sumstat_nucleotide_div {coala} | R Documentation |
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.
sumstat_nucleotide_div(name = "pi", population = 1, transformation = identity)
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. |
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: 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()
model <- coal_model(5, 2) + feat_mutation(5) + sumstat_nucleotide_div() stats <- simulate(model) print(stats$pi)