coala (version 0.4.0)

sumstat_sfs: Summary Statistic: Site Frequency Spectrum

Description

The Site Frequency Spectrum (SFS) counts how many SNPs are in a sample according to their number of derived alleles.

Usage

sumstat_sfs(name = "sfs", population = "all", transformation = identity)

Arguments

name

The name of the summary statistic. When simulating a model, the value of the statistics are written to an entry of the returned list with this name. Summary statistic names must be unique in a model.

population

The population for which the statistic is calculated. Can also be "all" to calculate it from all populations.

transformation

An optional function for transforming the results of the statistic. If specified, the results of the transformation are returned instead of the original values.

See Also

To create a demographic model: coal_model

To calculate this statistic from data: calc_sumstats_from_data

Other summary statistics: sumstat_dna, sumstat_file, sumstat_four_gamete, sumstat_ihh, sumstat_jsfs, sumstat_mcmf, sumstat_nucleotide_div, sumstat_omega, sumstat_seg_sites, sumstat_tajimas_d, sumstat_trees

Examples

model <- coal_model(20, 500) +
  feat_mutation(2) +
  sumstat_sfs()
stats <- simulate(model)
barplot(stats$sfs)