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.sa

Answer 1

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