Detecting Punctuated Evolution in Dinosaurs and Viruses

The development of this package has been suspended indefinitely.

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 fallpaddy:

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

To use fallpaddy, load as usual:

library(fallpaddy)

I customized fallpaddy to my preference, not yours. So, please don't hold me accountable if you find yourself cursing out loud 😇. If you're curious about how I string the functions together to analyze real-world data, please check out the vignette for this package by navigating the directory above or:

browseVignettes("fallpaddy")

You can see all of the functions available in this package:

?fallpaddy

And to access documentation for a function, say the sim_punc function, for example:

?sim_punc

If you have questions, thoughts, or suggestions, you can email me at sadikin.kevin@gmail.com 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.

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

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 😉.

P.S. The package name comes from the first poem of the Ogura Hyakunin Isshu (lit. "One Hundred Poets, One Poem [Each]"). All thanks go to Chihayafuru for educating me on the beauty of Japanese poetry!

The fall paddy shacks have rough thatching
as my sleeves are wet with dew.