Access and manipulate the population strata for genind or genlight objects.
The following methods allow the user to quickly change the strata of a genind or genlight object.
strata(x, formula = NULL, combine = TRUE, value) strata(x) <- value nameStrata(x, value) nameStrata(x) <- value splitStrata(x, value, sep = "_") splitStrata(x, sep = "_") <- value addStrata(x, value, name = "NEW") addStrata(x, name = "NEW") <- value
x |
a genind or genlight object |
formula |
a nested formula indicating the order of the population strata. |
combine |
if |
value |
a data frame OR vector OR formula (see details). |
sep |
a |
name |
an optional name argument for use with addStrata if supplying a vector. Defaults to "NEW". |
strata() - Use this function to view or define population stratification of a genind or genlight object.
nameStrata() - View or rename the different levels of strata.
splitStrata() - Split strata that are combined with a common separator. This function should only be used once during a workflow.
Rationale: It is often difficult to import files with several levels of strata as most data formats do not allow unlimited population levels. This is circumvented by collapsing all population strata into a single population factor with a common separator for each observation.
addStrata() - Add levels to your population
strata. This is ideal for adding groups defined by
find.clusters. You can input a data frame or a vector, but if
you put in a vector, you have the option to name it.
modifying: strata(myData) <- myStrata
preserving:
myNewData <- strata(myData, value = myStrata)
They essentially do
the same thing except that the modifying assignment method (the one with
the "<-") will modify the object in place whereas the non-assignment
method will preserve the original object (unless you overwrite it). Due to
convention, everything right of the assignment is termed value. To
avoid confusion, here is a guide to the argument value for
each function:
strata() value = a
data.frame that defines the strata for each individual in the
rows.
nameStrata() value = a vector or
a formula that will define the names.
splitStrata() value = a formula argument with
the same number of levels as the strata you wish to split.
addStrata() value = a vector or
data.frame with the same length as the number of individuals
in your data.
The preferred use of these functions is with a formula
object. Specifically, a hierarchical formula argument is used to assign the
levels of the strata. 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 hiearchical
formulas when specifying hierarchies as other types of formulas (eg.
~Country*City*Neighborhood) will give incorrect results.
Zhian N. Kamvar
# 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 strata strata(microbov) <- data.frame(other(microbov)) microbov # And change the names so we know what they are nameStrata(microbov) <- ~Country/Breed/Species ## Not run: # let's see what the strata looks like by Species and Breed: head(strata(microbov, ~Breed/Species)) # If we didn't want the last column combined with the first, we can set # combine = FALSE head(strata(microbov, ~Breed/Species, combine = FALSE)) #### USING splitStrata #### # For the sake of example, we'll imagine that we have imported our data set # with all of the stratifications combined. setPop(microbov) <- ~Country/Breed/Species strata(microbov) <- NULL # This is what our data would look like after import. microbov # To set our strata here, we need to use the functions strata and splitStrata strata(microbov) <- data.frame(x = pop(microbov)) microbov # shows us that we have "one" level of stratification head(strata(microbov)) # all strata are separated by "_" splitStrata(microbov) <- ~Country/Breed/Species microbov # Now we have all of our strata named and split head(strata(microbov)) # all strata are appropriately named and split. ## End(Not run)
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