I received an email from one of my students expressing deep frustation with a seemingly simple problem. He had a factor containing names of potato lines and wanted to set some levels to NA. Using simple letters as example names he was baffled by the result of the following code:

lines = factor(LETTERS)
lines
# [1] A B C D E F G H...
# Levels: A B C D E F G H...

linesNA = ifelse(lines %in% c('C', 'G', 'P'), NA, lines)
linesNA
#  [1]  1  2 NA  4  5  6 NA  8...

The factor has been converted to numeric and there was no trace of the level names. Even forcing the conversion to be a factor loses the level names. Newbie frustation guaranteed!

linesNA = factor(ifelse(lines %in% c('C', 'G', 'P'), NA, lines))
linesNA
# [1] 1    2    <NA> 4    5    6    <NA> 8...
# Levels: 1 2 4 5 6 8...

Under the hood factors are numerical vectors (of class factor) that have associated character vectors to describe the levels (see Patrick Burns’s R Inferno PDF for details). We can deal directly with the levels using this:

linesNA = lines
levels(linesNA)[levels(linesNA) %in% c('C', 'G', 'P')] = NA
linesNA
# [1] A    B    <NA> D    E    F    <NA> H...
#Levels: A B D E F H...

We could operate directly on lines (without creating linesNA), which is there to maintain consistency with the previous code. Another way of doing the same would be:

linesNA = factor(as.character(ifelse(lines %in%
                 c('C', 'G', 'P'), NA, lines)))
linesNA
# [1] A    B    <NA> D    E    F    <NA> H...
#Levels: A B D E F H...

I can believe that there are good reasons for the default behavior of operations on factors, but the results can drive people crazy (at least rhetorically speaking).