There are some differences between the way that R, SAS, SPSS, and Stata represented labelled data and missing values. While SAS, SPSS, and Stata share some obvious similarities, R is little different. This vignette explores the differences, and shows you how haven bridges the gap.
Base R has one data type that effectively maintains a mapping between integers and character labels: the factor. This however, is not the primary use of factors: they are instead designed to automatically generate useful contrasts for linear models. Factors differ from the labelled values provided by the other tools in important ways:
SPSS and SAS can label numeric and character values, not just integer values.
The value do not need to be exhaustive. It is common to label the
special missing values (e.g.
.D = did not respond,
.N = not applicable), while leaving other values as
Value labels in SAS are a little different again. In SAS, labels are
just special case of general formats. Formats include currencies and
dates, but user-defined just assigns labels to individual values
(including special missings value). Formats have names and existing
independently of the variables they are associated with. You create a
named format with
PROC FORMAT and then associated with
variables in a
DATA step (the names of character formats
thealways start with
To allow you to import labelled vectors into R, haven provides the S3
labelled class, created with
labelled(). This class allows
you to associated arbitrary labels with numeric or character
x1 <- labelled( sample(1:5), c(Good = 1, Bad = 5) ) x1 #> <labelled<integer>> #>  3 5 1 4 2 #> #> Labels: #> value label #> 1 Good #> 5 Bad x2 <- labelled( c("M", "F", "F", "F", "M"), c(Male = "M", Female = "F") ) x2 #> <labelled<character>> #>  M F F F M #> #> Labels: #> value label #> M Male #> F Female
The goal of haven is not to provide a labelled vector that you can use everywhere in your analysis. The goal is to provide an intermediate datastructure that you can convert into a regular R data frame. You can do this by either converting to a factor or stripping the labels:
See the documentation for
as_factor() for more options
to control exactly what the factor uses for levels.
zap_labels() have data
frame methods if you want to apply the same strategy to every column in
a data frame:
df <- tibble::data_frame(x1, x2, z = 1:5) #> Warning: `data_frame()` was deprecated in tibble 1.1.0. #> ℹ Please use `tibble()` instead. #> This warning is displayed once every 8 hours. #> Call `lifecycle::last_lifecycle_warnings()` to see where this warning was #> generated. df #> # A tibble: 5 × 3 #> x1 x2 z #> <int+lbl> <chr+lbl> <int> #> 1 3 M [Male] 1 #> 2 5 [Bad] F [Female] 2 #> 3 1 [Good] F [Female] 3 #> 4 4 F [Female] 4 #> 5 2 M [Male] 5 zap_labels(df) #> # A tibble: 5 × 3 #> x1 x2 z #> <int> <chr> <int> #> 1 3 M 1 #> 2 5 F 2 #> 3 1 F 3 #> 4 4 F 4 #> 5 2 M 5 as_factor(df) #> # A tibble: 5 × 3 #> x1 x2 z #> <fct> <fct> <int> #> 1 3 Male 1 #> 2 Bad Female 2 #> 3 Good Female 3 #> 4 4 Female 4 #> 5 2 Male 5
All three tools provide a global “system missing value” which is
.. This is roughly equivalent to R’s
NA, although neither Stata nor SAS propagate missingness in
numeric comparisons: SAS treats the missing value as the smallest
possible number (i.e.
-inf), and Stata treats it as the
largest possible number (i.e.
Each tool also provides a mechanism for recording multiple types of missingness:
Stata has “extended” missing values,
SAS has “special” missing values,
SPSS has per-column “user” missing values. Each column can declare up to three distinct values or a range of values (plus one distinct value) that should be treated as missing.
Stata and SAS only support tagged missing values for numeric columns. SPSS supports up to three distinct values for character columns. Generally, operations involving a user-missing type return a system missing value.
Haven models these missing values in two different ways:
For SAS and Stata, haven provides “tagged” missing values which
extend R’s regular
NA to add a single character
For SPSS, haven provides a subclass of
also provides user defined values and ranges.
To support Stata’s extended and SAS’s special missing value, haven implements a tagged NA. It does this by taking advantage of the internal structure of a floating point NA. That allows these values to behave identical to NA in regular R operations, while still preserving the value of the tag.
The R interface for creating with tagged NAs is a little clunky
because generally they’ll be created by haven for you. But you can
create your own with
Note these tagged NAs behave identically to regular NAs, even when
printing. To see their tags, use
To test if a value is a tagged NA, use
and to extract the value of the tag, use
My expectation is that tagged missings are most often used in
conjuction with labels (described below), so labelled vectors print the
tags for you, and
as_factor() knows how to relabel:
SPSS’s user-defined values work differently to SAS and Stata. Each
column can have either up to three distinct values that are considered
as missing, or a range. Haven provides
labelled_spss() as a
labelled() to model these additional
x1 <- labelled_spss(c(1:10, 99), c(Missing = 99), na_value = 99) x2 <- labelled_spss(c(1:10, 99), c(Missing = 99), na_range = c(90, Inf)) x1 #> <labelled_spss<double>> #>  1 2 3 4 5 6 7 8 9 10 99 #> Missing values: 99 #> #> Labels: #> value label #> 99 Missing x2 #> <labelled_spss<double>> #>  1 2 3 4 5 6 7 8 9 10 99 #> Missing range: [90, Inf] #> #> Labels: #> value label #> 99 Missing
These objects are somewhat dangerous to work with in R because most R functions don’t know those values are missing:
Because of that danger, the default behaviour of
read_spss() is to return regular labelled objects where
user-defined missing values have been converted to
read_spss() to return
objects, you’ll need to set
user_na = TRUE.
I’ve defined an
is.na() method so you can find them
And the presence of that method does mean many functions with an
na.rm argument will work correctly:
But generally you should either convert to a factor, convert to regular missing vaues, or strip the all the labels: