clonal_index: Indices for clonal data

In dbailleul/RClone: Partially Clonal Populations Analysis

Description

clonal_index computes main genotypic diversity and richness indices.

Usage

clonal_index(data1, vecpop = NULL, listMLL = NULL)

Arguments

data1	a RClone table with one allele per column, haploid or diploid data.
vecpop	vector, option, vecpop indicates the population name of each unit of data1, if data1 contains several populations. If data1 contains only one population, leave vecpop = NULL.
listMLL	option, a custom list of MLL.

Details

clonal_index returns:

• the number of units N,

• the number of unique genotypes G,

• the clonal diversity index R (Dorken & Eckert 2001; Ellstrand & Roose 1987),

• the Shannon-Wiener index estimator H'' (Pielou 1966),

• the Pielou evenness index J' (Pielou 1975),

• the Simpson complement unbiased D' (Pielou 1969 ; Gini 1912 ; Peet 1974),

• the Simpson complement index V (Hurlbert 1971 ; Fager 1972),

• the reciprocal of Simpson index unbiased Hill (Hurlbert 1971 ; Hill 1973).

Value

a table (one population) or a list of tables (several population) with genotypic indices.

Author(s)

Creator/Author: Diane Bailleul <[e-mail]>
Author: Sophie Arnaud-Haond <[e-mail]>
Contributor: Solenn Stoeckel

The R implementation of RClone was written by Diane Bailleul.

The design was inspired by GenClone program described in Arnaud-Haond & Belkhir (2007).

References

Arnaud-Haond et al., 2007, Standardizing methods to address clonality in population studies.

See Also

Pareto_index

Examples

data(posidonia)

clonal_index(posidonia)

dbailleul/RClone documentation built on May 17, 2021, 3:04 p.m.