Introduction to pgmcs

Zhuoer Dong

2022-05-14

library(pgmcs)

suppressWarnings(RNGversion('3.5.2'))

Web App

The package is very simple to use, all you need is a browser, like Chrome.

• dynamic mode
• static mode

But if you can’t stand the low speed, and the unstable connection demanding frequent refresh, you may consider the following approach.

Run on your own computer

In this way, you can free from the above troubles. It’s very easy, you just need to install R, which is even simpler than QQ.

1. install R (use this for Windows users.)

2. open R and install this package

if (!('remotes' %in% .packages(T))) install.packages('remotes');
remotes::install_github('dongzhuoer/pgmcs');

3. open R and run the application

shiny::runApp(system.file('shiny/pgmcs', package = 'pgmcs'))
shiny::runApp(system.file('shiny/pgmcs2', package = 'pgmcs'))

Command line interface

If you are familiar with R, you can get rid of the limit on population size and generation number, and try whatever parameters you like.

set.seed(0);
demo_population_simulation(100, 250, c(0, 490, 10), c(1, 1, 1), 'drift')

demo_population_simulation(100, 250, c(0, 490, 10), c(1, 1, 0.95), 'select A')

The following code reproduce the figures in 20.2 of Genetics From Genes to Genomes, 5th

Figure 20.8 at P671

Initial population are all heterozygotes.

set.seed(13);
demo_population_simulation(6, 30, c(0, 10, 0), c(1, 1, 1), "Small population: Lots of genetic drift");

set.seed(0);
demo_population_simulation(6, 30, c(0, 500, 0), c(1, 1, 1), "Large population: Little genetic drift");

Figure 20.13 at P676

499bb + 1Bb; WBB = 1.0, WBb = 1.0, Wbb = 0.98 (adjusted to 0.97)

set.seed(885);  # 57
demo_population_simulation(6, 900, c(0, 1, 499), c(1,1,0.97), "Natural selection together with genetic
drift")