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Examples

1. Obtain the neutral distribution of Tajima’s D

For 20 samples from a panmictic population:

 library(coala)
 model <- coal_model(20, 2000) +
   feat_mutation(2) +
   feat_recombination(1) +
   sumstat_tajimas_d()
 stats <- simulate(model, seed = 15)
 plot(density(stats$tajimas_d, na.rm = TRUE), 
      main = "Neutral Distribution of Tajiam's D")

2. Generate the site frequency spectrum

For a neutral model with two populations and migration:

model2a <- coal_model(c(10, 10), 100) +
   feat_mutation(10) +
   feat_recombination(5) +
   feat_migration(0.5, symmetric = TRUE) +
   sumstat_sfs(population = "all")
stats <- simulate(model2a, seed = 20)
barplot(stats$sfs / sum(stats$sfs), 
        names.arg = seq_along(stats$sfs), 
        col = 3)

And again, but now with a bottleneck in one population:

model2b <- model2a +
  feat_size_change(0.1, population = 2, time = 0.25) +
  feat_size_change(1, population = 2, time = 0.5)
stats <- simulate(model2b, seed = 25)
barplot(stats$sfs / sum(stats$sfs), 
        names.arg = seq_along(stats$sfs), 
        col = 4)

3. Plot the nucleotide diversity against the mutation rate:

model3 <- coal_model(10, 50) +
  feat_mutation(par_prior("theta", sample.int(100, 1))) +
  sumstat_nucleotide_div()
stats <- simulate(model3, nsim = 40)
mean_pi <- sapply(stats, function(x) mean(x$pi))
theta <- sapply(stats, function(x) x$pars[["theta"]])
plot(theta, mean_pi, pch = 19, col = "orange")
abline(lm(mean_pi ~ theta), col = "red2", lty = 3)

If you have a nice example for using coala, feel free to extend this vignette via a pull request on GitHub!

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.