An R Package to Quantify Tree Balance

For a given phylogenetic tree, calculates the Total Cophenetic Index. Reference: A. Mir, F. Rossello, L. A. Rotger (2013). A new balance index for phylogenetic trees. Math. Biosci. 241, 125-136 .


Build Status CRAN Status Badge CRAN Downloads Project Status: Inactive - The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows. R package implementing the Total Cophenetic Index measure of Mir et al. (2013).

The total cophenetic index describes how balanced a phylogenetic tree is, by measuring the how deep the most recent common ancestor of each pair of leaves lies within the tree.

See also

This functionality is now available via Rogter's package https://github.com/LuciaRotger/CollessLike R package.

References

A. Mir, F. Rossello, L. A. Rotger, A new balance index for phylogenetic trees. Math. Biosci. 241, 125-136 (2013).

News

TotalCopheneticIndex v1.0.1

  • Fixes some small errors in documentation and package metadata.
  • Small improvements to performance and code hygiene.
  • Add unit tests.
  • Link to CollessLike package.

TotalCopheneticIndex v1.0.0

  • Fixes some small errors in documentation and package metadata.
  • Provides accurate citation to the package.

TotalCopheneticIndex v0.1.0

  • Initial release.

Reference manual

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install.packages("TotalCopheneticIndex")

1.0.1 by Martin R. Smith, 4 months ago


https://github.com/ms609/tci


Report a bug at https://github.com/ms609/tci/issues


Browse source code at https://github.com/cran/TotalCopheneticIndex


Authors: Martin R. Smith [aut, cre, cph]


Documentation:   PDF Manual  


Unlimited license


Imports memoise

Suggests ape, CollessLike, knitr, testthat


See at CRAN