diff --git a/man/IterateHWE.Rd b/man/IterateHWE.Rd index 4b22228..743b4d1 100644 --- a/man/IterateHWE.Rd +++ b/man/IterateHWE.Rd @@ -69,6 +69,13 @@ assuming no population structure: \code{\link{AddGenotypePriorProb_HWE}}, \code{\link{AddGenotypeLikelihood}}, \code{\link{AddPloidyChiSq}}, and \code{\link{AddGenotypePosteriorProb}}. +\code{IterateHWE_LD} runs each of the functions listed for \code{IterateHWE} +once, then runs \code{\link{AddAlleleLinkages}}. It then runs +\code{\link{AddAlleleFreqHWE}}, \code{\link{AddGenotypePriorProb_HWE}}, +\code{\link{AddGenotypePriorProb_LD}}, \code{\link{AddGenotypeLikelihood}}, +\code{\link{AddPloidyChiSq}}, and \code{\link{AddGenotypePosteriorProb}} +iteratively until allele frequencies converge. + For \code{IteratePopStruct}, the following functions are run iteratively, modeling population structure: \code{\link{AddPCA}}, \code{\link{AddAlleleFreqByTaxa}},