hierarchy-methods: Access and manipulate the population hierarchy for genind or...

In adegenet: Exploratory Analysis of Genetic and Genomic Data

Access and manipulate the population hierarchy for genind or genlight objects.

Description

The following methods allow the user to quickly change the hierarchy or population of a genind or genlight object.

Usage

hier(x, formula = NULL, combine = TRUE, value)

hier(x) <- value

Arguments

x	a genind or genlight object
formula	a nested formula indicating the order of the population hierarchy to be returned.
combine	if TRUE (default), the levels will be combined according to the formula argument. If it is FALSE, the levels will not be combined.
value	a formula specifying the full hierarchy of columns in the strata slot. (See Details below)

Details

You must first specify your strata before you can specify your hierarchies. Hierarchies are special cases of strata in that the levels must be nested within each other. An error will occur if you specify a hierarchy that is not truly hierarchical.

Details on Formulas

The preferred use of these functions is with a formula object. Specifically, a hierarchical formula argument is used to name which strata are hierarchical. An example of a hierarchical formula would be:

~Country/City/Neighborhood

This convention was chosen as it becomes easier to type and makes intuitive sense when defining a hierarchy. Note: it is important to use hierarchical formulas when specifying hierarchies as other types of formulas (eg. ~Country*City*Neighborhood) will give incorrect results.

Author(s)

Zhian N. Kamvar

See Also

strata genind as.genind

Examples

# let's look at the microbov data set:
data(microbov)
microbov

# We see that we have three vectors of different names in the 'other' slot. 
?microbov
# These are Country, Breed, and Species
names(other(microbov))

# Let's set the hierarchy
strata(microbov) <- data.frame(other(microbov))
microbov

# And change the names so we know what they are
nameStrata(microbov) <- ~Country/Breed/Species

# let's see what the hierarchy looks like by Species and Breed:
hier(microbov) <- ~Species/Breed
head(hier(microbov, ~Species/Breed))

adegenet documentation built on Feb. 16, 2023, 6 p.m.