Summary statistics

Source: R/summary_SFS_class.R

Calculates summary statistics useful for analyzing DNA.

## S3 method for class 'SFS_class'
summary(SFS)

Arguments

SFS

vector with the site frequency spectrum of class 'SFS_class'.

Value

List containing the following components:

Watterson

Watterson's estimator.

pairwDiff

The pairwise difference estimator.

TajimaD

Tajima's D

See also

mutRate, TajimaD

Examples

# Using the function SFS:
DNAmat <- matrix(c(0,1,0,0,
                   0,1,0,1,
                   0,0,0,0,
                   0,0,0,0), 4,4, byrow=TRUE)
summary(SFS(DNAmat))
#> Summary statistics:
#> Estimators of the mutation rate:
#>  Watterson's estimator: 1.090909 
#>  Pairwise difference estimator: 1.166667 
#> Tajima's D: 0.5915801 

# Creating SFS by hand:
SFS <- c(2,1,0,0,0,1,0,0)
class(SFS) <- "SFS_class"
summary(SFS)
#> Summary statistics:
#> Estimators of the mutation rate:
#>  Watterson's estimator: 1.471748 
#>  Pairwise difference estimator: 1.333333 
#> Tajima's D: -0.3822722