Cleaning up factor levels (collapsing multiple levels/labels)
As the question is titled Cleaning up factor levels (collapsing multiple levels/labels), the forcats package should be mentioned here as well, for the sake of completeness. forcats appeared on CRAN in August 2016.
There are several convenience functions available for cleaning up factor levels:
x <- c("Y", "Y", "Yes", "N", "No", "H")
library(forcats)
Collapse factor levels into manually defined groups
fct_collapse(x, Yes = c("Y", "Yes"), No = c("N", "No"), NULL = "H")
#[1] Yes Yes Yes No No <NA>
#Levels: No Yes
Change factor levels by hand
fct_recode(x, Yes = "Y", Yes = "Yes", No = "N", No = "No", NULL = "H")
#[1] Yes Yes Yes No No <NA>
#Levels: No Yes
Automatically relabel factor levels, collapse as necessary
fun <- function(z) {
z[z == "Y"] <- "Yes"
z[z == "N"] <- "No"
z[!(z %in% c("Yes", "No"))] <- NA
z
}
fct_relabel(factor(x), fun)
#[1] Yes Yes Yes No No <NA>
#Levels: No Yes
Note that fct_relabel() works with factor levels, so it expects a factor as first argument. The two other functions, fct_collapse() and fct_recode(), accept also a character vector which is an undocumented feature.
Reorder factor levels by first appearance
The expected output given by the OP is
[1] Yes Yes Yes No No <NA>
Levels: Yes No
Here the levels are ordered as they appear in x which is different from the default (?factor: The levels of a factor are by default sorted).
To be in line with the expected output, this can be achieved by using fct_inorder() before collapsing the levels:
fct_collapse(fct_inorder(x), Yes = c("Y", "Yes"), No = c("N", "No"), NULL = "H")
fct_recode(fct_inorder(x), Yes = "Y", Yes = "Yes", No = "N", No = "No", NULL = "H")
Both return the expected output with levels in the same order, now.
Since R 3.5.0 (2018-04-23) you can do this in one clear and simple line:
x = c("Y", "Y", "Yes", "N", "No", "H") # The 'H' should be treated as NA
tmp = factor(x, levels= c("Y", "Yes", "N", "No"), labels= c("Yes", "Yes", "No", "No"))
tmp
# [1] Yes Yes Yes No No <NA>
# Levels: Yes No
1 line, maps multiple values to the same level, sets NA for missing levels" – h/t @Aaron
UPDATE 2: See Uwe's answer which shows the new "tidyverse" way of doing this, which is quickly becoming the standard.
UPDATE 1: Duplicated labels (but not levels!) are now indeed allowed (per my comment above); see Tim's answer.
ORIGINAL ANSWER, BUT STILL USEFUL AND OF INTEREST:
There is a little known option to pass a named list to the levels function, for exactly this purpose. The names of the list should be the desired names of the levels and the elements should be the current names that should be renamed. Some (including the OP, see Ricardo's comment to Tim's answer) prefer this for ease of reading.
x <- c("Y", "Y", "Yes", "N", "No", "H", NA)
x <- factor(x)
levels(x) <- list("Yes"=c("Y", "Yes"), "No"=c("N", "No"))
x
## [1] Yes Yes Yes No No <NA> <NA>
## Levels: Yes No
As mentioned in the levels documentation; also see the examples there.
value: For the 'factor' method, a vector of character strings with length at least the number of levels of 'x', or a named list specifying how to rename the levels.
This can also be done in one line, as Marek does here: https://stackoverflow.com/a/10432263/210673; the levels<- sorcery is explained here https://stackoverflow.com/a/10491881/210673.
> `levels<-`(factor(x), list(Yes=c("Y", "Yes"), No=c("N", "No")))
[1] Yes Yes Yes No No <NA>
Levels: Yes No
Perhaps a named vector as a key might be of use:
> factor(unname(c(Y = "Yes", Yes = "Yes", N = "No", No = "No", H = NA)[x]))
[1] Yes Yes Yes No No <NA>
Levels: No Yes
This looks very similar to your last attempt... but this one works :-)