Installing

A stable tested version of evobiR is available from the CRAN repository or the most recent version may be installed from github using the devtools package:

Installing from CRAN

install.packages("evobiR")

Installing from github

library(devtools)
install_github("coleoguy/evobir", build_vignettes = TRUE)

Introduction

evobiR is a bit of a catch all package that I began developing during graduate school. It now contains a variety of functions including some didactic, but with a definite focus on functions that are useful in comparative methods or population genetics.

Teaching with evobiR

All of the function in evobiR that are designed for teaching have been wrapped into shiny apps. These shiny apps are available online but are also included in evobiR to make it easy for instructors to use them on their own system and to make it easy for you to modify them to your own purposes. To access these apps we use the ViewEvo function:

Wright Fisher simulator:

ViewEvo("wf.model")

This app provides a convenient interface for students to experiment with the interaction of drift and selection. Students are able to control: initial allele frequency, population size, generations to run simulation, fitness of all genotypes, iterations to simulate, genotype or allele to plot, and mutation rate among alleles. The app will also show the expected outcome assuming infinite population size and reports the number of times that each allele is lost or fixed.

web app version

 

Brownian motion simulator:

ViewEvo("bm.model")

This app provides a simple color blind friendly Brownian motion simulation where students can choose the generations, replicates, and rate of evolution. This is app has a second interactive component that allows students to view the distribution of outcomes at any generation they select.

web app version