This function estimates the population parameter \(\theta\) using micro-satellite data with three different estimators.
theta.msat(x)
a numeric matrix with loci as rows and the three estimates of
\(\theta\) as columns.
an object of class "loci"
.
Emmanuel Paradis
The three estimators are based on (i) the variance of the number of repeats, (ii) the expected homozygosity (both described in Kimmel et al., 1998), and (iii) the mean allele frequencies (Haasl and Payseur, 2010).
The data must be micro-satellites, so the allele names must be the allele sizes (see the example). If the data are expressed in repeat counts, then only the first estimator is affected.
Kimmel, M., Chakraborty, R., King, J. P., Bamshad, M., Watkins, W. S. and Jorde, L. B. (1998) Signatures of population expansion in microsatellite repeat data. Genetics, 148, 1921--1930.
Haasl, R. J. and Payseur, B. A. (2010) The number of alleles at a microsatellite defines the allele frequency spectrum and facilitates fast accurate estimation of \(\theta\). Molecular Biology and Evolution, 27, 2702--2715.
theta.h
, theta.tree
data(jaguar)
theta.msat(jaguar)
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