How can I keep NA when I change levels

Question

I build a vector of factors containing NA.

my_vec <- factor(c(NA,\"a\",\"b\"),exclude=NULL)
levels(my_vec)
# [1] \"a\" \"b\" NA 

I change on

Answer 1

You have to quote NA, otherwise R treats it as a null value rather than a factor level. Factor levels sort alphabetically by default, but obviously that's not always useful, so you can specify a different order by passing a new list order to levels()

require(plyr)
my_vec <- factor(c("NA","a","b1","b2"))
vec2 <- revalue(my_vec,c("b1"="c","b2"="c"))

#now reorder levels

my_vec2 <- factor(vec2, levels(vec2)[c(1,3,2)])

Levels: a NA c

Answer 2

I finally created a function that first replaces the NA value with a temp one (inspired by @lmo), then does the replacement I wanted the standard way, then puts NA back in its place using @rawr's suggestion.

my_vec <- factor(c(NA,"a","b1","b2"),levels = c("a",NA,"b1","b2"),exclude=NULL)
my_vec <- level_sub(my_vec,c("b1","b2"),"c")
my_vec
# 1] <NA> a    c    c   
# Levels: a <NA> c

As a bonus level_sub can be used with na_rep = NULL which will remove the NA, and it will look good in pipe chains :).

level_sub <- function(x,from,to,na_rep = "NA"){
  if(!is.null(na_rep)) {levels(x)[is.na(levels(x))] <- na_rep}
  levels(x)[levels(x) %in% from] <- to
  if(!is.null(na_rep)) {attr(x, 'levels')[levels(x) == na_rep] <- NA}
  x
}

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Nevertheless it seems that R really doesn't want you to add NA to factors.

levels(my_vec) <- c(NA,"a") will have a strange behavior but that doesn't stop here. While subset will keep NA levels in your columns, rbind will quietly remove them! I wouldn't be surprised if further investigation revealed that half R functions remove NA factors, making them very unsafe to work with...