shapeEffect: Shape effect

In ms609/TreeDistData: Analysis of Phylogenetic Tree Distance Measures

Shape effect

Description

Results of tests exploring the influence of tree shape on reconstructed tree distances.

Usage

shapeEffect

Format

A list of length 25. Each entry of the list is named according to the abbreviation of the corresponding method (see 'Methods tested' below).

Each entry is itself a list of ten elements. Each element contains a numeric vector listing the distances between each pair of trees with shape x and shape y, where:

⁠x = 1, 1, 1, 1, 2, 2, 2, 3, 3, 4⁠ and ⁠y = 1, 2, 3, 4, 2, 3, 4, 3, 4, 4⁠.

As trees are not compared with themselves (to avoid zero distances), elements where x = y contain 4 950 distances, whereas other elements contain 5 050 distances.

Details

For each of the four binary unrooted tree shapes on eight leaves, I labelled leaves at random until I had generated 100 distinct trees.

I measured the distance from each tree to each of the other 399 trees.

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

\insertRef

Li1996TreeDist

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Kendall2016TreeDistData

\insertRef

Nye2006TreeDist

\insertRef

Robinson1981TreeDist

\insertRef

Smith2019TreeDist

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SmithDistTreeDist

\insertRef

Steel1993TreeDist

\insertRef

Valiente2009TreeDist

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