R2.test: 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 as an object of class "DNAbin".
B
the number of replicates used for the simulation procedure.
theta
the value of the $theta$ population parameter
used in simulation procedure.
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
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.