Saving missing categories from R to Stata

March 15, 2019
By

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I’m finishing a project from the RECSM institute where we developed a Shiny application to download data from the European Social Survey with Spanish translated labels. This was one hell of a project since I had to build some wrappers around the Google Translate API to generate translations for over 1300 questions and stream line this to be interactive while users download the data. That’s a long story which I will not delve into.

This post is about a bug I found in the haven package while doing the project. The bug is simple to explain and I filed it in haven already:

Let’s define a labelled double with only one tagged NA value.

library(haven)
#> Warning: package 'haven' was built under R version 3.4.4

tst <-
  labelled(
    c(
      1:5,
      tagged_na("d")
    ),
    c(
      "Agree Strongly" = 1,
      "Agree" = 2,
      "Neither agree nor disagree" = 3,
      "Disagree" = 4,
      "Disagree strongly" = 5,
      "No answer" = tagged_na("d")
    )
  )

tst
## 
## [1]     1     2     3     4     5 NA(d)
## 
## Labels:
##  value                      label
##      1             Agree Strongly
##      2                      Agree
##      3 Neither agree nor disagree
##      4                   Disagree
##      5          Disagree strongly
##  NA(d)                  No answer
write_dta(data.frame(freehms = tst), "test.dta", version = 13)

If I load this in Stata and type tab freehms, all labels are correct:

Now, if I take the code above and add another tagged NA value, then write_dta drops the last label for some reason:

library(haven)

tst <-
  labelled(c(1:5,
             tagged_na('d'),
             ## Only added this
             tagged_na('c')
          ),
        c('Agree Strongly' = 1,
          'Agree' = 2,
          'Neither agree nor disagree' = 3,
          'Disagree' = 4,
          'Disagree strongly' = 5,
          'No answer' = tagged_na('d'),
            ## And this
          'Dont know' = tagged_na('c')
          )
        )

tst
## 
## [1]     1     2     3     4     5 NA(d) NA(c)
## 
## Labels:
##  value                      label
##      1             Agree Strongly
##      2                      Agree
##      3 Neither agree nor disagree
##      4                   Disagree
##      5          Disagree strongly
##  NA(d)                  No answer
##  NA(c)                  Dont know
write_dta(data.frame(freehms = tst), "test.dta", version = 13)

Well, the bug is evident (notice the 5 without a label?). However, since the project is on a deadline I had to come up with a solution. It’s very simple: avoid tagged NA’s but recode them as traditional labels. Here’s a solution:

library(sjlabelled)
library(sjmisc)

# Labels tags present in the ESS data
old_label_names <- c("a", "b", "c", "d")

# Grab the labels with tagged NA's with a regex
na_available <- unname(gsub("NA|\\(|\\)", "", get_na(tst, TRUE)))

# Identify which of the existent labels are actually valid ESS missings
which_ones_use <- old_label_names %in% na_available

# Subset only the ones which need recoding
value_code <- c(666, 777, 888, 999)[which_ones_use]
new_label_names <- c(".a", ".b", ".c", ".d")[which_ones_use]

# Recode them
for (i in seq_along(na_available)) {
  tst <- replace_na(tst,
                    value = value_code[i],
                    na.label = new_label_names[i],
                    tagged.na = na_available[i]
                    )
}

tst
## 
## [1]   1   2   3   4   5 888 999
## 
## Labels:
##  value                      label
##      1             Agree Strongly
##      2                      Agree
##      3 Neither agree nor disagree
##      4                   Disagree
##      5          Disagree strongly
##    888                         .c
##    999                         .d

There we go. Those labels would clearly be interpreted as missings and Stata would read them as traditional labels (well, it’s not perfect, but it’s a workaround). What I did was wrap the above code into a function and apply it to all questions in all rounds (> 1300!).

recode_stata_labels <- function(x) {
  # Labels tags present in the ESS data
  old_label_names <- c("a", "b", "c", "d")

  # Grab the labels with tagged NA's with a regex
  na_available <- unname(gsub("NA|\\(|\\)", "", get_na(x, TRUE)))

  # Identify which of the existent labels are actually valid ESS missings
  which_ones_use <- old_label_names %in% na_available

  # Subset only the ones which need recoding
  value_code <- c(666, 777, 888, 999)[which_ones_use]
  new_label_names <- c(".a", ".b", ".c", ".d")[which_ones_use]

  for (i in seq_along(na_available)) {
    x <- replace_na(x,
                    value = value_code[i],
                    na.label = new_label_names[i],
                    tagged.na = na_available[i]
    )
  }

  x
}

Now, what happens if a labelled class only has tagged NA’s?

tst <-
  labelled(c(1:5,
             tagged_na('d'),
             tagged_na('c')
             ),
           c('No answer' = tagged_na('d'), 'Dont know' = tagged_na('c')))

tst
## 
## [1]     1     2     3     4     5 NA(d) NA(c)
## 
## Labels:
##  value     label
##  NA(d) No answer
##  NA(c) Dont know
recode_stata_labels(tst)
## Error: `x` must be a double vector

That’s weird. I was in such a rush that I didn’t really want to debug the source code in haven. However, I had the intuition that this was related to the fact that there were only tagged NA’s as labels. How do I fixed it? Just add a toy label at the beginning of the function and remove it after the recoding.

recode_stata_labels <- function(x) {
    # I add a random label (here) and delete it at the end (end of the function)
    x <- add_labels(x, labels = c('test' = 111111))

    # Note that this vector is in the same order as the `value_code` and `new_label_names`
    # because they're values correspond to each other in this order.
    old_label_names <- c("a", "b", "c", "d")

    na_available <- unname(gsub("NA|\\(|\\)", "", sjlabelled::get_na(x, TRUE)))
    which_ones_use <- old_label_names %in% na_available

    value_code <- c(666, 777, 888, 999)[which_ones_use]
    new_label_names <- c(".a", ".b", ".c", ".d")[which_ones_use]

    for (i in seq_along(na_available)) {
      x <- replace_na(x, value = value_code[i], na.label = new_label_names[i], tagged.na = na_available[i])
    }

    x <- remove_labels(x, labels = "test")

  x
}

recode_stata_labels(tst)
## 
## [1]   1   2   3   4   5 888 999
## 
## Labels:
##  value label
##    888    .c
##    999    .d

There we are. The replace_na function is actually doing most of the work and I found it extremely useful (comes from the sjmisc package).

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