poppr (version 1.1.5)

genclone-class: Genclone class

Description

Genclone is an S4 class that extends the genind from the adegenet package. It will have all of the same attributes as the genind, but it will contain two extra slots that will help retain information about population hierarchies and multilocus genotypes.

Extends

Class "genind", directly.

Details

The genclone class will allow for more optimized methods of clone correcting and analyzing data over multiple levels of population hierarchy.

Previously, for hierarchical analysis to work in a genind object, the user had to place a data frame in the other slot of the object. The suggested name of the data frame was population_hierarchy, and this was used to be able to store the hierarchical information inside the object so that the user did not have to keep track of that information. This method worked, but it became apparent that it was a bit confusing to the user as the method for changing the population of an object became:

pop(object) <- other(object)$population_hierarchy$population_name

That is a lot to keep track of. The new hierarchy slot will allow the user to change the population factor with one function and a formula:

setpop(object) <- ~Population/Subpopulation

making this become slightly more intuitive and tractable.

Previously for genind objects, multilocus genotypes were not retained after a data set was subset by population. The new mlg slot allows us to assign the multilocus genotypes and retain that information no matter how we subset the data set.

See Also

as.genclone sethierarchy setpop genind