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wavess

Within-host adaptive virus evolution sequence simulator.

The goal of wavess is to simulate within-host virus sequence evolution optionally including recombination, a latent infected cell reservoir, and three types of selection (conserved sites, comparison to a fit sequence, antibody-mediated immunity, and cytotoxic T-cell mediated immunity). The package also provides functions to pre-process data for input into the simulator, as well as post-processing functions to analyze the simulation output. The post-processing functions can also be used on real data. The default settings for the simulator assume that the sequences being simulated are HIV gp120.

Website: molevolepid.github.io/wavess/

Manuscript: wavess: An R package for simulation of adaptive within-host virus sequence evolution

**Note that another manuscript is in prep describing the CTL response and variable recombination rate. Release v1.1 includes the variable recombination rate. Upcoming release v1.2 will include the CTL response. Installing as described below includes the CTL response implementation.

Installation

You can install the development version of wavess from GitHub with:

# install.packages("devtools")
devtools::install_github("MolEvolEpid/wavess")

This will not install the vignettes locally, but you can still see the vignettes on the website. If you’d like to install the vignettes locally, you can use the command:

# install.packages("devtools")
devtools::install_github("MolEvolEpid/wavess", build_vignettes = TRUE, force = TRUE)

Vignettes

Please go to the website and see the following vignettes for examples:

Citation 

citation("wavess")

Contributing

You are of course welcome to fork the package for your own use. If you would like for your changes to be incorporated into the latest version of wavess, please open an issue related to your proposed change, create a pull request with the implemented change, or reach out to , , or .