README.md

In suryakevin/drugcandy: Detecting Punctuated Evolution in Dinosaurs and Viruses

Detecting Punctuated Evolution in Dinosaurs and Viruses

This package contains the tools to simulate, detect, and visualize punctuated evolution in any clades, from co-occurring species (e.g., present-day mammals) to serially-sampled viruses (e.g., SARS-CoV-2 genomes) and long-extinct taxa (e.g., Mesozoic dinosaurs).

To install drugcandy:

library(devtools)
install_github("suryakevin/drugcandy")

Load drugcandy as usual:

library(drugcandy)

I customized the codes to my needs, not yours. So, I don't hold any responsibility if you find yourself slamming your desk using this package :innocent:. If you're curious about how I string the functions together, please check out the vignette for this package by navigating the directory above or:

browseVignettes("drugcandy")

You can see all functions available in this package by:

?drugcandy

And you can access documentation for each function by, for example:

?fit_punc_model

If you have questions, thoughts, or suggestions, you can email me or open new issues or pull requests (if you're comfortable with these git functionalities).

If you end up using this package (thanks!), please cite the following paper. If it's still not published yet, you can use the bibliography format typical for any other R packages.

Surya, K., Gardner, J.D. & Organ, C. Detecting punctuated evolution in SARS-CoV-2 over the first year of the pandemic. Submitted.

You should also cite relevant publications from the Reading Evolutionary Biology Group since they were the ones who established the foundational statistical methods used here for detecting punctuated evolution. You know which papers I mean if you've done your homework :wink:.

P.S. You don't want to know what the package name means, but it's not about illegal drugs (or any forms of substance, really) or candy, in case you're curious or concerned.

suryakevin/drugcandy documentation built on May 6, 2022, 6:37 p.m.