Description Usage Arguments Details Value Author(s) References Examples
View source: R/allelicrichness.R
These functions analyse allelic richness.
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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 n used in the rarefaction method; by default, the smallest observed number of genotypes within a population. |
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.
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Loading required package: ape
Loading required package: adegenet
Loading required package: ade4
Registered S3 method overwritten by 'spdep':
method from
plot.mst ape
/// adegenet 2.1.3 is loaded ////////////
> overview: '?adegenet'
> tutorials/doc/questions: 'adegenetWeb()'
> bug reports/feature requests: adegenetIssues()
Registered S3 method overwritten by 'pegas':
method from
print.amova ade4
Attaching package: ‘pegas’
The following object is masked from ‘package:ade4’:
amova
The following object is masked from ‘package:ape’:
mst
FCA742 FCA723 FCA740 FCA441 FCA391 F98
Green Corridor 13.666781 6.667388 6.000000 4.913465 8.609116 4.264864
Morro do Diabo 7.273041 3.614526 3.814504 3.696214 5.821907 3.255633
Ivinhema 10.075582 3.915132 4.669092 4.227038 6.147078 4.157132
Porto Primavera 12.122143 6.547597 4.725376 4.446950 7.420281 3.650175
F53 F124 F146 F85 F42 FCA453
Green Corridor 10.142035 8.541292 4.142035 13.317372 9.462459 6.000000
Morro do Diabo 5.702842 5.699537 3.358572 6.246868 6.039535 4.418142
Ivinhema 7.936982 6.590136 3.433005 7.506622 5.042223 4.643040
Porto Primavera 9.945373 7.502866 4.630582 9.506712 7.935866 5.698888
FCA741
Green Corridor 4.000000
Morro do Diabo 2.696205
Ivinhema 3.227038
Porto Primavera 3.446950
FCA742 FCA723 FCA740 FCA441 FCA391 F98 F53 F124
0.1846344 0.6511533 0.6831464 0.7232569 0.5000337 0.7640041 0.3806827 0.4930452
F146 F85 F42 FCA453 FCA741
0.7590793 0.3213005 0.4899983 0.6508319 0.8047877
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