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jude.ryan at ubs.com

2008-Dec-03 21:40 UTC

[R] reading version 9 SAS datasets in R

Hi,

 

I am trying to read a SAS version 9.1.3 SAS dataset into R (to preserve
the SAS labels), but am unable to do so (I have read in a CSV version).
I first created a transport file using the SAS code:

 

libname ces2 'D:\CES Analysis\Data';

filename transp 'D:\CES Analysis\Data\fadata.xpt';

 

/* create a transport file - R cannot read file created by proc cport */

proc cport data=ces2.fadata file=transp;

run;

 

I then tried to read it in R using:

 
> library(foreign)
> library(Hmisc)
> fadata2 <- sasxport.get("D:\\CES Analysis\\Data\\fadata.xpt")
Error in lookup.xport(file) : file not in SAS transfer format

 

Next I tried using the libname statement and the xport engine to create
a transport file. The problem with this method is that variable names
cannot be more than 8 characters as this method creates a SAS version 6
transport file. 

 

libname to_r xport 'D:\CES Analysis\Data\fadata2.xpt';

 

data to_r.fadata2;

  set ces2.fadata;

run;

 

But I get an error message in the SAS log:

 

493  libname to_r xport 'D:\CES Analysis\Data\fadata2.xpt';

NOTE: Libref TO_R was successfully assigned as follows:

      Engine:        XPORT

      Physical Name: D:\CES Analysis\Data\fadata2.xpt

494

495  data to_r.fadata2;

496    set ces2.fadata;

497  run;

 

ERROR: The variable name BUS_TEL_N is illegal for the version 6 file
TO_R.FADATA2.DATA.

NOTE: The SAS System stopped processing this step because of errors.

WARNING: The data set TO_R.FADATA2 was only partially opened and will
not be saved.

 

Next I tried other ways of reading a SAS dataset in R, as shown below:

 

fadata2 <- sas.get("D:\\CES Analysis\\Data", mem=fadata)

Error in sas.get("D:\\CES Analysis\\Data", mem = fadata) : 

  Unix file, "D:\CES Analysis\Data/c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, .sd2 D:\CES Analysis\Data/c(NA, 64716,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 64716, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 

In addition: Warning message:

In sas.get("D:\\CES Analysis\\Data", mem = fadata) :

  D:\CES Analysis\Data/formats.sc? or formats.sas7bcat  not found.
Formatting ignored. 

 
> ls()
[1] "fadata"
> ?read.xport
> fadata2 <- read.xport("D:\\CES Analysis\\Data\\fadata.xpt")
Error in lookup.xport(file) : file not in SAS transfer format
> ?read.ssd
> fadata2 <- read.ssd("D:\\CES Analysis\\Data",
"fadata")
SAS failed.  SAS program at
D:\DOCUME~1\re06572\LOCALS~1\Temp\RtmpLqCVUx\file72ae2cd6.sas 

The log file will be file72ae2cd6.log in the current directory

Warning messages:

1: In system(paste(sascmd, tmpProg)) : "sas" not found

2: In read.ssd("D:\\CES Analysis\\Data", "fadata") :

  SAS return code was -1
> sashome <- "C:\\Program Files\\SAS\\SAS 9.1"
> fadata2 <- read.ssd(file.path(sashome, "core",
"sashelp"), "fadata",sascmd=file.path(sashome, "sas.exe"))

SAS failed.  SAS program at
D:\DOCUME~1\re06572\LOCALS~1\Temp\RtmpLqCVUx\file6df11649.sas 

The log file will be file6df11649.log in the current directory

Warning message:

In read.ssd(file.path(sashome, "core", "sashelp"),
"fadata", sascmd file.path(sashome,  :

  SAS return code was 2
> 
 

Is there any way I can read in a SAS version 9 dataset in R, so that I
can preserve the SAS labels?

If I have to change the SAS variable names to be 8 characters or less,
to create a SAS version 6 transport file, I could probably do without
the SAS labels as I have already read in the data into R from a CSV
file.

 

Thanks in advance for any help.

 

Jude

 

___________________________________________
Jude Ryan
Director, Client Analytic Services
Strategy & Business Development
UBS Financial Services Inc.
1200 Harbor Boulevard, 4th Floor
Weehawken, NJ 07086-6791
Tel. 201-352-1935
Fax 201-272-2914
Email: jude.ryan at ubs.com

 


























Please do not transmit orders or instructions regarding a UBS account by e-mail.
The information provided in this e-mail or any attachments is not an official
transaction confirmation or account statement. For your protection, do not
include account numbers, Social Security numbers, credit card numbers, passwords
or other non-public information in your e-mail. Because the information
contained in this message may be privileged, confidential, proprietary or
otherwise protected from disclosure, please notify us immediately by replying to
this message and deleting it from your computer if you have received this
communication in error. Thank you.



UBS Financial Services Inc.

UBS International Inc.

UBS Financial Services Incorporated of Puerto Rico

UBS AG

Nordlund, Dan (DSHS/RDA)

2008-Dec-03 22:11 UTC

head link

[R] reading version 9 SAS datasets in R

> -----Original Message-----
> From: r-help-bounces at r-project.org 
> [mailto:r-help-bounces at r-project.org] On Behalf Of jude.ryan at ubs.com
> Sent: Wednesday, December 03, 2008 1:40 PM
> To: r-help at r-project.org
> Cc: juderyan61 at yahoo.com
> Subject: [R] reading version 9 SAS datasets in R
> 
> Hi,
> 
>  
> 
> I am trying to read a SAS version 9.1.3 SAS dataset into R 
> (to preserve
> the SAS labels), but am unable to do so (I have read in a CSV 
> version).
> I first created a transport file using the SAS code:
> 
>  
> 
> libname ces2 'D:\CES Analysis\Data';
> 
> filename transp 'D:\CES Analysis\Data\fadata.xpt';
> 
>  
> 
> /* create a transport file - R cannot read file created by 
> proc cport */
> 
> proc cport data=ces2.fadata file=transp;
> 
> run;
> 
>  
> 
> I then tried to read it in R using:
> 
>  
> 
> > library(foreign)
> 
> > library(Hmisc)
> 
> > fadata2 <- sasxport.get("D:\\CES
Analysis\\Data\\fadata.xpt")
> 
> Error in lookup.xport(file) : file not in SAS transfer format
> 
>  
> 
> Next I tried using the libname statement and the xport engine 
> to create
> a transport file. The problem with this method is that variable names
> cannot be more than 8 characters as this method creates a SAS 
> version 6
> transport file. 
> 
>  
> 
> libname to_r xport 'D:\CES Analysis\Data\fadata2.xpt';
> 
>  
> 
> data to_r.fadata2;
> 
>   set ces2.fadata;
> 
> run;
> 
>  
> 
> But I get an error message in the SAS log:
> 
>  
> 
> 493  libname to_r xport 'D:\CES Analysis\Data\fadata2.xpt';
> 
> NOTE: Libref TO_R was successfully assigned as follows:
> 
>       Engine:        XPORT
> 
>       Physical Name: D:\CES Analysis\Data\fadata2.xpt
> 
> 494
> 
> 495  data to_r.fadata2;
> 
> 496    set ces2.fadata;
> 
> 497  run;
> 
>  
> 
> ERROR: The variable name BUS_TEL_N is illegal for the version 6 file
> TO_R.FADATA2.DATA.
> 
> NOTE: The SAS System stopped processing this step because of errors.
> 
> WARNING: The data set TO_R.FADATA2 was only partially opened and will
> not be saved.
> 
>  
> 
> Next I tried other ways of reading a SAS dataset in R, as shown below:
> 
>  
> 
> fadata2 <- sas.get("D:\\CES Analysis\\Data", mem=fadata)
> 
> Error in sas.get("D:\\CES Analysis\\Data", mem = fadata) : 
> 
>   Unix file, "D:\CES Analysis\Data/c(1, 1, 1, 1, 1, 1, 1, 1, 
> 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
> 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
> 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
> 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
> 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
> 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 
> 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, .sd2 D:\CES 
> Analysis\Data/c(NA, 64716,
> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
> NA, NA, NA,
> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
> NA, NA, NA,
> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 64716, NA,
> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
> NA, NA, NA,
> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
> NA, NA, NA,
> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
> 
> In addition: Warning message:
> 
> In sas.get("D:\\CES Analysis\\Data", mem = fadata) :
> 
>   D:\CES Analysis\Data/formats.sc? or formats.sas7bcat  not found.
> Formatting ignored. 
> 
>  
> 
> > ls()
> 
> [1] "fadata"
> 
> > ?read.xport
> 
> > fadata2 <- read.xport("D:\\CES
Analysis\\Data\\fadata.xpt")
> 
> Error in lookup.xport(file) : file not in SAS transfer format
> 
> > ?read.ssd
> 
> > fadata2 <- read.ssd("D:\\CES Analysis\\Data",
"fadata")
> 
> SAS failed.  SAS program at
> D:\DOCUME~1\re06572\LOCALS~1\Temp\RtmpLqCVUx\file72ae2cd6.sas 
> 
> The log file will be file72ae2cd6.log in the current directory
> 
> Warning messages:
> 
> 1: In system(paste(sascmd, tmpProg)) : "sas" not found
> 
> 2: In read.ssd("D:\\CES Analysis\\Data", "fadata") :
> 
>   SAS return code was -1
> 
> > sashome <- "C:\\Program Files\\SAS\\SAS 9.1"
> 
> > fadata2 <- read.ssd(file.path(sashome, "core",
"sashelp"), "fadata",
> sascmd=file.path(sashome, "sas.exe"))
> 
> SAS failed.  SAS program at
> D:\DOCUME~1\re06572\LOCALS~1\Temp\RtmpLqCVUx\file6df11649.sas 
> 
> The log file will be file6df11649.log in the current directory
> 
> Warning message:
> 
> In read.ssd(file.path(sashome, "core", "sashelp"),
"fadata", sascmd > file.path(sashome,  :
> 
>   SAS return code was 2
> 
> > 
> 
>  
> 
> Is there any way I can read in a SAS version 9 dataset in R, so that I
> can preserve the SAS labels?
> 
> If I have to change the SAS variable names to be 8 characters or less,
> to create a SAS version 6 transport file, I could probably do without
> the SAS labels as I have already read in the data into R from a CSV
> file.
> 
>  
> 
> Thanks in advance for any help.
> 
>  
> 
> Jude
> 
>  
> 
> ___________________________________________
> Jude Ryan
> Director, Client Analytic Services
> Strategy & Business Development
> UBS Financial Services Inc.
> 1200 Harbor Boulevard, 4th Floor
> Weehawken, NJ 07086-6791
> Tel. 201-352-1935
> Fax 201-272-2914
> Email: jude.ryan at ubs.com
> 
>  
> 
> 
Jude,

Since it appears that you have access to SAS, I would look at using the
sas.get() function in the Hmisc package.  While the function appears to still be
broken in the Windows version, there is an easy fix that has been posted to
R-help in the past.  If you want to try this, you can search the R-help archives
for posts on sas.get or you can email me off-list and I will send you the fix
with instructions.  This will avoid any v6 limitations.

Hope this is helpful,

Dan

Daniel J. Nordlund
Washington State Department of Social and Health Services
Planning, Performance, and Accountability
Research and Data Analysis Division
Olympia, WA  98504-5204

Frank E Harrell Jr

2008-Dec-03 22:51 UTC

head link

[R] reading version 9 SAS datasets in R

jude.ryan at ubs.com wrote:> Hi,
> 
>  
> 
> I am trying to read a SAS version 9.1.3 SAS dataset into R (to preserve
> the SAS labels), but am unable to do so (I have read in a CSV version).
> I first created a transport file using the SAS code:
> 
>  
> 
> libname ces2 'D:\CES Analysis\Data';
> 
> filename transp 'D:\CES Analysis\Data\fadata.xpt';
Try

FILENAME transp SASV5XPT 'D:\CES Analysis\Data\fadata.xpt';

Frank
> 
>  
> 
> /* create a transport file - R cannot read file created by proc cport */
> 
> proc cport data=ces2.fadata file=transp;
> 
> run;
> 
>  
> 
> I then tried to read it in R using:
> 
>  
> 
>> library(foreign)
> 
>> library(Hmisc)
> 
>> fadata2 <- sasxport.get("D:\\CES
Analysis\\Data\\fadata.xpt")
> 
> Error in lookup.xport(file) : file not in SAS transfer format
> 
>  
> 
> Next I tried using the libname statement and the xport engine to create
> a transport file. The problem with this method is that variable names
> cannot be more than 8 characters as this method creates a SAS version 6
> transport file. 
> 
>  
> 
> libname to_r xport 'D:\CES Analysis\Data\fadata2.xpt';
> 
>  
> 
> data to_r.fadata2;
> 
>   set ces2.fadata;
> 
> run;
> 
>  
> 
> But I get an error message in the SAS log:
> 
>  
> 
> 493  libname to_r xport 'D:\CES Analysis\Data\fadata2.xpt';
> 
> NOTE: Libref TO_R was successfully assigned as follows:
> 
>       Engine:        XPORT
> 
>       Physical Name: D:\CES Analysis\Data\fadata2.xpt
> 
> 494
> 
> 495  data to_r.fadata2;
> 
> 496    set ces2.fadata;
> 
> 497  run;
> 
>  
> 
> ERROR: The variable name BUS_TEL_N is illegal for the version 6 file
> TO_R.FADATA2.DATA.
> 
> NOTE: The SAS System stopped processing this step because of errors.
> 
> WARNING: The data set TO_R.FADATA2 was only partially opened and will
> not be saved.
> 
>  
> 
> Next I tried other ways of reading a SAS dataset in R, as shown below:
> 
>  
> 
> fadata2 <- sas.get("D:\\CES Analysis\\Data", mem=fadata)
> 
> Error in sas.get("D:\\CES Analysis\\Data", mem = fadata) : 
> 
>   Unix file, "D:\CES Analysis\Data/c(1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, .sd2 D:\CES Analysis\Data/c(NA, 64716,
> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 64716, NA,
> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,
> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, 
> 
> In addition: Warning message:
> 
> In sas.get("D:\\CES Analysis\\Data", mem = fadata) :
> 
>   D:\CES Analysis\Data/formats.sc? or formats.sas7bcat  not found.
> Formatting ignored. 
> 
>  
> 
>> ls()
> 
> [1] "fadata"
> 
>> ?read.xport
> 
>> fadata2 <- read.xport("D:\\CES
Analysis\\Data\\fadata.xpt")
> 
> Error in lookup.xport(file) : file not in SAS transfer format
> 
>> ?read.ssd
> 
>> fadata2 <- read.ssd("D:\\CES Analysis\\Data",
"fadata")
> 
> SAS failed.  SAS program at
> D:\DOCUME~1\re06572\LOCALS~1\Temp\RtmpLqCVUx\file72ae2cd6.sas 
> 
> The log file will be file72ae2cd6.log in the current directory
> 
> Warning messages:
> 
> 1: In system(paste(sascmd, tmpProg)) : "sas" not found
> 
> 2: In read.ssd("D:\\CES Analysis\\Data", "fadata") :
> 
>   SAS return code was -1
> 
>> sashome <- "C:\\Program Files\\SAS\\SAS 9.1"
> 
>> fadata2 <- read.ssd(file.path(sashome, "core",
"sashelp"), "fadata",
> sascmd=file.path(sashome, "sas.exe"))
> 
> SAS failed.  SAS program at
> D:\DOCUME~1\re06572\LOCALS~1\Temp\RtmpLqCVUx\file6df11649.sas 
> 
> The log file will be file6df11649.log in the current directory
> 
> Warning message:
> 
> In read.ssd(file.path(sashome, "core", "sashelp"),
"fadata", sascmd > file.path(sashome,  :
> 
>   SAS return code was 2
> 
> 
>  
> 
> Is there any way I can read in a SAS version 9 dataset in R, so that I
> can preserve the SAS labels?
> 
> If I have to change the SAS variable names to be 8 characters or less,
> to create a SAS version 6 transport file, I could probably do without
> the SAS labels as I have already read in the data into R from a CSV
> file.
> 
>  
> 
> Thanks in advance for any help.
> 
>  
> 
> Jude
> 
>  
> 
> ___________________________________________
> Jude Ryan
> Director, Client Analytic Services
> Strategy & Business Development
> UBS Financial Services Inc.
> 1200 Harbor Boulevard, 4th Floor
> Weehawken, NJ 07086-6791
> Tel. 201-352-1935
> Fax 201-272-2914
> Email: jude.ryan at ubs.com
> 
>  
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> 
> Please do not transmit orders or instructions regarding a UBS account by
e-mail. The information provided in this e-mail or any attachments is not an
official transaction confirmation or account statement. For your protection, do
not include account numbers, Social Security numbers, credit card numbers,
passwords or other non-public information in your e-mail. Because the
information contained in this message may be privileged, confidential,
proprietary or otherwise protected from disclosure, please notify us immediately
by replying to this message and deleting it from your computer if you have
received this communication in error. Thank you.
> 
> 
> 
> UBS Financial Services Inc.
> 
> UBS International Inc.
> 
> UBS Financial Services Incorporated of Puerto Rico
> 
> UBS AG
> ______________________________________________
> 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

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