genclone: Summary function of RClone package

In RClone: Partially Clonal Populations Analysis

Description

genclone computes main genetic/genotypic diversity/richness indices.

Usage

GenClone(data1, haploid = FALSE, coords = NULL, vecpop = NULL, listMLL = NULL, 
			nbrepeat = NULL, bar = FALSE)

Arguments

data1	a Rclone table with one allele per column.
haploid	logical, option, haploid indicates the ploidy level of data1.
coords	a table with coordinates of every units in data1.
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.
nbrepeat	numeric, option, if pvalue = TRUE, nbrepeat is the number of resampling to enable pvalues computation.
listMLL	option, a custom list of MLL.
bar	option, if TRUE, displays a progression bar.

Details

GenClone returns results of several functions of RClone: a summary of MLG_tab, Fis on ramets and genets with pvalues (resample the population nbrepeat times, with simulated sexual events), B_Pareto from Pareto_index, Sp from autocorrelation and indexes from clonal_index.

If no coordinate at all are available, let coords = NULL as it or create a table with always the same number (i.e. "999", "-1", etc.). If coordinates are available for some populations only, for the population with missing coordinates: replace all the coordinates by the same number, as "999". GenClone cannot handle mix situation with missing coordinates only for some units of the population.

Value

GenClone returns a table with:

• N, the number of units in data1,

• Lineage, MLG or MLL,

• nb_L, the number of MLG/MLL,

• nb_all, the mean number of alleles,

• SE, the standard error of nb_all,

• Fis, on ramets if diploid data

• pval_2sides, the two-sided p-value of Fis if nbrepeat,

• Fis_WR, on genets if diploid data

• pval_2sides, the two-sided p-value of Fis_WR if nbrepeat,

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

• Pareto_index, the index of Pareto

• Sp_Loiselle, Sp index computed on ramets with Loiselle kinship results used to quantify Spatial Genetic Structure (Vekemans and Hardy, 2004)

• pval_2sides, the two-sided p-value of Sp_Loiselle if nbrepeat,

• Sp_Ritland, Sp index computed on ramets with Ritland kinship results used to quantify SGS

• pval_2sides, the two-sided p-value of Sp_Ritland if nbrepeat,

• Sp_L_WR, Sp index computed on genets with Loiselles kinship results used to quantify SGS

• pval_2sides, the two-sided p-value of Sp_L_WR if nbrepeat,

• Sp_R_WR, , Sp index computed on genets with Ritland kinship results used to quantify SGS

• pval_2sides, the two-sided p-value of Sp_R_WR if nbrepeat,

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

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

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

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

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

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

clonal_index

Examples

data(posidonia)
data(coord_posidonia)

#GenClone(posidonia) #without coordinates
#GenClone(posidonia, coords = coord_posidonia) #with coordinates
#GenClone(posidonia, coords = coord_posidonia, nbrepeat = 1000)
##time consuming

RClone documentation built on May 15, 2021, 5:07 p.m.