In DomBennett/om..partitionfinder: PartitionFinder2

knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)

Run `partitionfinder` with `outsider` in R

Select best-fit partitioning schemes and models of molecular evolution for phylogenetic analyses.

Install and look up help

library(outsider)
module_install(repo = "dombennett/om..partitionfinder")
# module_help(repo = "dombennett/om..partitionfinder")

Examples

The module comes with three functions for each program comprising the "PartitionFinder2" software.

PartitionFinder - For nucleotide data
PartitionFinderMorphology - For morphological data
PartitionFinderProtein - For protein data

The module ships with example datasets. These data can be accessed by using the example_fetch function.

At a minimum all that is required is to provide a input folder containing the configuration file and the data. In the arguments, there is no need to call python, this is done by the module. For example, on the command-line if you wrote python PartitionFinder.py example where "example" is the name of the input folder, in R this would be partitionfinder("example").

If required, additional arguments can be provided as a character vector. E.g.

python PartitionFinder.py --raxml example/

In R becomes ...

partitionfinder(c('--raxml', 'example/'))

Each argument must be a separate charcter in the argument list vector.

DNA

library(outsider)
PartitionFinder <- module_import('PartitionFinder',
                                 repo = 'dombennett/om..partitionfinder')
# show help
PartitionFinder('-h')

# data
example_fetch <- module_import('example_fetch',
                               repo = 'dombennett/om..partitionfinder')
example_fetch(type = 'nucleotide')

# run on the "nucleotide" example folder
PartitionFinder(arglist = 'nucleotide')

Morphology

library(outsider)
PartitionFinderMorphology <- module_import('PartitionFinderMorphology',
                                 repo = 'dombennett/om..partitionfinder')
example_fetch <- module_import('example_fetch',
                               repo = 'dombennett/om..partitionfinder')
# bring PartitionFinder examples to working directory
example_fetch(type = 'morphology')
# run on the "morphology" example folder
PartitionFinderMorphology(arglist = c('--raxml', 'morphology'))

Protein

library(outsider)
PartitionFinderProtein <- module_import('PartitionFinderProtein',
                                        repo = 'dombennett/om..partitionfinder')
example_fetch <- module_import('example_fetch',
                               repo = 'dombennett/om..partitionfinder')
# bring PartitionFinder examples to working directory
example_fetch(type = 'aminoacid')
# run on the "aminoacid" example folder
PartitionFinderProtein(arglist = 'aminoacid')

for (fldr in c('nucleotide', 'morphology', 'aminoacid')) {
  if (fldr %in% ls() && dir.exists(wd)) {
    unlink(x = fldr, recursive = TRUE, force = TRUE)
  }
}
module_uninstall(repo = "dombennett/om..partitionfinder")

Links

Find out more by visiting the PartitionFinder's homepage.

Please cite

Lanfear, R., Frandsen, P. B., Wright, A. M., Senfeld, T., Calcott, B. 2016 PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses. Molecular biology and evolution. DOI: dx.doi.org/10.1093/molbev/msw260
Bennett et al. (2020). outsider: Install and run programs, outside of R, inside of R. Journal of Open Source Software, In review