R: Ramos-Onsins-Rozas Test of Neutrality

R2.test {pegas} | R Documentation

## Ramos-Onsins–Rozas Test of Neutrality

### Description

This function computes Ramos-Onsins and Rozas's test of neutrality for a set of DNA sequences.

### Usage

    R2.test(x, B = 1000, theta = 1, plot = TRUE, quiet = FALSE, ...)

### Arguments

`x` | a DNA matrix (object of class `"DNAbin"`).
`B` | the number of replicates used for the simulation procedure.
`theta` | the value of the theta population parameter used in the simulation.
`plot` | a logical value specifying whether to plot the results (`TRUE` by default).
`quiet` | a logical value specifying whether to not display the progress of the simulations. The default is `FALSE` meaning that a progress bar is displayed by default.
`...` | further arguments passed to `hist`.

### Value

a list with two elements: `R2` the value of the test statistic R_2, and `P.val` the associated P-value. If `B = 0` a single value, the test statistic, is returned

### Note

The simulation procedure probably needs to be tested and improved. However the results make sense so far.

### Author(s)

Emmanuel Paradis

### References

Ramos-Onsins, R. and Rozas, R. (2002) Statistical properties of new neutrality tests against population growth. Molecular Biology and Evolution, 19, 2092–2100.

Sano, J. and Tachida, G. (2005) Gene genealogy and properties of test statistics of neutrality under population growth. Genetics, 169, 1687–1697.

### See Also

`read.dna`, `dist.dna`

### Examples

    data(woodmouse)
    R2.test(woodmouse, quiet = TRUE)

[Package pegas version 1.1 Index]