coala (version 0.7.2)

sumstat_nucleotide_div: Summary Statistic: Nucleotide Diversity

Description

The summary statistic calculates the nucleotide diversity (\(\pi\)) per locus, which is the mean number of pairwise difference for two individuals. It is a commonly used estimator for the scaled mutation rate \(\theta\).

Usage

sumstat_nucleotide_div(name = "pi", population = 1, transformation = identity)

Value

On simulation, this returns a vector with the value of pi for each locus.

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. Default is population 1.

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.

Details

The nucleotide diversity was introduced by

Nei and Li (1979). "Mathematical Model for Studying Genetic Variation in Terms of Restriction Endonucleases". PNAS 76 (10): 5269-73. doi:10.1073/pnas.76.10.5269.

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_omega(), sumstat_seg_sites(), sumstat_sfs(), sumstat_tajimas_d(), sumstat_trees()

Examples

model <- coal_model(5, 2) +
  feat_mutation(5) +
  sumstat_nucleotide_div()
stats <- simulate(model)
print(stats$pi)