[R] follow-up on Error when reading a SAS transport file (with sasxport.get from Hmisc)
Peter Dalgaard
p.dalgaard at biostat.ku.dk
Fri Oct 10 21:50:45 CEST 2008
Jean-Louis Abitbol wrote:
> I have done what P. Dalgaard has suggested and I don't find a
> descrepancy between the number of values and the number of labels: there
> 15 each...
>
> Any hint on what might go wrong here ?
>
Actually, I think you got it:
> factor(1,c(NA,1:4),c(1:5))
Error in factor(1, c(NA, 1:4), c(1:5)) :
invalid labels; length 5 should be 1 or 4
but
> factor(1,c(NA,1:4),c(1:5),exclude=NULL)
[1] 2
Levels: 1 2 3 4 5
so the issue is more than likely that your SAS format puts a label on
"." (missing). You probably need something like
factor(x, f$value, f$label, exclude=if (!any(is.na(f$value))) NA)
> Here is the output
>
> The SAS format from proc contents
>
> VISITF
> . = INEXTXT
> -10 = Visit 1 [Screening]
> 0 = Visit 2 [Baseline]
> 1 = CRF Tracking
> 6 = Visit 6
> 7 = Tel.Contact (day 7)
> 14 = Visit 3
> 21 = Tel.Contact (day 21)
> 28 = Visit 4
> 35 = Tel.Contact (day 35)
> 43 = Visit 5 [EOT]
> 65 = Visit 6 [Follow-up]
> 777 = End of Study
> 888 = Concomitant Med.
> 999 = Adverse Events
>
> the cat output with sep=" * " (manual CR edit due to line length)
>
> Processing SAS dataset ADMIN .x= * 43 * 28 * 0 * 14 * 43 * 0 * 28 *
> 14 * 28 * 43 * 14 * 0 * 28 * 14 * 0
> * 43 * 43 * 28 * 14 * 0 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 14
> * 0 * 43 * 28 * 43 * 28 * 14 * 0 * 43
> * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 14 * 0 * 0 * 43 * 28 * 14 * 0 *
> 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0
> * 14 * 0 * 43 * 28 * 0 * 28 * 43 * 14 * 14 * 0 * 28 * 43 * 0 * 43 * 0 *
> 43 * 14 * 0 * 28 * 0 * 43 * 28 * 14 * 43
> * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 0 * 43 * 43 * 28 *
> 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14
> * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28
> * 14 * 0 * 28 * 14 * 0 * 43 * 14 * 0 * 43
> * 28 * 0 * 14 * 43 * 28 * 14 * 43 * 28 * 0 * 28 * 14 * 0 * 43 * 0 * 43
> * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28
> * 14 * 0 * 0 * 28 * 14 * 0 * 43 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 *
> 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43
> * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 28
> * 14 * 0 * 14 * 28 * 43 * 0 * 43 * 14
> * 28 * 0 * 28 * 14 * 43 * 0 * 0 * 14 * 0 * 28 * 43 * 43 * 28 * 14 * 0
> * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0
> * 14 * 0 * 43 * 28 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 *
> 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28
> * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 14 * 0 * 43 * 28 * 0
> * 43 * 28 * 14 * 28 * 43 * 0 * 14
> * 0 * 43 * 28 * 14 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 *
> 14 * 0 * 43 * 28 * 14 * 0 * 43
> * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 14 * 0 * 28 * 14 * 0 * 14 * 0 *
> 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0
> * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 0 * 43 *
> 28 * 14 * 0 * 14 * 43 * 28 * 28 * 14
> * 0 * 43 * 43 * 28 * 0 * 14 * 28 * 0 * 14 * 43 * 43 * 28 * 14 * 0 *
> 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0
> * 28 * 14 * 0 * 43 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 *
> 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28
> * 14 * 0 * 43 * 28 * 14 * 0 * 0 * 28 * 14 * 0 * 0 * 14 * 0 * 43 * 28
> * 0 * 43 * 14 * 28 * 14 * 43 * 28
> * 0 * 0 * 43 * 28 * 14 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 *
> 28 * 14 * 0 * 43 * 14 * 0 * 43 * 28
> * 14 * 0 * 0 * 43 * 28 * 14 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 *
> 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0
> * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 0 * 43 *
> 28 * 14 * 0 * 14 * 28 * 43 * 14 * 28
> * 0 * 43 * 43 * 28 * 0 * 14 * 28 * 0 * 14 * 43 * 43 * 28 * 14 * 0 *
> 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0
> * 28 * 14 * 0 * 43 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 *
> 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28
> * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 28 * 14 * 0 * 43 *
> 14 * 0 * 28 * 43 * 14 * 0 * 43 * 28
> * 43 * 28 * 0 * 14 * 43 * 14 * 0 * 28 * 0 * 43 * 28 * 14 * 43 * 28 *
> 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28
> * 14 * 0 * 0 * 43 * 28 * 14 * 14 * 0 * 28 * 14 * 0 * 43 * 28 * 14 *
> 0 * 0 * 43 * 28 * 14 * 0 * 43 * 28
> * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 28 * 14 * 0 * 43 *
> 14 * 0 * 43 * 28 * 14 * 28 * 0 * 28
> * 43 * 0 * 14 * 43 * 28 * 14 * 0 * 14 * 0 * 43 * 28 * 43 * 28 * 14 *
> 0 * 43 * 28 * 14 * 0 * 0 * 43 * 28
> * 14 * 0 * 0 * 43 * 28 * 14 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 *
> 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0
> * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28 * 14 * 0 * 0 * 43 *
> 28 * 14 * 14 * 43 * 28 * 0 * 14 * 0
> * 14 * 0 * 43 * 28 * 43 * 14 * 0 * 28 * 0 * 43 * 28 * 14 * 43 * 28 *
> 14 * 0 * 43 * 28 * 14 * 0 * 43 * 28
> * 14 * 0 * 0 * 28 * 14 * 28 * 14 * 0 *
> f$value= * NA * -10 * 0 * 1 * 6 * 7 * 14 * 21 * 28 * 35 * 43 * 65 * 777
> * 888 * 999 *
> f$label= * INEXTXT * Visit 1 [Screening] * Visit 2 [Baseline] * CRF
> Tracking * Visit 6 * Tel.Contact (day 7) * Visit 3
> * Tel.Contact (day 21) * Visit 4 * Tel.Contact (day 35) * Visit 5 [EOT]
> * Visit 6 [Follow-up] * End of Study * Concomitant Med. * Adverse Events
> *
> Erreur dans factor(x, f$value, f$label) :
> invalid labels; length 15 should be 1 or 14
>
> Thanks again, JL
>
>
> On Thu, 09 Oct 2008 17:33:06 +0200, "Peter Dalgaard"
> <P.Dalgaard at biostat.ku.dk> said:
>
>> Jean-Louis Abitbol wrote:
>>
>>> Dear All,
>>>
>>> I get the following error when using either SASxport or Hmisc to read an
>>> .xpt file:
>>>
>>>
>>>
>>>> w <- read.xport("D:/consult/Trophos/dnp/base/TRO_ds_20081006.xpt")
>>>>
>>>>
>>> Erreur dans factor(x, f$value, f$label) :
>>> invalid labels; length 15 should be 1 or 14
>>>
>>>
>>>> z<- sasxport.get("D:/consult/Trophos/dnp/base/TRO_ds_20081006.xpt")
>>>>
>>>>
>>> Erreur dans factor(x, f$value, f$label) :
>>> invalid labels; length 15 should be 1 or 14
>>>
>>> I don't understand what is wrong with the labels ! Is there a limit for
>>> their length ?
>>> Could the problem be in the formats label ?
>>>
>>>
>> Hmmnoo...
>>
>> This is happening in R code, and the error is the same as you'd get from
>>
>>
>>> factor(1,levels=1:4,labels=1:5)
>>>
>> Error in factor(1, levels = 1:4, labels = 1:5) :
>> invalid labels; length 5 should be 1 or 4
>>
>> So, not going into the actual code, I would suspect that it is
>> encountering a problem where a user format has values and labels out of
>> sync. This could well be a bug in the package(s), but I wouldn't rule
>> out that your data could have gotten into some inconsistent state. You
>> might try debugging to the trouble spot and see what is actually in
>> f$value and f$label at that point.
>>
>>
>>> Just in case this might help this is the output from
>>> test <- lookup.xport("D:/consult/Trophos/dnp/base/TRO_ds_20081006.xpt")
>>> print(test)
>>>
>>> for the first SAS dataset:
>>> SAS xport file
>>> --------------
>>> Filename: `D:/consult/Trophos/dnp/base/TRO_ds_20081006.xpt'
>>>
>>> Variables in data set `ADMIN':
>>> dataset name type format flength fdigits iformat iflength
>>> ifdigits label nobs
>>> ADMIN CEN numeric 5 0 0
>>> 0 Centre 696
>>> ADMIN PNO numeric 6 0 0
>>> 0 Pat./Subj. number 696
>>> ADMIN VISIT numeric VISITF 0 0 0
>>> 0 Visit no. 696
>>> ADMIN VISITR numeric 0 0 0
>>> 0 Visit repeat 696
>>> ADMIN PRO character 0 0 0
>>> 0 Project number 696
>>> ADMIN STUDY character 0 0 0
>>> 0 Study number 696
>>> ADMIN COLLDAT numeric DATE 7 0 0
>>> 0 Date collected (study medication) 696
>>> ADMIN COMM_O character 0 0 0
>>> 0 Comment 696
>>> ADMIN INEXMET numeric YESNOF 0 0 0
>>> 0 In-/exclusion criteria still met? 696
>>> ADMIN LABEL_NO numeric 4 0 0
>>> 0 Medication number (label) 696
>>> ADMIN RAND_NO numeric 4 0 0
>>> 0 Lowest randomisation/medication number 696
>>> ADMIN RETMED numeric 4 0 0
>>> 0 Number of capsules returned 696
>>> ADMIN PAGE numeric 0 0 0
>>> 0 Page 696
>>> ADMIN PAGER numeric 0 0 0
>>> 0 Page repeat 696
>>> ADMIN CT_RECID character $ 40 0 $ 40
>>> 0 for merge with notes and flags 696
>>> ADMIN RNO numeric 4 0 0
>>> 0 Randomisation number 696
>>> ADMIN SAF numeric NOYESZF 0 0 0
>>> 0 696
>>> ADMIN ITT numeric NOYESZF 0 0 0
>>> 0 696
>>> ADMIN PP numeric NOYESZF 0 0 0
>>> 0 696
>>> ADMIN SEX numeric SEXF 0 0 0
>>> 0 Sex 696
>>> ADMIN AGE_C numeric 4 0 0
>>> 0 Age calc 696
>>> ADMIN TRT numeric TRTF 0 0 0
>>> 0 696
>>> ADMIN CRF_VERS character 0 0 0
>>> 0 CRF Version no. 696
>>>
>>> Thanks for any help,
>>>
>>> Best wishes, Jean-Louis
>>>
>>> PS: sessionInfo()
>>> R version 2.7.1 RC (2008-06-20 r45965)
>>> i386-pc-mingw32
>>>
>>> locale:
>>> LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> other attached packages:
>>> [1] SASxport_1.2.3 Hmisc_3.4-3 foreign_0.8-29 RWinEdt_1.8-0
>>>
>>> loaded via a namespace (and not attached):
>>> [1] chron_2.3-24 cluster_1.11.11 grid_2.7.1 lattice_0.17-15
>>>
>>>
>>> Jean-Louis Abitbol, MD
>>> Chief Medical Officer
>>> Trophos SA, Parc scientifique de Luminy, Case 931
>>> Luminy Biotech Entreprises
>>> 13288 Marseille Cedex 9 France
>>> Email: jlabitbol at trophos.com ---- Backup Email: abitbol at sent.com
>>> Cellular: (33) (0)6 24 47 59 34
>>> Direct Line: (33) (0)4 91 82 82 73-Switchboard: (33) (0)4 91 82 82 82
>>> Fax: (33) (0)4 91 82 82 89
>>>
>>> ______________________________________________
>>> 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.
>>>
>>>
>> --
>> O__ ---- Peter Dalgaard Øster Farimagsgade 5, Entr.B
>> c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
>> (*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
>> ~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
>>
>>
>>
>>
--
O__ ---- Peter Dalgaard Øster Farimagsgade 5, Entr.B
c/ /'_ --- Dept. of Biostatistics PO Box 2099, 1014 Cph. K
(*) \(*) -- University of Copenhagen Denmark Ph: (+45) 35327918
~~~~~~~~~~ - (p.dalgaard at biostat.ku.dk) FAX: (+45) 35327907
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