View source: R/allelicrichness.R
allelicrichness | R Documentation |
These functions analyse allelic richness.
allelicrichness(x, pop = NULL, method = "extrapolation", min.n = NULL)
rarefactionplot(x, maxn = nrow(x), type = "l", xlab = "Sample size",
ylab = "Expected number of alleles", plot = TRUE, ...)
rhost(x, pop = NULL, method = "extrapolation")
x |
an object of class |
pop |
a vector or factor giving the population assignment of each
row of |
method |
a character string which should be one of “extrapolation”, “rarefaction”, “raw” or an unambiguous abbreviation of these. |
min.n |
the value of |
maxn |
the largest sample size used to calculate the rarefaction curve. |
type , xlab , ylab |
arguments passed to |
plot |
a logical value specifying whether to do the rarefaction
plot ( |
... |
arguments passed to and from methods. |
allelicrichness
computes for each locus in x
the
estimated allelic richness. Three methods are available: the
extrapolation method (Foulley and Ollivier 2006), the rarefaction
method (Hurlbert 1971), and the raw numbers of alleles.
rarefactionplot
computes the rarefaction curves of the number
of alleles with respect to sample size using Hurlbert's (1971)
method. A plot is made by default.
allelicrichness
returns a numeric matrix.
rarefactionplot
returns invisibly a list of matrices with the
coordinates of the rarefaction plots for each locus.
rhost
returns a numeric vector.
Emmanuel Paradis
El Mousadik, A. and Petit, R. J. (1996) High level of genetic differentiation for allelic richness among populations of the argan tree [Argania spinosa (L. Skeels)] endemic to Morocco. Theoretical and Applied Genetics, 92, 832–836.
Foulley, J. L. and Ollivier, L. (2006) Estimating allelic richness and its diversity. Livestock Science, 101, 150–158.
Hurlbert, S. H. (1971) The nonconcept of species diversity: a critique and alternative parameters. Ecology, 52, 577–586.
data(jaguar)
rarefactionplot(jaguar)
allelicrichness(jaguar)
rhost(jaguar)
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