geotreespace: an R Package for the Statistical Measure of Phylogeographic Incopatibilities

geotreespace implements new mathematical measures (metrics) of phylogeographic concordance or incompatibilities,: the Pairwise Most-Recent Common Ancestor (MRCA) incompatibility $I_{mrca}$ and the Maximum Agreement Sub-Phylogeography (MASPG) $I_{maspg}$. These metrics are for detecting differences between geographical histories in terms of distances between phylogeographies. The metrics can be applied to any phylogeography, and more generally to any phylogeny where each tip has been assigned a geographical discrete location or any other continuous/discrete 'trait' independent of the sequence. A non-zero value of an incompatibility metric between two phylogeographies implies that they are incompatible, and could be evidence of recombination.

Installing geotreespace

To install the development version from github:

library(devtools)
install_github("BenSinger01/geotreespace")

Then, to load the package, use: library("geotreespace")

Content overview

The main functions implemented in geotreespace are:

• mrcaDist: comparison of two phylogeographic trees using the MRCA incompatibility measure

• multiMrcaDist: comparison of a list of phylogeographic trees using the MRCA incompatibility measure

• maspgDist: comparison of two phylogeographic trees using the MASPG incompatibility metric

• multiMaspgDist: Comparison of a list of phylogeographic trees using the MASPG incompatibility metric

Other functions are central to the computations of distances between trees:

• mrcaVec: function to find the location of the most recent common ancestor (MRCA) of each pair of tips in a tree

Reporting bugs

Bugs can be reported using the package’s issue system.

Authors

Authors:

• Benjamin John Singer

• Antonello Di Nardo

• Luca Ferretti