[R] reading version 9 SAS datasets in R
Frank E Harrell Jr
f.harrell at vanderbilt.edu
Wed Dec 3 23:51:06 CET 2008
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
>
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>
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> 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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