genetic_diversity: Estimate genetic diversity among strata in a Population,
In MarianaLag/Mlag: Tools Related to the Spatial Analysis of Genetic Marker Data

Description Usage Arguments Value Author(s) Examples

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.

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

`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

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

Rodney J. Dyer rjdyer@vcu.edu

 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")