TreeSearch

R package for phylogenetic tree search under inapplicable-corrected parsimony and custom optimality criteria

https://github.com/ms609/treesearch

Science Score: 59.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
Found 32 DOI reference(s) in README
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Academic publication links
Links to: zenodo.org
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Committers with academic emails
2 of 6 committers (33.3%) from academic institutions
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Scientific vocabulary similarity
Low similarity (16.4%) to scientific vocabulary

Keywords

bioinformatics morphological-analysis phylogenetics r-package research-tool tree-search

Keywords from Contributors

consensus-tree phylogenetic-trees graphics plotting-in-r ternary-plots

Last synced: 6 months ago · JSON representation

Repository

R package for phylogenetic tree search under inapplicable-corrected parsimony and custom optimality criteria

Basic Info

Host: GitHub
Owner: ms609
License: gpl-3.0
Language: R
Default Branch: main
Homepage: https://ms609.github.io/TreeSearch/
Size: 123 MB

Statistics

Stars: 8
Watchers: 5
Forks: 4
Open Issues: 51
Releases: 26

Topics

bioinformatics morphological-analysis phylogenetics r-package research-tool tree-search

Created over 8 years ago · Last pushed 6 months ago

Metadata Files

Readme Changelog Contributing License Code of conduct Codemeta

TreeSearch

"TreeSearch" (Smith 2023) is an R package that contains a "shiny" user interface for interactive tree search and exploration of results, including character visualization, rogue taxon detection (Smith 2022a), tree space mapping (Smith 2022b), and cluster consensus trees.

Inapplicable character states are handled using the algorithm of Brazeau, Guillerme and Smith (2019) using the "Morphy" C library (Brazeau et al. 2017). Implied weighting (Goloboff, 1993), Profile Parsimony (Faith and Trueman, 2001) and Successive Approximations (Farris, 1969) are implemented; custom optimality criteria and search approaches can also be defined.

Installing in R

Full installation instructions, including notes on installing R, are available in a vignette.

Install and load the stable version from CRAN as follows:

```r install.packages("TreeSearch") library("TreeSearch")

Launch the Shiny App with:

TreeSearch::EasyTrees() ```

Install and load the development version of "TreeSearch" with:

r if(!require("curl")) install.packages("curl") if(!require("remotes")) install.packages("remotes") remotes::install_github("ms609/TreeSearch") library("TreeSearch")

Installing stand-alone application

The TreeSearch user interface can be run as a stand-alone application without installing R. Download the latest release for your platform. If your preferred platform is not supported, please contact the maintainer.

Installation on Windows

You may need to obtain the ffmpeg library before you can run TreeSearch.

This is best installed using 'Chocolatey'.

Once chocolatey is installed, open a PowerShell window with administrative privileges, and type choco install ffmpeg; then restart your computer.

Quick start

Launch a graphical user interface by typing TreeSearch::EasyTrees() in the R console.

For more control over search settings, see ?MaximizeParsimony().

Flow charts listing common actions facilitated by TreeSearch

Documentation

Package functions reference manual
Getting started
Using the GUI
Analysing tree spaces
Loading phylogenetic data into R
Parsimony search with inapplicable data
Calculating concavity profiles for Profile Parsimony
Tree search with profile parsimony

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

References

Brazeau M. D., Smith M. R., Guillerme T. (2017). MorphyLib: a library for phylogenetic analysis of categorical trait data with inapplicability. doi: 10.5281/zenodo.815372.

Brazeau, M. D., Guillerme, T. and Smith, M. R. (2019). An algorithm for morphological phylogenetic analysis with inapplicable data. Systematic Biology, 68(4), 619-631. doi: 10.1093/sysbio/syy083.

Faith D. P., Trueman J. W. H. (2001). Towards an inclusive philosophy for phylogenetic inference. Systematic Biology, 50(3), 331–350. doi: 10.1080/10635150118627.

Farris, J. S. (1969). A successive approximations approach to character weighting. Systematic Biology, 18(4), 374–385. doi: 10.2307/2412182.

Goloboff, P. A. (1993). Estimating character weights during tree search. Cladistics, 9(1), 83–91. doi: 10.1111/j.1096-0031.1993.tb00209.x.

Goloboff, P. A., Torres, A., Arias, J. S. (2018). Weighted parsimony outperforms other methods of phylogenetic inference under models appropriate for morphology. Cladistics, 34(4), 407–437. doi: 10.1111/cla.12205.

Smith, M. R. (2022a). Using information theory to detect rogue taxa and improve phylogenetic trees. Systematic Biology, 71(5), 1088–1094. doi: 10.1093/sysbio/syab099

Smith, M. R. (2022b). Robust analysis of phylogenetic tree space. Systematic Biology, 71(5), 1255–1270. doi: 10.1093/sysbio/syab100

Smith, M. R. (2023). TreeSearch: morphological phylogenetic analysis in R. R Journal, 14(4), 305-315. doi: 10.32614/RJ-2023-019

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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GitHub Events

Total

Create event: 9
Release event: 1
Issues event: 25
Watch event: 3
Delete event: 5
Issue comment event: 35
Push event: 209
Pull request event: 16
Fork event: 1

Last Year

Create event: 9
Release event: 1
Issues event: 25
Watch event: 3
Delete event: 5
Issue comment event: 35
Push event: 209
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Fork event: 1

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Committers: 3
Avg Commits per committer: 29.333
Development Distribution Score (DDS): 0.205

Top Committers

Name	Email	Commits
Martin Smith	m**s@g**m	1,349
Martin R. Smith	1****9	294
Martin R. Smith	p**8@d**k	89
GitHub Actions	a**s@g**m	32
Martin R. Smith	m**h@d**k	31
Fabrizio Sandri	1****i	1

Committer Domains (Top 20 + Academic)

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Total issues: 83
Total pull requests: 65
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Pull requests: 13
Average time to close issues: 2 months
Average time to close pull requests: about 10 hours
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ms609 (74)
HS6986 (2)
ad0012 (2)
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RussellGarwood (1)
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computingmachine (1)
KlausVigo (1)
EunokLee (1)

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ms609 (66)
FabrizioSandri (1)
KlausVigo (1)

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enhancement (9) app (8) search-optimization (5) on hold (3) up next (2) bug (2) help wanted (1) vignettes (1)

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Total packages: 1
Total downloads:
- cran 744 last-month

Total dependent packages: 3
Total dependent repositories: 4
Total versions: 28
Total maintainers: 1

cran.r-project.org: TreeSearch

Phylogenetic Analysis with Discrete Character Data

Homepage: https://ms609.github.io/TreeSearch/ (doc)
Documentation: http://cran.r-project.org/web/packages/TreeSearch/TreeSearch.pdf
License: GPL (≥ 3)
Latest release: 1.7.0
published 6 months ago

Versions: 28
Dependent Packages: 3
Dependent Repositories: 4
Downloads: 744 Last month

Rankings

Dependent packages count: 10.9%

Forks count: 12.2%

Dependent repos count: 14.6%

Average: 17.2%

Stargazers count: 21.9%

Downloads: 26.2%

Maintainers (1)

martin.smith@durham.ac.uk

Last synced: 6 months ago

Dependencies

DESCRIPTION cran

R >= 3.5.0 depends
Rcpp * imports
Rdpack >= 0.7 imports
Rogue > 2.0.0 imports
TreeDist >= 2.3.0 imports
TreeTools >= 1.7.0 imports
ape >= 5.6 imports
cli >= 3.0 imports
cluster * imports
fastmatch >= 1.1.3 imports
future * imports
promises * imports
protoclust * imports
shiny >= 1.6.0 imports
shinyjs * imports
stats * imports
Quartet * suggests
knitr * suggests
phangorn >= 2.2.1 suggests
rmarkdown * suggests
shinytest * suggests
spelling * suggests
testthat * 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/coverage.yml actions

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

.github/workflows/gcc-ASAN.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/memcheck.yml actions

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

.github/workflows/revdep.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

TreeSearch

Science Score: 59.0%

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README.md

TreeSearch

Installing in R

Launch the Shiny App with:

Installing stand-alone application

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