Nucleotide Diversity
This function computes the nucleotide diversity from a sample of DNA sequences or a set of haplotypes.
nuc.div(x, ...) ## S3 method for class 'DNAbin' nuc.div(x, variance = FALSE, pairwise.deletion = FALSE, ...) ## S3 method for class 'haplotype' nuc.div(x, variance = FALSE, pairwise.deletion = FALSE, ...)
x |
a matrix or a list which contains the DNA sequences. |
variance |
a logical indicating whether to compute the variance of the estimated nucleotide diversity. |
pairwise.deletion |
a logical indicating whether to delete the sites with missing data in a pairwise way. The default is to delete the sites with at least one missing data for all sequences. |
... |
further arguments to be passed. |
This is a generic function with methods for classes "DNAbin"
and "haplotype". The first method uses the sum of the number of
differences between pairs of sequences divided by the number of
comparisons (i.e. n(n - 1)/2, where n is the number of
sequences). The second method uses haplotype frequencies. It could be
that both methods give (slightly) different results because of missing
or ambiguous nucleotides: this is generally solved by setting
pairwise.deletion = TRUE.
The variance of the estimated diversity uses formula (10.9) from Nei
(1987). This applies only if all sequences are of the same lengths,
and cannot be used if pairwise.deletion = TRUE. A bootstrap
estimate may be in order if you insist on using the latter option.
A numeric vector with one or two values if variance = TRUE.
Emmanuel Paradis
Nei, M. (1987) Molecular evolutionary genetics. New York: Columbia University Press.
data(woodmouse) nuc.div(woodmouse) nuc.div(woodmouse, TRUE) nuc.div(woodmouse, FALSE, TRUE)
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