[R] Numeric class and sasxport.get

Frank E Harrell Jr f.harrell at vanderbilt.edu
Wed Feb 4 18:30:20 CET 2009

Sebastien Bihorel wrote:
> Thanks a lot Frank,
> One last question, though. I was tempted to remove all attributes of my 
> variables after the sasxport.get call using
> foo <- sasxport.get(...)
> foo <- as.data.frame(lapply(unclass(foo),as.vector))
> Since I never worked with the objects of class 'labeled', I was 
> wondering what I will loose by removing this attribute.

Not a good idea, for many reasons including dates and other types.

And the labelled type is need if you subset the data, in order to keep 
the labels.

Note that your original issue is related to "class" being "soft" for 
integers and regular numerics:

  x <- 1:3
 > attributes(x)
 > class(x)
[1] "integer"
 > x <- runif(3)
 > class(x)
[1] "numeric"
 > attributes(x)


> *Sebastien Bihorel, PharmD, PhD*
> PKPD Scientist
> Cognigen Corp
> Email: sebastien.bihorel at cognigencorp.com 
> <mailto:sebastien.bihorel at cognigencorp.com>
> Phone: (716) 633-3463 ext. 323
> Frank E Harrell Jr wrote:
>> Sebastien.Bihorel at cognigencorp.com wrote:
>>> The problem is actually not related to a broken command but a attempt of
>>> operational qualification of R. A few years ago, my company developed a
>>> set of scripts for the 'operational qualification' of Splus. We are
>>> switching to R so I am currently trying to port the scripts to R.
>>> All Splus scripts imported SAS data using the importData function, 
>>> which I
>>> substituted by sasxport.get. One particular script returns the class of
>>> each variable of the imported data frame; the output must match the
>>> expected values: numeric, factor, integer, etc... The R 'translation' 
>>> with
>>> sasxport.get is thus problematic.
>>> If there is no easy tweak of the function, we will probably have to 
>>> remove
>>> this script from our list of 'qualification' scripts.
>>> Although it would be nice
>> Then my advice is to write your own wrapper function for sasxport.get 
>> that takes its output, looks for labelled variables, and adds a new 
>> class of your choosing depending on properties of the variable, making 
>> sure that you write methods needed for that class (if any).  Then test 
>> your new function, not sasxport.get explicitly.
>> Frank
>>>> Sebastien Bihorel wrote:
>>>>> Frank,
>>>>> It is a non existing issue for me if the variables of class "labelled"
>>>>> (and only "labelled") can only be numerical variables (integer or
>>>>> numeric).
>>>>> Sebastien
>>>> 'labelled' can apply to any type of vector.  I'm not clear on the
>>>> problem this causes you.  Please provide a command that is broken by
>>>> this behavior.
>>>> Frank
>>>>> Frank E Harrell Jr wrote:
>>>>>> Sebastien Bihorel wrote:
>>>>>>> Dear R-users,
>>>>>>> The sasxport.get function (from the Hmisc package) automatically
>>>>>>> defines the class of imported variables. I have noticed that the
>>>>>>> class of theoretically numeric variables is simply "labelled",
>>>>>>> although character variables might end up been defined as "labelled"
>>>>>>> "Date" or "labelled" "factor".
>>>>>>> Is there a way to tell sasxport.get to define numeric variable as
>>>>>>> "labelled" "integer" or "labelled" "numeric"?
>>>>>> Sebastien,
>>>>>> If that would fix a problem you're having we could look into it.
>>>>>> Otherwise I'd tend to leave well enough alone.
>>>>>> Frank
>>>>>>> Thank you
>>>>>>> Sebastien
>>>>>>> ______________________________________________
>>>>>>> R-help at r-project.org mailing list
>>>>>>> https://stat.ethz.ch/mailman/listinfo/r-help
>>>>>>> PLEASE do read the posting guide
>>>>>>> http://www.R-project.org/posting-guide.html
>>>>>>> and provide commented, minimal, self-contained, reproducible code.
>>>> -- 
>>>> Frank E Harrell Jr   Professor and Chair           School of Medicine
>>>>                       Department of Biostatistics   Vanderbilt 
>>>> University

Frank E Harrell Jr   Professor and Chair           School of Medicine
                      Department of Biostatistics   Vanderbilt University

More information about the R-help mailing list