theta.s {ape} | R Documentation |
This function computes the population parameter THETA using the
number of segregating sites s
in a sample of n
DNA sequences.
theta.s(s, n, variance = FALSE)
s |
a numeric giving the number of segregating sites. |
n |
a numeric giving the number of sequences. |
variance |
a logical indicating whether the variance of the
estimated THETA should be returned (TRUE ), the default being
FALSE . |
a numeric vector of length one with the estimated theta (the default),
or of length two if the standard error is returned
(variance = TRUE
).
The number of segregating sites needs to be computed beforehand, for
instance with the function seg.sites
(see example below).
Emmanuel Paradis paradis@isem.univ-montp2.fr
Watterson, G. (1975) On the number of segragating sites in genetical models without recombination. Theoretical Population Biology, 7, 256–276.
Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics, 123, 585–595.
theta.h
, theta.k
, seg.sites
,
nuc.div
data(woodmouse) y <- seg.sites(woodmouse) s <- length(y) n <- length(woodmouse) theta.s(s, n) theta.s(s, n, variance = TRUE)