TreeDist

Calculate distances between phylogenetic trees in R

Science Score: 59.0%

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Keywords

phylogenetic-trees r r-package rstats tree-distances trees

Keywords from Contributors

consensus-tree phylogenetics graphics plotting-in-r ternary-plots bioinformatics morphological-analysis research-tool tree-search comparison

Last synced: 6 months ago · JSON representation

Repository

Calculate distances between phylogenetic trees in R

Basic Info

Host: GitHub
Owner: ms609
Language: R
Default Branch: main
Homepage: https://ms609.github.io/TreeDist/
Size: 64.9 MB

Statistics

Stars: 33
Watchers: 4
Forks: 6
Open Issues: 25
Releases: 27

Topics

phylogenetic-trees r r-package rstats tree-distances trees

Created over 6 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing Code of conduct Codemeta

TreeDist

'TreeDist' is an R package that implements a suite of metrics that quantify the topological distance between pairs of unweighted phylogenetic trees. It also includes a simple 'Shiny' application to allow the visualization of distance-based tree spaces, and functions to calculate the information content of trees and splits.

'TreeDist' primarily employs metrics in the category of 'generalized Robinson–Foulds distances': they are based on comparing splits (bipartitions) between trees, and thus reflect the relationship data within trees, with no reference to branch lengths.

Generalized RF distances

The Robinson-Foulds distance simply tallies the number of non-trivial splits (sometimes inaccurately termed clades, nodes or edges) that occur in both trees – any splits that are not perfectly identical contribute one point to the distance score of zero, however similar or different they are. By overlooking potential similarities between almost-identical splits, this conservative approach has undesirable properties.

'Generalized' RF metrics generate matchings that pair splits in one tree with similar splits in the other. Each pair of splits is assigned a similarity score; the sum of these scores in the optimal matching then quantifies the similarity between two trees.

Different ways of calculating the the similarity between a pair of splits lead to different tree distance metrics, implemented in the functions below:

MutualClusteringInfo(), SharedPhylogeneticInfo()

Smith (2020) scores matchings based on the amount of information that one partition contains about the other. The Mutual Phylogenetic Information assigns zero similarity to split pairs that cannot both exist on a single tree; The Mutual Clustering Information metric is more forgiving, and exhibits more desirable behaviour; it is the recommended metric for tree comparison. (Its complement, ClusteringInfoDistance(), returns a tree distance.)
NyeSimilarity()

Nye et al. (2006) score matchings according to the size of the largest split that is consistent with both of them, normalized against the Jaccard index. This approach is extended by Böcker et al. (2013) with the Jaccard-Robinson-Foulds metric (function JaccardRobinsonFoulds()).
MatchingSplitDistance()

Bogdanowicz and Giaro (2012) and Lin et al. (2012) independently proposed counting the number of 'mismatched' leaves in a pair of splits. MatchingSplitInfoDistance() provides an information-based equivalent (Smith 2020).

The package also implements the variation of the path distance proposed by Kendal and Colijn (2016) (function KendallColijn()), approximations of the Nearest-Neighbour Interchange (NNI) distance (function NNIDist(); following Li et al. (1996)), and calculates the size (function MASTSize()) and information content (function MASTInfo()) of the Maximum Agreement Subtree.

For an implementation of the Tree Bisection and Reconnection (TBR) distance, see the package 'TBRDist'.

Installation

Install and load the library from CRAN as follows: r install.packages('TreeDist') library('TreeDist')

You can install the development version of the package with: r if(!require("curl")) install.packages("curl") if(!require("remotes")) install.packages("remotes") remotes::install_github("ms609/TreeDist")

Tree space analysis

Construct tree spaces and readily visualize projected landscapes, avoiding common analytical pitfalls (Smith, 2022), using the inbuilt graphical user interface (Shiny GUI):

r TreeDist::MapTrees()

Serious analysts should consult the vignette for a command-line interface.

Documentation

References

Böcker, S. et al. (2013) The Generalized Robinson-Foulds metric. Algorithms in Bioinformatics. WABI 2013. Lecture Notes in Computer Science, 8126, 156–69.
Bogdanowicz, D. and Giaro, K. (2012) Matching split distance for unrooted binary phylogenetic trees. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9, 150–160.
Kendall, M. and Colijn, C. (2016) Mapping phylogenetic trees to reveal distinct patterns of evolution. Mol Biol Evol, 33, 2735–2743.
Li, M., Tromp, J. and Zhang, L.-X. (1996) Some notes on the nearest neighbour interchange distance. Computing and Combinatorics, Goos, G., Hartmanis, J., Leeuwen, J., Cai, J.-Y., and Wong, C. K., eds. Springer, Berlin. 343–351.
Nye, T.M.W. et al. (2006) A novel algorithm and web-based tool for comparing two alternative phylogenetic trees. Bioinformatics, 22, 117–119.
Smith, M.R. (2020) Information theoretic Generalized Robinson-Foulds metrics for comparing phylogenetic trees. Bioinformatics, 36, 5007–5013.
Smith, M.R. (2022) Robust analysis of phylogenetic tree space. Systematic Biology, 71, 1255–1270.

Please note that the 'TreeDist' project is released with a Contributor Code of Conduct. By contributing to this project, you agree to abide by its terms.

Owner

Name: Martin R. Smith
Login: ms609
Kind: user
Location: Durham, UK
Company: Department of Earth Sciences, Durham University

Website: https://orcid.org/0000-0001-5660-1727
Twitter: PalaeoSmith
Repositories: 21
Profile: https://github.com/ms609

Palaeontology & phylogenetics

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        "issueNumber": "5",
        "datePublished": "2022",
        "isPartOf": {
          "@type": [
            "PublicationVolume",
            "Periodical"
          ],
          "volumeNumber": "71",
          "name": "Systematic Biology"
        }
      }
    },
    {
      "@type": "SoftwareSourceCode",
      "datePublished": "2020",
      "author": [
        {
          "@type": "Person",
          "givenName": [
            "Martin",
            "R."
          ],
          "familyName": "Smith",
          "email": "martin.smith@durham.ac.uk"
        }
      ],
      "name": "TreeDist: Distances between Phylogenetic Trees. R package version 2.11.1",
      "identifier": "10.5281/zenodo.3528124",
      "@id": "https://doi.org/10.5281/zenodo.3528124",
      "sameAs": "https://doi.org/10.5281/zenodo.3528124",
      "isPartOf": {
        "@type": "PublicationIssue",
        "datePublished": "2020",
        "isPartOf": {
          "@type": [
            "PublicationVolume",
            "Periodical"
          ],
          "name": "Comprehensive R Archive Network"
        }
      }
    }
  ]
}

GitHub Events

Total

Create event: 11
Release event: 2
Issues event: 5
Watch event: 4
Delete event: 10
Issue comment event: 36
Push event: 161
Pull request review event: 6
Pull request review comment event: 6
Pull request event: 17

Last Year

Create event: 11
Release event: 2
Issues event: 5
Watch event: 4
Delete event: 10
Issue comment event: 36
Push event: 161
Pull request review event: 6
Pull request review comment event: 6
Pull request event: 17

Committers

Last synced: 9 months ago

All Time

Total Commits: 2,237
Total Committers: 4
Avg Commits per committer: 559.25
Development Distribution Score (DDS): 0.19

Past Year

Commits: 109
Committers: 2
Avg Commits per committer: 54.5
Development Distribution Score (DDS): 0.156

Top Committers

Name	Email	Commits
Martin Smith	m**s@g**m	1,812
Martin R. Smith	1****9	349
GitHub Actions	a**s@g**m	48
Martin R. Smith	p**8@d**k	28

Committer Domains (Top 20 + Academic)

durham.ac.uk: 1 github.com: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 57
Total pull requests: 85
Average time to close issues: 6 months
Average time to close pull requests: 17 days
Total issue authors: 13
Total pull request authors: 3
Average comments per issue: 1.12
Average comments per pull request: 0.55
Merged pull requests: 67
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 4
Pull requests: 14
Average time to close issues: 27 days
Average time to close pull requests: about 14 hours
Issue authors: 3
Pull request authors: 2
Average comments per issue: 0.75
Average comments per pull request: 0.29
Merged pull requests: 2
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

ms609 (39)
Jigyasa3 (5)
liamxg (2)
ghost (2)
ammaraziz (1)
roblanf (1)
jc17659 (1)
danimelsz (1)
aguang (1)
rforster1 (1)
Sidduppal (1)
Cassie818 (1)
cdp-rna (1)
qwer62667771 (1)

Pull Request Authors

ms609 (87)
SermetPekin (4)
Copilot (2)

Top Labels

Issue Labels

enhancement (3)

Pull Request Labels

Packages

Total packages: 2
Total downloads:
- cran 1,376 last-month
Total docker downloads: 123

Total dependent packages: 3
(may contain duplicates)
Total dependent repositories: 6
(may contain duplicates)
Total versions: 35
Total maintainers: 1

cran.r-project.org: TreeDist

Calculate and Map Distances Between Phylogenetic Trees

Homepage: https://ms609.github.io/TreeDist/
Documentation: http://cran.r-project.org/web/packages/TreeDist/TreeDist.pdf
License: GPL (≥ 3)
Latest release: 2.10.1
published 6 months ago

Versions: 25
Dependent Packages: 3
Dependent Repositories: 5
Downloads: 1,376 Last month
Docker Downloads: 123

Rankings

Dependent packages count: 10.6%

Stargazers count: 11.9%

Forks count: 12.3%

Average: 12.4%

Dependent repos count: 13.2%

Downloads: 13.8%

Maintainers (1)

martin.smith@durham.ac.uk

Last synced: 6 months ago

conda-forge.org: r-treedist

Homepage: https://ms609.github.io/TreeDist/, https://github.com/ms609/TreeDist
License: GPL-3.0-or-later
Latest release: 2.5.0
published over 3 years ago

Versions: 10
Dependent Packages: 0
Dependent Repositories: 1

Rankings

Dependent repos count: 24.1%

Average: 45.1%

Stargazers count: 51.0%

Dependent packages count: 51.5%

Forks count: 53.9%

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 3.4.0 depends
stats * depends
Rdpack >= 0.7 imports
TreeTools >= 1.7.1.9000 imports
ape >= 5.0 imports
cli >= 3.0 imports
colorspace * imports
memoise * imports
phangorn >= 2.2.1 imports
shiny * imports
shinyjs * imports
MASS * suggests
Quartet * suggests
Rcpp >= 1.0.8 suggests
Rogue * suggests
Ternary >= 1.1.2 suggests
TreeDistData > 0.1.0 suggests
TreeSearch * suggests
Umatrix * suggests
bookdown * suggests
cluster * suggests
ggplot2 * suggests
hypervolume * suggests
kdensity * suggests
knitr * suggests
parallel * suggests
plotly * suggests
protoclust * suggests
readxl * suggests
rgl * suggests
rmarkdown * suggests
spelling * suggests
testthat >= 3.0 suggests
uwot * suggests
vdiffr >= 1.0.0 suggests

.github/workflows/R-CMD-check.yml actions

actions/checkout v2 composite
r-lib/actions/check-r-package v2 composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite
r-lib/actions/setup-r-dependencies v2 composite

.github/workflows/RcppDeepState.yml actions

FabrizioSandri/RcppDeepState-action main composite
actions/checkout v2 composite

.github/workflows/codemeta.yml actions

actions/cache v2 composite
actions/checkout v2 composite
r-lib/actions/setup-r v2 composite

.github/workflows/memcheck.yml actions

actions/cache v2 composite
actions/checkout v2 composite
r-lib/actions/setup-pandoc master composite
r-lib/actions/setup-r v2 composite

.github/workflows/pkgdown.yml actions

actions/cache v2 composite
actions/checkout v2 composite
r-lib/actions/setup-pandoc master composite
r-lib/actions/setup-r master composite

.github/workflows/revdepcheck.yml actions

actions/cache v2 composite
actions/checkout v2 composite
actions/upload-artifact main composite
r-lib/actions/setup-pandoc v2 composite
r-lib/actions/setup-r v2 composite

.github/workflows/rhub.yaml actions

actions/checkout v3 composite
r-hub/rhub2/actions/rhub-check v1 composite
r-hub/rhub2/actions/rhub-setup v1 composite
r-hub/rhub2/actions/rhub-setup-r v1 composite

TreeDist

Science Score: 59.0%

Keywords

Keywords from Contributors

Repository

Basic Info

Statistics

Topics

Metadata Files

README.md

TreeDist

Generalized RF distances

Installation

Tree space analysis

Documentation

See also

References

Owner

CodeMeta (codemeta.json)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

cran.r-project.org: TreeDist

Rankings

Maintainers (1)

conda-forge.org: r-treedist

Rankings

Dependencies