pop_rare_gen_index: Compute population-level rarefied genetic indices with ADZE...
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pop_rare_gen_index

R Documentation

Compute population-level rarefied genetic indices with ADZE software

Description

The function computes population-level rarefied genetic indices from an object of class genind with the ADZE software.

Usage

pop_rare_gen_index(x, max_g = NULL, pop_names = NULL, OS = "linux")

Arguments

`x`	An object of class `genind` from package adegenet.
`max_g`	(optional default = NULL) The maximum standardized sample size used by ADZE software (MAX_G) in ADZE manual. It is equal to twice the minimum number of individuals considered for the rarefaction analysis. By default, it is equal to twice the number of individuals in the smallest population. Ohterwise, it must be either a numeric or integer value.
`pop_names`	(optional) A character vector indicating population names. It is of the same length as the number of populations. Without this argument, populations are given the names they have initially in the 'genind' object (which is sometimes only a number). The order of the population names must match with their order in the 'genind' object. The function does not reorder them. Users must be careful.
`OS`	A character string indicating whether you use a Linux ('linux') or Windows ('win') operating system.

Value

An object of class data.frame whose rows correspond to populations and columns to population attributes (ID, size, genetic indices). By default, the first column corresponds to the population names (ID). The order of the columns depends on the vector 'indices'.