poppr (version 2.9.6)

mll.reset: Reset multilocus lineages

Description

This function will allow you to reset multilocus lineages for your data set.

Usage

mll.reset(x, value)

Value

an object of the same type as x

Arguments

x

a genclone or snpclone object.

value

a character vector that specifies which levels you wish to be reset.

Author

Zhian N. Kamvar

See Also

mll mlg.table mll.custom

Examples

# This data set was a subset of a larger data set, so the multilocus
# genotypes are not all sequential
data(Pinf)
mll(Pinf) <- "original"
mll(Pinf)

# If we use mll.reset, then it will become sequential
Pinf.new <- mll.reset(Pinf, TRUE) # reset all
mll(Pinf.new)

if (FALSE) {

# It is possible to reset only specific mll definitions. For example, let's
# say that we wanted to filter our multilocus genotypes by nei's distance
mlg.filter(Pinf, dist = nei.dist, missing = "mean") <- 0.02

# And we wanted to set those as custom genotypes,
mll.custom(Pinf) <- mll(Pinf, "contracted")
mll.levels(Pinf) <- .genlab("MLG", nmll(Pinf, "custom"))

# We could reset just the original and the filtered if we wanted to and keep
# the custom as it were.

Pinf.new <- mll.reset(Pinf, c("original", "contracted"))

mll(Pinf.new, "original")
mll(Pinf.new, "contracted")
mll(Pinf.new, "custom")

# If "original" is not one of the values, then that is used as a baseline.
Pinf.orig <- mll.reset(Pinf, "contracted")
mll(Pinf.orig, "contracted")
mll(Pinf.new, "contracted")
}