Often it is useful to keep a "codebook" to document the contents of a dataset. (By
"dataset" I mean
a rectangular structure such as a dataframe.)
The codebook has as many rows as the dataset has columns (variables, fields).
The columns (fields)
of the codebook may include:
• variable name
• type (character, factor, integer, etc)
• variable label (e.g., a variable called "bmi2" might be labeled
"BMI hand-input by
clinic personnel, must be checked"
• permissible values
• which values indicate missing (and potentially different kinds
of missing)
Some statistics software (e.g., SPSS and Stata) provides at least a subset of
this kind of
information automatically in a convenient form. For instance, in Stata one can define a
"label" for
a variable and it is thenceforth linked to the variable. In output from certain
modeling and
graphics functions, Stata by default uses the label rather than the variable
name.
Furthemore: In Stata, if "myvariable" is labeled numeric (in R lingo, a
factor), and I type
codebook myvariable
then Stata tells me, among other things, the "levels" of myvariable.
Does a tool of this sort exist in R?
The prompt() function is related to this, but prompt(someDataFrame) creates a
text file on disk. The
text file is associated with, but not unambiguously linked to, someDataFrame.
The epicalc function codebook() provides a summary of a dataframe similar to
that created by
summary() but easier to read. But this is not a way to define and keep track of
labels that are
linked to variables.
To link a dataframe to its codebook, one could do the following "by hand":
Create a list, say,
"somedata", where somedata$DATA is a dataframe that contains the data, and
somedata$VARIABLE is also
a dataframe, but serves as the codebook. For instance, the following function
creates a template
into which one could subsequently edit to insert variable labels and turn into
somedata$VARIABLE.
fnJunk <-function( THESEDATA ) {
# From a dataframe, make the start of a codebook.
if(!is.data.frame(THESEDATA)) stop("!is.data.frame(THESEDATA)")
data.frame(
Variable=names(THESEDATA)
, class=sapply(THESEDATA, class)
, type=sapply(THESEDATA, typeof)
, label=""
, comment=""
)
}
But the following automatic behavior would be nice:
• We should be able to treat somedata exactly as we treat a
dataframe, so that the
fact that it possesses a "codebook" is merely an added benefit, not an
interference with the
usual tasks.
• If we delete a column of somedata$DATA, the associated row of
somedata$VARIABLE
should be automatically deleted.
• If we add a column to somedata$DATA, the associated column
should be inserted in
somedata$VARIABLE, and some of the fields automatically populated such
as variable name and
type. It could get fancier. For instance:
• If we try to add a value to a field in somedata$DATA which is
not permitted by the
"permissible values" listed for this field in somedata$VARIABLE, we get
an error.
Has anyone already thought this through, maybe defined a class and associated
methods?
Thanks
Jacob A. Wegelin
Assistant Professor
Department of Biostatistics
Virginia Commonwealth University
730 East Broad Street Room 3006
P. O. Box 980032
Richmond VA 23298-0032
U.S.A.
E-mail: [email protected]
URL: http://www.people.vcu.edu/~jwegelin______________________________________________
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