I received an email from one of my students expressing deep frustration 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 frustration 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).