How can I import SAS format files into R?

Question

I am trying to analyze data from the 2012-2013 NATS survey, from this location. There are three files in the zip folder there, labelled 2012-2013 NATS format.sas, formats.sas7bcat and nats2012.sas7bdat. The third file contains the actual data, but the second file contains the labels that go with the data; that is, as an example, if the variable 'Race' in the raw data file has categories 1,2,3 and 4, the labels show that these categories stand for 'Caucasian', 'African-American','Hispanic' and 'Other'. I have been able to import the sas7bdat file into R, using the 'sas7bdat' package, but when I try to do cross-tabulations, I am not able to see which category each cell represents. For example, if I try to do this:

table(SMOKSTATUS_R, RACEETHNIC)

What I get is:

RACEETHNIC
SMOKSTATUS_R     1     2     3     4     5     6     7     8     9
           1  4045   455    55     7    63     0   675   393   373
           2  1183   222    38     2    26     0   217   255   154
           3 14480   957   238    14    95     3  1112   950   369
           4 23923  2532  1157    23   147     1  1755  3223   909
           5    81    18     4     0     1     0    11    17     9

As far as I can tell, the only way to inlcude the labels to the data is manually typing them in, but there are 240 variables and besides, there are labels currently existing, in the form of the format.sas7bcat file. Is there any way to import the format file into R, so that the labels can be attached to the variables? This is how it is done in SAS, but I do not have access t oSAS right now. Thanks for all the help.

Do a search on the foreign package -- here's the reference manual — JasonAizkalns
Just read the SAS program that has the code to define the formats and parse that. I am not familiar with NATS, but most people that publish SAS code to define formats produce the code in a very structured format that lends itself to being parsed easily. Or use SAS to export the format catalog to a SAS dataset that you can read from R. — Tom
readsas7dbat or haven are other packages; see this question and answer of mine. — MichaelChirico
I usually load into SAS then export as a single Stata file and load that into R with foreign. I find that works the best, since it preserves the format statements as metadata. — Carl
Isn't that too roundabout a way? Anyway, thanks all for your suggestions, but I am going to wait till next week to work in SAS directly. @MichaelChirico I can't create an Xport file from the SAS dataset either, which rules out using the package foreign along with the ones you mentioned. — KVemuri

rawr rawr · Accepted Answer · 2015-10-29T22:19:29

This should be a one-liner:

library('haven')
sas <- read_sas('nats2012.sas7bdat', 'formats.sas7bcat')

with(sas, table(SMOKSTATUS_R, RACEETHNIC))
#             RACEETHNIC
# SMOKSTATUS_R     1     2     3     4     5     6     7     8     9
#            1  4045   455    55     7    63     0   675   393   373
#            2  1183   222    38     2    26     0   217   255   154
#            3 14480   957   238    14    95     3  1112   950   369
#            4 23923  2532  1157    23   147     1  1755  3223   909
#            5    81    18     4     0     1     0    11    17     9

table(names(attr(sas[, 'SMOKSTATUS_R'], 'labels')[sas[, 'SMOKSTATUS_R']]),
      names(attr(sas[, 'RACEETHNIC'], 'labels')[sas[, 'RACEETHNIC']]))

#                          Amer. Indian, AK Nat. Only, Non-Hispanic
# Current everyday smoker                                        63
# Current some days smoker                                       26
# Former smoker                                                  95
# Never smoker                                                  147
# Unknown                                                         1

Use haven to read in the data, but that also gives you some useful attributes, namely the variable labels:

attributes(sas$SMOKSTATUS_R)
# $label
# [1] "SMOKER STATUS (4-level)"
# 
# $class
# [1] "labelled"
# 
# $labels
# Current everyday smoker Current some days smoker            Former smoker 
#                       1                        2                        3 
# Never smoker                  Unknown 
#            4                        5 
# 
# $is_na
# [1] FALSE FALSE FALSE FALSE FALSE

You can easily write this into a function to use more generally:

do_fmt <- function(x, fmt) {
  lbl <- if (!missing(fmt))
    unlist(unname(fmt)) else attr(x, 'labels')

  if (!is.null(lbl))
    tryCatch(names(lbl[match(unlist(x), lbl)]),
             error = function(e) {
               message(sprintf('formatting failed for %s', attr(x, 'label')),
                       domain = NA)
               x
             }) else x
}

table(do_fmt(sas[, 'SMOKSTATUS_R']),
      do_fmt(sas[, 'RACEETHNIC']))

#                          Amer. Indian, AK Nat. Only, Non-Hispanic
# Current everyday smoker                                        63
# Current some days smoker                                       26
# Former smoker                                                  95
# Never smoker                                                  147
# Unknown                                                         1

And apply to the entire data set

sas[] <- lapply(sas, do_fmt)
sas$SMOKSTATUS_R[1:4]
# [1] "Never smoker"  "Former smoker" "Former smoker" "Never smoker"

Although sometimes this fails like below. This looks like something wrong with the haven package

attr(sas$SMOKTYPE, 'labels')
# INAPPLICABLE            REFUSED                 DK    NOT ASCERTAINED 
#     -4.00000           -0.62500           -0.50000           -0.46875 
# PREMADE CIGARETTES      ROLL-YOUR-OWN               BOTH 
#            1.00000            2.00000            3.00000

So instead of this, you can parse the format.sas file with some simple regexes

locf <- function(x) {
  x <- data.frame(x, stringsAsFactors = FALSE)
  x[x == ''] <- NA
  indx <- !is.na(x)

  x[] <- lapply(seq_along(x), function(ii) {
    idx <- cumsum(indx[, ii])
    idx[idx == 0] <- NA
    x[, ii][indx[, ii]][idx]
  })
  x[, 1]
}

fmt <- readLines('~/desktop/2012-2013-NATS-Format/2012-2013-NATS-Format.sas')
## not sure if comments are allowed in the value definitions, but
## this will check for those in case
fmt <- gsub('\\*.*;|\\/\\*.*\\*\\/', '', fmt)

vars <- gsub('(?i)value\\W+(\\w*)|.', '\\1', fmt, perl = TRUE)
vars <- locf(vars)

regex <- '[\'\"].*[\'\"]|[\\w\\d-]+'
vals <- gsub(sprintf('(?i)\\s*(%s)\\s*(=)\\s*(%s)|.', regex, regex),
               '\\1\\2\\3', fmt, perl = TRUE)

View(dd <- na.omit(data.frame(values = vars, formats = vals,
                              stringsAsFactors = FALSE)))

sp <- split(dd$formats, dd$values)
sp <- lapply(sp, function(x) {
  x <- Filter(nzchar, x)
  x <- strsplit(x, '=')
  tw <- function(x) gsub('^\\s+|\\s+$', '', x)
  sapply(x, function(y)
    setNames(tw(y[1]), tw(y[2])))
})

So the smoke type formats (one of them that failed above), for example, gets parsed like this:

sp['A5_']
# $A5_
# 'INAPPLICABLE'            'REFUSED'                 'DK' 
#           "-1"                 "-7"                 "-8" 
# 'NOT ASCERTAINED' 'PREMADE CIGARETTES'      'ROLL-YOUR-OWN'  'BOTH' 
#              "-9"                  "1"                  "2"     "3"

And then you can use the function again to apply to the data

table(do_fmt(sas['SMOKTYPE'], sp['A5_']))

# 'BOTH'                 'DK'       'INAPPLICABLE' 
#   736                   17                51857 
# 'PREMADE CIGARETTES'            'REFUSED'      'ROLL-YOUR-OWN' 
#                 7184                    2                  396

How can I import SAS format files into R?

2 Answers