genclone: Summary function of RClone package

Description Usage Arguments Details Value Author(s) References See Also Examples

Description

genclone computes main genetic/genotypic diversity/richness indices.

Usage

1
2
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:

Author(s)

Creator/Author: Diane Bailleul <[email protected]>
Author: Sophie Arnaud-Haond <[email protected]>
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

1
2
3
4
5
6
7
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

dbailleul/RClone documentation built on May 12, 2017, 8:56 p.m.