README.md

In cedatorma/recpd: RecPD

RecPD

The RecPD package was developed to calculate the recombination-adjusted phylogenetic diversity of a given feature (phenotype, variant, etc. in binary presence/absence format) found across a given species phylogenetic tree utilizing ancestral state reconstruction.

RecPD also provides functions for:

• Visualizing feature ancestral lineage reconstructions.
• Derived measures such as: nRecPD (a measure of the degree of feature recombination), Span, Clustering, Longevity, and Lability.
• RecPDcor - a measure of pairwise feature lineage correlation.

For a more detailed description of the RecPD methodology, and its advantage over using simple Prevalence to measure feature diversity in microbial population genetics studies, see Bundalovic-Torma C. & Guttman D. PLoS CompBiol. (2022).

Installation

You can install the development version of RecPD from GitHub

# install.packages("devtools")
devtools::install_github("cedatorma/recpd")

Tutorial and Usage Examples

See the ./vignettes directory for a tutorial providing a general overview of RecPD and the various functionalities offered in the package.

cedatorma/recpd documentation built on April 25, 2022, 10:14 p.m.