Population Genetics - More Simulations with R¶

There some nice R packages available for learning population genetics. Here we focus on the package HardyWeinberg and learnPopGen. For both packages help options and documentation are available (see below).

R Packages for PopGen¶

HardyWeinberg¶

The HardyWeinberg package offers several functions for various tests (e.g. HWE), genetic marker data simulations, graphical tools (e.g. ternary plots) and provided data sets.

Example: Simulation for marker data¶

Npop <- 100 # number of individuals
Nind <-  10 # number of popualtions
# Matrix with genotype counts:
pop <- HWData(Nind, Npop)
pop

learnPopGen¶

R package learnPopGen was developed to learn population genetics, quantitative genetics, and evolutionary theory.

Example: Migration, Selection, and Drift (msd)¶

learnPopGen::msd(p0 = c(0.5, 0.5),                 # starting frequency for the A1 allele
                 Ne = c(100, 100),                 # effective population
                 w = list(c(1, 1, 1), c(1, 1, 1)), # fitnesses of the three genotypes
                 m = c(0.05, 0.05),                # rates of migration
                 ngen = 500,                       # number of generations
                 colors = c("red", "blue")         # population color id
)

R Script with Examples¶

With the help of both packages, I have written some R code examples. It extends the do-it-yourself example by a lot. I wrapped everything into a Rmarkdown file. There should be no problem to run individual code chunks. I also knitted an HTML page in case you have difficulties to do it yourself. I hope you learn something from the code and constrictive feedback is appreciated.

I also provide a zip file containing the Rmarkdown script and the HTML file.

Note

The HTML report works well with the interent browser Firefox, Chrome or Epic but there are troubles with Safari. You can download the HTML file and open it locally. This works even for Safari in my case.