genetic_diversity: Estimate genetic diversity among strata in a Population,

In dyerlab/gstudio: Tools Related to the Spatial Analysis of Genetic Marker Data

Estimate genetic diversity among strata in a Population,

Description

This function is the main one used for estimating genetic diversity among strata. Given the large number of genetic diversity metrics, not all potential types are included.

Usage

genetic_diversity(
  x,
  stratum = NULL,
  loci = NULL,
  mode = c("A", "Ae", "A95", "He", "Ho", "Hi", "Hos", "Hes", "Fis", "Pe")[2],
  small.N = FALSE,
  ...
)

Arguments

x	A data.frame object with locus columns.
stratum	The strata by which the genetic distances are estimated. This can be an optional parameter when estimating distance measures calculated among individuals (default='Population').
loci	The set of loci to use (default NULL will use all)
mode	The particular genetic diversity metric that you are going to use. The gstudio package currently includes the following individual distance measures: A Number of alleles Ae Effective number of alleles (default) A95 Number of alleles with frequency at least five percent He Expected heterozygosity Ho Observed heterozygosity Hes Expected subpopulation heterozygosity (Nei's Corrected) Hos Expected subpopulation heterozygosity (Nei's Corrected) Fis Wright's Inbreeding coefficient (size corrected). Pe Locus polymorphic index.
small.N	Apply small N correction
...	Other parameters

Value

A data.frame with columns for strata, diversity (mode), and potentially P(mode=0).

Author(s)

Rodney J. Dyer [e-mail]

Examples

 AA <- locus( c("A","A") )
 AB <- locus( c("A","B") )
 BB <- locus( c("B","B") )
 locus <- c(AA,AA,AA,AA,BB,BB,BB,AB,AB,AA)
 locus2 <- c(AB,BB,AA,BB,BB,AB,AB,AA,AA,BB)
 Population <- c(rep("Pop-A",5),rep("Pop-B",5))
 df <- data.frame( Population, TPI=locus, PGM=locus2 )
 genetic_diversity( df, mode="Ae")

dyerlab/gstudio documentation built on Jan. 17, 2025, 11:17 a.m.