Pareto_index: Pareto index

In dbailleul/RClone: Partially Clonal Populations Analysis

Description

Pareto_index computes parameters of the Pareto distribution.

Usage

Pareto_index(data1, vecpop = NULL, listMLL = NULL, full = FALSE, graph = FALSE, 
				legends = 1, export = FALSE)

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.
full	option, if TRUE, gives more detailed results.
graph	option, if TRUE, displays plot of the inverse cumulated frequency of the number of lineages.
export	option, if TRUE, graph is saved as .eps into working directory.
legends	option, numerical, with graph = TRUE, legends = 1 gives the log-log regression equation; legends = 2 gives the Pareto index, the r2 and the p-value of the regression.

Details

Pareto's Beta is given as -slope of the linear regression of the inverse cumulated frequency of the number of lineages (Pareto 1897 in Vidondo 1997).

The distribution of clonal size in the population c_Pareto is computed as slope+1 (Schroeder 1991).

Value

A list of:

Pareto	Pareto's Beta,
c_Pareto	distribution of clonal size in the population,
coefficients and regression_results	summary of the linear regression,
coords_Pareto	x and y coordinates of the inverse cumulated frequencies.

For several populations, a list of lists per population.

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)

Pareto_index(posidonia, graph = TRUE, legends = 2)

res <- Pareto_index(posidonia, full = TRUE)[[4]]

xi <- res[,1]
yi <- res[,2]
exp(summary(lm(log10(yi)~log10(xi)))$coefficients[1]) ##true b of y=ax+b

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