poppr (version 2.5.0)

mll: Access and manipulate multilocus lineages.

Description

The following methods allow the user to access and manipulate multilocus lineages in genclone or snpclone objects.

Usage

mll(x, type = NULL)
nmll(x, type = NULL)
mll(x) <- value

Arguments

x

a '>genclone or '>snpclone object.

type

a character specifying "original", "contracted", or "custom" defining they type of mlgs to return. Defaults to what is set in the object.

value

a character specifying which mlg type is visible in the object. See details.

Value

an object of the same type as x.

Details

'>genclone and '>snpclone objects have a slot for an internal class of object called '>MLG. This class allows the storage of flexible mll definitions:

• "original" - naive mlgs defined by string comparison. This is default.

• "contracted" - mlgs defined by a genetic distance threshold.

• "custom" - user-defined MLGs

See Also

mll.custom mlg.table

Examples

# NOT RUN {
data(partial_clone)
pc <- as.genclone(partial_clone)
mll(pc)
mll(pc) <- "custom"
mll(pc)
mll.levels(pc) <- LETTERS
mll(pc)
# }