R has factors, which are very cool (and somewhat analogous to labeled levels in Stata). Unfortunately, the factor list sticks around even if you remove some data such that no examples of a particular level still exist
# Create some fake data
x <- as.factor(sample(head(colors()),100,replace=TRUE))
x <- x[x!="aliceblue"]
levels(x) # still the same levels
table(x) # even though one level has 0 entries!
The solution is simple: run factor() again:
x <- factor(x)
If you need to do this on many factors at once (as is the case with a data.frame containing several columns of factors), use drop.levels() from the gdata package:
x <- x[x!="antiquewhite1"]
df <- data.frame(a=x,b=x,c=x)
df <- drop.levels(df)
Now I'm going to quit monkeying around and get to sleep.