poppr (version 2.3.0)

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

data(partial_clone)
pc <- as.genclone(partial_clone)
mll(pc)
mll(pc) <- "custom"
mll(pc)
mll.levels(pc) <- LETTERS
mll(pc)