The primary user-facing data types in the R statistical computing environment behave as vectors. That is: one dimensional arrays of scalar values that have a nice operational algebra. There are additional types (lists, data frames, matrices, environments, and so-on) but the most common data types are vectors. In fact vectors are so common in R that scalar values such as the number
5 are actually represented as length-1 vectors. We commonly think about working over vectors of “logical”, “integer”, “numeric”, “complex”, “character”, and “factor” types. However, a “factor” is not a R vector. In fact “factor” is not a first-class citizen in R, which can lead to some ugly bugs.
For example, consider the following R code.
levels <- c('a','b','c')
f <- factor(c('c','a','a',NA,'b','a'),levels=levels)
##  c a a <NA> b a
## Levels: a b c
##  "factor"
This example encoding a series of 6 observations into a known set of factor-levels (
'c'). As is the case with real data some of the positions might be missing/invalid values such as
NA. One of the strengths of R is we have a uniform explicit representation of bad values, so with appropriate domain knowledge we can find and fix such problems. Suppose we knew (by policy or domain experience) that the level
'a' was a suitable default value to use when the actual data is missing/invalid. You would think the following code would be the reasonable way to build a new revised data column.
fRevised <- ifelse(is.na(f),'a',f)
##  "3" "1" "1" "a" "2" "1"
##  "character"
Notice the new column
fRevised is an absolute mess (and not even of class/type factor). This sort of fix would have worked if
f had been a vector of characters or even a vector of integers, but for factors we get gibberish.
We are going to work through some more examples of this problem. Continue reading