bullseye: Bullseye test results

In ms609/TreeDistData: Analysis of Phylogenetic Tree Distance Measures

Description

Implementation and results of a 'Bullseye' test, after that proposed by Kuhner and Yamato (2015).

Usage

bullseyeTrees

bullMoDiInferred

bullMoDiScores

bullseyeMorphInferred

bullseyeMorphScores

Format

bullseyeTrees is a list with four elements, named 5 leaves, 10 leaves, 20 leaves and 50 leaves. Each element contains 1 000 trees with n leaves, randomly sampled (note: not from the uniform distribution) using ape::rtree().

The bullseyeMorph prefix refers to the 'subsampling' experiment described by Smith (2020); the bullMoDi prefix refers to the 'miscoding' experiment.

bull...Inferred is a list with four elements, named as in bullseyeTrees. Each element contains 1 000 sub-elements. Each sub-element is a list of ten trees, which have been inferred from progressively more degraded datasets, originally simulated from the corresponding tree in bullseyeTrees.

bull...Scores is a list with four elements, named as in bullseyeTrees. Each element contains a three dimensional array, in which the first dimension corresponds to the progressive degrees of degradation, labelled according to the number of characters present or the percentage of tokens switched; the second dimension is named with an abbreviation of the tree similarity / distance metric used to score the trees (see 'Methods tested' below), and the third dimension contains 1 000 entries corresponding to the trees in bullseyeTrees. Each cell contains the distance between the inferred tree and the generative tree under the stated tree distance metric.

An object of class list of length 4.

An object of class list of length 4.

An object of class list of length 4.

An object of class list of length 4.

Details

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

Kuhner2015TreeDistData

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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.