Summary Statistic: Nucleotide Diversity
The summary statistic calculates the nucleotide diversity (π) per locus, which is the mean number of pairwise difference for two individuals. It is a commonly used estimator for the scaled mutation rate θ.
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.
The population for which the statistic is calculated. Can also be "all" to calculate it from all populations.
An optional function for transforming the results of the statistic. If specified, the results of the transformation are returned instead of the original values.
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.
On simulation, this returns a vector with the value of pi for each locus.
To create a demographic model:
To calculate this statistic from data:
Other summary statistics:
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