AllDists: All distances between a pair of trees

In ms609/TreeDistData: Analysis of Phylogenetic Tree Distance Measures

All distances between a pair of trees

Description

AllDists() calculates the distances between two trees, using a suite of distance measures.

Usage

AllDists(tr1, tr2, verbose = FALSE)

Arguments

tr1, tr2	Phylogenetic trees of class phylo.
verbose	Logical specifying whether to print messages allowing the user to keep track of progress.

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.

Author(s)

Martin R. Smith ([e-mail])

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

See Also

Other pairwise tree distances: CompareAllTrees()

Examples

library('TreeTools', quietly = TRUE, warn.conflict = FALSE)
AllDists(BalancedTree(8), PectinateTree(8))
AllDists(list(BalancedTree(6), PectinateTree(6)), BalancedTree(6))

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