theta.s | 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(x, ...)
## S3 method for class 'DNAbin'
theta.s(x, variance = FALSE, ...)
## Default S3 method:
theta.s(x, n, variance = FALSE, ...)
x |
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 ( |
... |
arguments passed to methods. |
A numeric vector of length one with the estimated theta (the default),
or of length two if the standard error is returned
(variance = TRUE
).
Emmanuel Paradis
Watterson, G. A. (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
, theta.tree
data(woodmouse)
theta.s(woodmouse)
theta.s(woodmouse, variance = TRUE)
## using the default:
s <- length(seg.sites(woodmouse))
n <- nrow(woodmouse)
theta.s(s, n)
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