theta.h | R Documentation |
This function computes the population parameter THETA using the homozygosity (or mean heterozygosity) from gene frequencies.
theta.h(x, standard.error = FALSE)
x |
a vector or a factor. |
standard.error |
a logical indicating whether the standard error
of the estimated theta should be returned ( |
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.
The standard error is computed with an approximation due to Chakraborty and Weiss (1991).
A numeric vector of length one with the estimated theta (the default),
or of length two if the standard error is returned
(standard.error = TRUE
).
Emmanuel Paradis
Zouros, E. (1979) Mutation rates, population sizes and amounts of electrophoretic variation at enzyme loci in natural populations. Genetics, 92, 623–646.
Chakraborty, R. and Weiss, K. M. (1991) Genetic variation of the mitochondrial DNA genome in American Indians is at mutation-drift equilibrium. American Journal of Physical Anthropology, 86, 497–506.
heterozygosity
, theta.s
,
theta.k
, theta.tree
data(jaguar)
## compute frequencies:
S <- summary(jaguar)
## compute THETA for all loci:
sapply(S, function(x) theta.h(x$allele))
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