typeof returns integer for something that is clearly a factor

If what you wanted was to know what class attribute was held by a vector then use class. If you wanted to test whether a vector was a factor then use is.factor.

the value returned by typeof being integer for factors is a language feature that confused me as well in my early days of R programming. The typeof function is giving information that's at a "lower" level of abstraction. Factor variables (and also Dates) are stored as integers. Learn to use class or str rather than typeof (or mode). They give more useful information. You can look at the full "structure" of a factor variable with dput:

 dput( factor( rep( letters[1:5], 2) ) )
# structure(c(1L, 2L, 3L, 4L, 5L, 1L, 2L, 3L, 4L, 5L), 
            .Label = c("a", "b", "c", "d", "e"), class = "factor")

The character values that are usually thought of as the factor values are actually stored in an attribute (which is what "levels" returns), while the "main" part of the variable is a set of integer indices pointing to teh various level "attributes), named .Label, so mode returns "numeric" and typeof returns "integer". For this reason one usually needs to use as.character that will coerce to what most people think of as factors, namely their character representations.