Multiple missing values in R? Solved.

As a former SPSS trained user, ever since I started using R there was always a rather annoying background question: why is there a single missing value in base R, and why isn’t it possible to use more missing values?

As far as I understand, the main reason might have something to do with the scientific domain of the original R creators, who were definitely not from the social sciences. A single missing value is more than enough for any other scientific domain, and R simply went on the original design, ignoring the use of multiple missing values that are universally offered by all other major statistical software like SAS, SPSS and Stata.

More recently, some good initiatives led to the packages haven and labelled, who are almost (but not) perfect. In this post, I am going to write about my own solution to this situation, published on CRAN in the package declared.

This package offers a custom type of vector, that is not different from regular R vectors in the sense that it contains exactly the same missing values, so normal functionality is maintained for any statistical operation. What it additionally does, is to keep a record of the position of each and every missing value, and assign meaning to those positions. This way, it achieves the best of both worlds: declare and use multiple missing values, whilst being fully compatible with base R design.

The following is an illustrative example, for a hypothetical variable about the number of children in a household:

library(declared)
children <- declared(
  c(2, -91, 0, 3, -92, 4, 2, 1, 0, 3, -91, 0, 1, 2, 1, 0, -91, 2, 5, 2, 1, 3),
  label = "Number of children in the household",
  labels = c("Prefer not to say" = -91, "Not applicable" = -92),
  na_values = c(-91, -92)
)
#> <declared<integer>[22]> Number of children in the household
#>  [1]       2 NA(-91)       0       3 NA(-92)       4       2       1       0
#> [10]       3 NA(-91)       0       1       2       1       0 NA(-91)       2
#> [19]       5       2       1       3
#> Missing values: -91, -92

#> Labels:
#>  value             label
#>    -91 Prefer not to say
#>    -92    Not applicable

The values -91 and -92 are properly declared and recognised as missing, as it can be seen in the print method which prepends the NA in front of the value.

Let’s see how this vector looks in base R:

baseRchildren <- children |> drop()
#> [1]  2 NA  0  3 NA  4  2  1  0  3 NA  0  1  2  1  0 NA  2  5  2  1  3

Any statistical operation, even basic descriptives, on such vectors results into an NA:

baseRchildren |> mean()
#> [1] NA

In R, the value NA is equivalent to an empty cell (with no information about why it is missing) and this requires attention. To obtain the expected result, one has to employ the argument na.rm (remove missing values before calculating the mean), deactivated by default to alert users about potential problems in the data.

baseRchildren |> mean(na.rm = TRUE)
#> [1] 1.777778

However, in this particular example the values are not “empty”. There are particular and known reasons for each value where the number of children is not provided, hence these values should not be problematic. Package declared solves this by default:

children |> mean()
#> [1] 1.777778

In this example, the argument na.rm is not necessary because the (declared) NA values are not empty cells, despite being stored as regular NA values. For this reason, a dedicated function is provided, called is.empty(), to differentiate between pure NA and the four declared missing values:

children |> is.na() |> sum()
#> [1] 4

children |> is.empty() |> sum()
#> [1] 0

# adding one pure empty value
c(children, NA) |> is.empty() |> sum()
#> [1] 1

Declared vectors are useful for both numeric and categorical variables. In fact, missing values can be recorded no matter what kind of variables there are in a dataset. In addition to declaring such values, it is in fact possible to also declare value labels for the response categories, to create a special kind of object that is inbetween numerical vectors and R factors.

orientation <- declared(
  c(1:3, -91),
  labels = c("Left" = 1, "Middle" = 2, "Right" = 3, "Don't know" = -91),
  na_value = -91,
  label = "Respondent's political orientation"
)
#> <declared<integer>[4]> Respondent's political orientation
#> [1]       1       2       3 NA(-91)
#> Missing values: -91

#> Labels:
#>  value     label
#>     1       Left
#>     2     Middle
#>     3      Right
#>   -91 Don't know

This is a typical example of a categorical variable, with all values corresponding to certain ordered categories. The only possible way to emulate this in base R is to use a factor:

factor(
  c("Left", "Middle", "Right", "Don't know"),
  levels = c("Left", "Middle", "Right", "Don't know"),
  ordered = TRUE
)
#> [1] Left       Middle     Right      Don't know
#> Levels: Left < Middle < Right < Don't know

R factors are unable to differentiate between valid categories and those which should be treated as missing, and the order of the categories needs to be specified separately using the argument levels. In addition, the original (questionnaire) values are lost, for instance the value -91 can not be preserved.

Unlike R factors, in the declared counterpart the values are still there, and labels are assigned for each category. To meet the expectations of various statistical procedures that allow for categorical variables, the function as.factor() coerces the vector:

> orientation |> as.factor(ordered = TRUE)
#> [1] Left   Middle Right  <NA>  
#> Levels: Left < Middle < Right

This is the expected behavior, since the value -91 corresponding to the category “Don’t know” is to be treated as missing, anyways. The declared missing values are correctly coerced to base R NA values.

There are many other utility functions in this package, probably too many to describe in a single post. Interested readers are invited to visit the package’s Vignettes from CRAN:
https://cran.r-project.org/web/packages/declared/index.html