 to 100.

Details

I generated a chain of 100 50-leaf trees, starting from a pectinate tree and deriving each tree in turn by performing an SPR operation on the previous tree. A consistent measure of tree similarity should correlate with the number of SPR operations separating a pair of trees in this chain. This said, because one SPR operation may counteract some of the difference introduced by a previous one, perfect correlation is unlikely.

For analysis of this data, see the accompanying vignette.

Methods tested

• pid: Phylogenetic Information Distance (Smith 2020)

• msid: Matching Split Information Distance (Smith 2020)

• cid: Clustering Information Distance (Smith 2020)

• qd: Quartet divergence (Smith 2019)

• nye: Nye et al. tree distance (Nye et al. 2006)

• jnc2, jnc4: Jaccard-Robinson-Foulds distances with k = 2, 4, conflicting pairings prohibited ('no-conflict')

• joc2, jco4: Jaccard-Robinson-Foulds distances with k = 2, 4, conflicting pairings permitted ('conflict-ok')

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

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

• masti: Information content of Maximum Agreement Subtree

• nni_l, nni_t, nni_u: Lower bound, tight upper bound, and upper bound for nearest-neighbour interchange distance (Li et al. 1996)

• spr: Approximate SPR distance

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

• rf: Robinson-Foulds distance (Robinson & Foulds 1981)

• icrf: Information-corrected Robinson-Foulds distance (Smith 2020)

• path: Path distance (Steel & Penny 1993)

Source

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

References

\insertRef

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 June 30, 2024, 7:21 p.m.