allelicrichness: Allelic Richness and Rarefaction Plots

In pegas: Population and Evolutionary Genetics Analysis System

Description

These functions analyse allelic richness.

Usage

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")

Arguments

x	an object of class "loci".
pop	a vector or factor giving the population assignment of each row of x, or a single numeric value specifying which column of x to use as population indicator. By default, the column labelled "population" is used.
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.
plot	a logical value specifying whether to do the rarefaction plot (TRUE by default).
...	arguments passed to and from methods.

Details

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.

Value

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.

Author(s)

Emmanuel Paradis

References

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.

Examples

data(jaguar)
rarefactionplot(jaguar)
allelicrichness(jaguar)
rhost(jaguar)

Example output

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 

pegas documentation built on Dec. 16, 2021, 5:09 p.m.