Population Parameter THETA using Expected Number of Alleles
This function computes the population parameter THETA using the expected number of alleles.
theta.k(x, n = NULL, k = NULL)
x |
a vector or a factor. |
n |
a numeric giving the sample size. |
k |
a numeric giving the number of alleles. |
This function can be used in two ways: either with a vector giving the
individual genotypes from which the sample size and number of alleles
are derived (e.g., theta.k(x)), or giving directly these two
quantities (e.g., theta.k(n = 50, k = 5)).
The argument x can be either a factor or a vector. If it is a
factor, then it is taken to give the individual alleles in the
population. If it is a numeric vector, then its values are taken to be
the numbers of each allele in the population. If it is a non-numeric
vector, it is a coerced as a factor.
Both arguments n and k must be single numeric values.
A numeric vector of length one with the estimated theta.
For the moment, no standard-error or confidence interval is computed.
Emmanuel Paradis
Ewens, W. J. (1972) The sampling theory of selectively neutral alleles. Theoretical Population Biology, 3, 87–112.
data(jaguar) ## compute frequencies: S <- summary(jaguar) ## compute THETA for all loci: sapply(S, function(x) theta.k(x$allele))
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