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phylobench: Phylogenetic Benchmarking

phylobench implements tests of phylogenetic analyses and compares the output with expected outputs.

Currently, the implemented benchmarks are:

  • Branching times calculation
  • Base frequencies from DNA sequences
  • Phylogenetically independent contrasts
  • Variance-covariance under Brownian motion
  • Neiborgh-joining
  • Random coalescent trees
  • Random Yule trees
  • Type I error rate of the Mantel test
  • Ultrametric trees
  • Topological distances
  • Splits from unrooted trees
  • Reordering of the edge matrix

New benchmarks are added easily by:

  • Writing a function, say FUN, which runs the benchmark and returns "OK" if the results are as expected. This function must have no argument or its arguments defined by default so that it can be called with FUN().
  • Modifying the list .list_of_tests (in the file phylobench/R/phylobench.R) by adding the new benchmark like this:
.list_of_tests <- list(...., "Title of the benchmark" = "FUN")
  • Optionally, a file phylobench/man/FUN.Rd describing the new benchmark may be created.

If the benchmark requires files, these must be placed in phylobench/inst/extdata/.

All the benchmarks are run when building the vignette, so they can be visualized once the package is installed with:

vignette("PhylogeneticBenchmarks")

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