poppr (version 2.3.0)

mll.reset: Reset multilocus lineages

Description

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

Usage

mll.reset(x, value)

Arguments

x

a genclone or snpclone object.

value

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

Value

an object of the same type as x

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)

## Not run: 
# 
# # 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")
# ## End(Not run)