Phylin

Phylin is an R package for the spatial interpolation of genetic distances. The inteprolation between samples is based on a modified kriging method that accepts a genetic distance matrix and generates a map of probability of lineage presence. This package also offers tools to generate a map of potential contact zones between groups with user-defined thresholds in the tree to account for old and recent divergence. Additionally, it has functions for IDW interpolation using genetic data and midpoints.

Installation

There are several option to install phylin:

• Install the version at CRAN as usual. This may not be the latest, latest version but it already passed all CRAN checks.

• To install the current development version found here, you need to download the built tar.gz package file and install it. Windows users may have to use Rtools to rebuild the package.

• Clone the repository with git and build the package in your computer.

• Use the devtools package in R. Example code:

    library(devtools)
    install_github("ptarroso/phylin", subdir="source")

Using phylin

Phylin has an example dataset and functions are documented and with example code. You can also check the online tutorial or the vignette also included in the package with:

vignette("phylin_tutorial")