Replacing multilocus lineages with one representative sample

mll.representative.R

# Replacing multilocus lineages with one representative sample
library(poppr)
data(monpop)
mlg.filter(monpop) <- 0 + .Machine$double.eps
mondf  <- genind2df(monpop, usepop = FALSE)
mid    <- mlg.id(monpop)
orders <- unlist(mid, use.names = FALSE)
monpop <- monpop[orders, ]
mondif <- mondf[orders, ]
n      <- vapply(mid, length, integer(1))
sam    <- vector(mode = "character", length = length(n))
for (i in seq(mid)){
  sam[i] <- sample(mid[[i]], 1) # for a random sample
  # sam[i] <- mid[[i]][length(mid[[i]])] # for the last sample
  # sam[i] <- mid[[i]][1] # for the first sample
}
monpop2 <- df2genind(mondf[rep(sam, n), ], ploidy = 1, 
                     ind.names = indNames(monpop),
                     pop = pop(monpop),
                     strata = strata(monpop))
other(monpop2) <- other(monpop)
monpop2 <- as.genclone(monpop2)