Peter Dalgaard wrote:
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)
Thanks Peter. We will make this change in Hmisc for the next release.
Thomas - please take note. Thanks.
Frank
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$label) : invalid labels; length
15 should be 1 or 14
Thanks again, JL
On Thu, 09 Oct 2008 17:33:06 +0200, "Peter Dalgaard"
<[EMAIL PROTECTED]> said:
Jean-Louis Abitbol wrote:
Dear All,
I get the following error when using either SASxport or Hmisc to
read an
.xpt file:
w <- read.xport("D:/consult/Trophos/dnp/base/TRO_ds_20081006.xpt")
Erreur dans factor(x, f$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: [EMAIL PROTECTED] ---- Backup Email: [EMAIL PROTECTED]
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
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--
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
~~~~~~~~~~ - ([EMAIL PROTECTED]) FAX: (+45) 35327907
--
Frank E Harrell Jr Professor and Chair School of Medicine
Department of Biostatistics Vanderbilt University
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