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R package for phylogenetic tree search under custom optimality criteria
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README.md

Build Status codecov CRAN Status Badge CRAN Downloads DOI Project Status: Active – – The project has reached a stable, usable state and is being actively developed.

TreeSearch

This package exists to allow parsimony-style tree searches in R.

It extends the basic functionality available in phangorn, with a view to making tree search faster and more efficient, and allowing user-defined optimality criteria to be employed.

Implied weighting and heuristic searches such as the Parsimony Ratchet are implemented (function: Ratchet).

Installation

Install and load the library from CRAN as follows:

install.packages('TreeSearch')
library('TreeSearch')

If you're feeling brave, you can install the development version thus:

if(!require(devtools)) install.packages("devtools")
devtools::install_github('ms609/TreeSearch')

Optimality criteria

TreeSearch allows the implementation of various optimality criteria, including

  • The Profile Parsimony approach introduced by Faith and Trueman (2001).
  • Successive Approximations weighting (Farris 1969).
  • Fitch parsimony with inapplicable data (Brazeau, Guillerme and Smith, 2019).

It is also possible to specify bespoke optimality criteria.

Documentation

References

Brazeau, M. D., Guillerme, T. and Smith, M. R. in press. An algorithm for morphological phylogenetic analysis with inapplicable data. Systematic Biology. doi:10.1093/sysbio/syy083.

D. P. Faith, J. W. H. Trueman, Towards an inclusive philosophy for phylogenetic inference. Syst. Biol. 50, 331–350 (2001). 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

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