genetic_structure: Estimation of , genetic structure statistics.
In MarianaLag/Mlag: Tools Related to the Spatial Analysis of Genetic Marker Data

Description Usage Arguments Value Note Examples

This function estimates common , genetic statistics.

genetic_structure(
  x,
  stratum = "Population",
  mode = c("Gst", "Gst_prime", "Dest")[1],
  nperm = 0,
  size.correct = TRUE,
  pairwise = FALSE,
  locus
)

`x`	An object of type `data.frame` with at least a single column of type `locus`
`stratum`	The stratum to use as groupings (default='Population').
`mode`	Whic statistic to estimate. Current options include: Gst Nei's Gst (not Berg and Hamrick) Gst_prime Hedrick's correction of Nei's Gst for diverse loci Dest Joost's estimate
`nperm`	The number of permutations used to test the hypothesis that the parameter = 0.
`size.correct`	A flag indicating that the estimate should be corrected for based upon sample sizes (default=TRUE).
`pairwise`	A flag indicating that the analysis should be done among all pairs of strata.
`locus`	An optional parameter specifying the locus or loci to be used in the analysis. If this is not specified, then all loci are used.

An object of type data.frame containing estimates for each locus and a multilocus estimate. If pairwise=TRUE, then it returns the multilocus (if more than one locus) estimate in a matrix format.

The multilocus estimation of these parameters is estimated following the suggestions of Culley et al. (2001) A comparison of two methods of calculating Gst, a genetic measure of population differentiation. American Journal of Botany 89(3): 460-465.

 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_structure( df, mode="Gst", nperm=999)
 genetic_structure( df, mode="Gst", pairwise=TRUE)
 genetic_structure( df, mode="Gst", pairwise=TRUE, locus="TPI" )