Re: [R] Reading sas7bdat files directly

[Ted]

Just wondering if the proposed loop for the metadata on this conversion was
implemented by any chance...before I go trying the Long routine...
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Re: [R] Reading sas7bdat files directly

[Chris Long]

The dsread output is little-endian, as that's the native format for 
floats on the Wintel platform.  The byte order should stay the same if 
converting directly to a float, using a data structure like (C/C++):

union {
 char bytes[8];
 double value;
}

If reading the values with a SAS HEX informat, the bytes will need to be 
reversed.  It's obviously trivial for me to add an endian-ness option, 
I'll do that later

Chris.

On 02/03/2010 02:06, Roger DeAngelis(xlr82sas) wrote:
> Hi,
>
>It looks like we may need to swap bytes(little endian to big endian). I
> will look into it tonight.
>
>As a side note, SAS reserves 28 floats for missing values. It should be
> easy to convert these to NaN on input to R.
>
> You can test this in SAS by converting the 16 char floats to ieee8. in SAS
> and doing a put. The result will be A, B...Z, . and _.
>
> SAS code that produced the listing is below.
>
> Here are the floats that map to the 28 missing values in SAS
>
> A  FD00
> B  FC00
> C  FB00
> D  FA00
> E  F900
> F  F800
> G  F700
> H  F600
> I  F500
> J  F400
> K  F300
> L  F200
> M  F100
> N  F000
> O  EF00
> P  EE00
> Q  ED00
> R  EC00
> S  EB00
> T  EA00
> U  E900
> V  E800
> W  E700
> X  E600
> Y  E500
> Z  E400
> _  FF00
> .  FE00
>
> data mis;
> retain A .A B .B C .C D .D E .E F .F G .G H .H I .I J .J K .K L .L M .M
> N .N O .O P .P Q .Q R .R S .S T .T U .U V .V W .W X .X Y .Y Z .Z
>_ ._ DOT .;
> array mis[28] A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ DOT;
>do idx=1 to 28;
>   hex=put(mis[idx],ieee8.);
>   xeh=put(hex,hex16.);
>   put @1 mis[idx] @6 xeh;
>end;
>
>
>

[[alternative HTML version deleted]]

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Re: [R] Reading sas7bdat files directly

[Roger DeAngelis(xlr82sas)]

Hi,

  It looks like we may need to swap bytes(little endian to big endian). I
will look into it tonight.

  As a side note, SAS reserves 28 floats for missing values. It should be
easy to convert these to NaN on input to R.

You can test this in SAS by converting the 16 char floats to ieee8. in SAS
and doing a put. The result will be A, B...Z, . and _.

SAS code that produced the listing is below.

Here are the floats that map to the 28 missing values in SAS

A  FD00 
B  FC00 
C  FB00 
D  FA00 
E  F900 
F  F800 
G  F700 
H  F600 
I  F500 
J  F400 
K  F300 
L  F200 
M  F100 
N  F000 
O  EF00 
P  EE00 
Q  ED00 
R  EC00 
S  EB00 
T  EA00 
U  E900 
V  E800 
W  E700 
X  E600 
Y  E500 
Z  E400 
_  FF00 
.  FE00 

data mis;   
retain A .A B .B C .C D .D E .E F .F G .G H .H I .I J .J K .K L .L M .M 
   N .N O .O P .P Q .Q R .R S .S T .T U .U V .V W .W X .X Y .Y Z .Z 
  _ ._ DOT .;   
array mis[28] A B C D E F G H I J K L M N O P Q R S T U V W X Y Z _ DOT;
  do idx=1 to 28;   
 hex=put(mis[idx],ieee8.);  
 xeh=put(hex,hex16.);   
 put @1 mis[idx] @6 xeh;
  end;  


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Re: [R] Reading sas7bdat files directly

[Nordlund, Dan (DSHS/RDA)]

> -Original Message-
> From: r-help-boun...@r-project.org [mailto:r-help-boun...@r-project.org] On
> Behalf Of Roger DeAngelis(xlr82sas)
> Sent: Monday, March 01, 2010 4:38 PM
> To: r-help@r-project.org
> Subject: Re: [R] Reading sas7bdat files directly
> 
> 
> Hi All,
> 
>  The hack below might help R users get going with Chris's DSREAD. I have not
> had a chance to look at  Monday's version of DSREAD, can't wait.
> 
> Note Duncan Murdoch was most gracious to supply me with a R function to
> translate floats in 16 char hex to R floats.
> 
> Your utility solves the 200 byte, 8 char name and potential precision
> errors with other methods of transfering SAS datasets to perl and R.
> Thanks.
> 
> Importing SAS datasets(sas7bdat) into R
> (32 bit windows 2000, 32 bit SAS 9.2 and
> 32 bit R version 2.9.0 (2009-04-17)
> 
>  Here is what I want to accomplish, the double floats below show data
> from SAS to R.
>  They are exactly the same in R and SAS memory, bit for bit.
> 
> 
>   R Internal SAS Internal
>   16 Byte Float  16 byte Float
> 
> 
> 3FFB  3FFB
> 4002AAAB  4002AAAB
> 400D  400D
> 3FF6  3FF6
> 3FFD  3FFD
> 4001999A  4001999A
> 4004CCCD  4004CCCD
> 3FF4924924924925  3FF4924924924925
> 3FF9249249249249  3FF9249249249249
> 3FFDB6DB6DB6DB6E  3FFDB6DB6DB6DB6E
> 4001249249249249  4001249249249249
> 3FF2E8BA2E8BA2E9  3FF2E8BA2E8BA2E9
> 3FF5D1745D1745D1  3FF5D1745D1745D1
> 3FF8BA2E8BA2E8BA  3FF8BA2E8BA2E8BA
> 3FFBA2E8BA2E8BA3  3FFBA2E8BA2E8BA3
> 3FF2762762762762  3FF2762762762762
> 3FF4EC4EC4EC4EC5  3FF4EC4EC4EC4EC5
> 3FF7627627627627  3FF7627627627627
> 3FF9D89D89D89D8A  3FF9D89D89D89D8A
> 1.7976931348623E  1.7976931348623E
> 0010  0010
> 
> 
> I don't believe this high accuracy transfer is possible  with any
> other method except ODBC,
> but SAS ODBC is unsatisfactory for me. If you use CSV with the maximum
> assured decimal
> precision(15 significant digits?). The CSV decimal numbers will only
> approximate the double floats.
> 
> I consider the Csv to be corrupt if the relative of absolute
> difference using the decimal
> Csv numbers and the memory floats is greater than 10^-12.  There are
> two sources of error first
> the SAS floats are decimally rounded and converted to decimal then the
> rounded decimal
> approximations are  converted into R floats.
> 
> 
> Status of R InternalCSV
> Csv   16 Byte Float
> 
> 
> Csv corrupt 3FFB   1.67>10^-12 different
> Csv corrupt 4002AAAB   2.33
> Csv corrupt 400D   3.67
> Csv OK  3FF6   1.4
> Csv OK  3FFD   1.8
> Csv OK  4001999A   2.2
> Csv OK  4004CCCD   2.6
> Csv corrupt 3FF4924924924925   1.28571428571429
> Csv corrupt 3FF9249249249249   1.57142857142857
> Csv corrupt 3FFDB6DB6DB6DB6E   1.85714285714286
> Csv corrupt 4001249249249249   2.14285714285714
> Csv corrupt 3FF2E8BA2E8BA2E9   1.18181818181818
> Csv corrupt 3FF5D1745D1745D1   1.36363636363636
> Csv corrupt 3FF8BA2E8BA2E8BA   1.54545454545455
> Csv corrupt 3FFBA2E8BA2E8BA3   1.72727272727273
> Csv corrupt 3FF2762762762762   1.15384615384615
> Csv corrupt 3FF4EC4EC4EC4EC5   1.30769230769231
> Csv corrupt 3FF7627627627627   1.46153846153846
> Csv corrupt 3FF9D89D89D89D8A   1.61538461538462
> Csv corrupt 1.7976931348623E   1.7976931348623E+308
> Csv corrupt 0010   2.2250738585072E-308
> 
> 
> Bacground
> 
> 
>   1. Provide absolutely loss less transfer
>  of character(max 32756 bytes per character variable)  and numeric
> data from SAS to R
>  Since SAS has only two datatypes so this code should be
> exhaustive.
> 
> 
>   2. This code is useful because:
>  a. The SAS ODBC driver requires the user to not only have
> SAS but the user must bring up a SAS session and
> the session has to be closed manually. (SAS issue not a
> foreign issue)
>  b. The foreign package also requires interaction with SAS. (SAS
> issue)
>  c. SASxport only supports 8 character SAS names and a max of
> 200 byte character values. (This is a SAS issue not a SASxport
> issue)
>  d. SASxport creates floating point doubles that have an 8 bit
> exponent
> and 56 bit mantissa while IEEE is 11 bit exponent and 53 bit
> mantissa
> (sometimes defined slightly differently depending of where you
> consider
> the sign bits). This results

Re: [R] Reading sas7bdat files directly

[Roger DeAngelis(xlr82sas)]

Hi All,

 The hack below might help R users get going with Chris's DSREAD. I have not
had a chance to look at  Monday's version of DSREAD, can't wait.

Note Duncan Murdoch was most gracious to supply me with a R function to
translate floats in 16 char hex to R floats.

Your utility solves the 200 byte, 8 char name and potential precision 
errors with other methods of transfering SAS datasets to perl and R. 
Thanks. 

Importing SAS datasets(sas7bdat) into R 
(32 bit windows 2000, 32 bit SAS 9.2 and 
32 bit R version 2.9.0 (2009-04-17) 

 Here is what I want to accomplish, the double floats below show data 
from SAS to R. 
 They are exactly the same in R and SAS memory, bit for bit. 


  R Internal SAS Internal 
  16 Byte Float  16 byte Float 


3FFB  3FFB 
4002AAAB  4002AAAB 
400D  400D 
3FF6  3FF6 
3FFD  3FFD 
4001999A  4001999A 
4004CCCD  4004CCCD 
3FF4924924924925  3FF4924924924925 
3FF9249249249249  3FF9249249249249 
3FFDB6DB6DB6DB6E  3FFDB6DB6DB6DB6E 
4001249249249249  4001249249249249 
3FF2E8BA2E8BA2E9  3FF2E8BA2E8BA2E9 
3FF5D1745D1745D1  3FF5D1745D1745D1 
3FF8BA2E8BA2E8BA  3FF8BA2E8BA2E8BA 
3FFBA2E8BA2E8BA3  3FFBA2E8BA2E8BA3 
3FF2762762762762  3FF2762762762762 
3FF4EC4EC4EC4EC5  3FF4EC4EC4EC4EC5 
3FF7627627627627  3FF7627627627627 
3FF9D89D89D89D8A  3FF9D89D89D89D8A 
1.7976931348623E  1.7976931348623E 
0010  0010 


I don't believe this high accuracy transfer is possible  with any 
other method except ODBC, 
but SAS ODBC is unsatisfactory for me. If you use CSV with the maximum 
assured decimal 
precision(15 significant digits?). The CSV decimal numbers will only 
approximate the double floats. 

I consider the Csv to be corrupt if the relative of absolute 
difference using the decimal 
Csv numbers and the memory floats is greater than 10^-12.  There are 
two sources of error first 
the SAS floats are decimally rounded and converted to decimal then the 
rounded decimal 
approximations are  converted into R floats. 


Status of R InternalCSV 
Csv   16 Byte Float 


Csv corrupt 3FFB   1.67>10^-12 different 
Csv corrupt 4002AAAB   2.33 
Csv corrupt 400D   3.67 
Csv OK  3FF6   1.4 
Csv OK  3FFD   1.8 
Csv OK  4001999A   2.2 
Csv OK  4004CCCD   2.6 
Csv corrupt 3FF4924924924925   1.28571428571429 
Csv corrupt 3FF9249249249249   1.57142857142857 
Csv corrupt 3FFDB6DB6DB6DB6E   1.85714285714286 
Csv corrupt 4001249249249249   2.14285714285714 
Csv corrupt 3FF2E8BA2E8BA2E9   1.18181818181818 
Csv corrupt 3FF5D1745D1745D1   1.36363636363636 
Csv corrupt 3FF8BA2E8BA2E8BA   1.54545454545455 
Csv corrupt 3FFBA2E8BA2E8BA3   1.72727272727273 
Csv corrupt 3FF2762762762762   1.15384615384615 
Csv corrupt 3FF4EC4EC4EC4EC5   1.30769230769231 
Csv corrupt 3FF7627627627627   1.46153846153846 
Csv corrupt 3FF9D89D89D89D8A   1.61538461538462 
Csv corrupt 1.7976931348623E   1.7976931348623E+308 
Csv corrupt 0010   2.2250738585072E-308 


Bacground 


  1. Provide absolutely loss less transfer 
 of character(max 32756 bytes per character variable)  and numeric 
data from SAS to R 
 Since SAS has only two datatypes so this code should be 
exhaustive. 


  2. This code is useful because: 
 a. The SAS ODBC driver requires the user to not only have 
SAS but the user must bring up a SAS session and 
the session has to be closed manually. (SAS issue not a 
foreign issue) 
 b. The foreign package also requires interaction with SAS. (SAS 
issue) 
 c. SASxport only supports 8 character SAS names and a max of 
200 byte character values. (This is a SAS issue not a SASxport 
issue) 
 d. SASxport creates floating point doubles that have an 8 bit 
exponent 
and 56 bit mantissa while IEEE is 11 bit exponent and 53 bit 
mantissa 
(sometimes defined slightly differently depending of where you 
consider 
the sign bits). This results is the loss of some very small 
and 
very large numbers. ( SAS issue not a SASxport issue) 


  3. How this code overcomes the issues above for import only. 


 You need the dsread exec in the previous mesage. Also the input 
SAS dataset must have 
16 byte character representations for the floats. I am working with 
the developer to see what we 
can do about this.. 
He will make it an option on the invocation to do the hex conversion 
for numerics. 


Here is the R code run inside a SAS datastep. Actually I can interact 
with the output of the R code 
in the same dataqstep. It is also possible to run perl, SAS procs and 
other SAS languages in the same datastep. 
Note the input pipe, no physical CSV file is produced). 


If there is interest I can provide the code that executes R. 


data _nu

Re: [R] Reading sas7bdat files directly

[Chris Long]

dsread (http://www.oview.co.uk/dsread) was updated yesterday, to include
various new features as suggested here and elsewhere.  Of particular
interest might be:

- you can now use the /c and /v options together to get dataset contents in
CSV format for easier importing;

- there is now a /l option for lossless representation of numerics in the
output.  Numerics will appear as (eg) '0xf03f' giving the exact
hex value of each of the eight bytes making up the IEEE float value.

Please continue to report bugs or feature requests here or on the above web
page.

Thanks,

Chris.
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Re: [R] Reading sas7bdat files directly

[Frank E Harrell Jr]

Chris Long wrote:

No problem, Frank, I'm glad that you think it will be useful.

I will be making changes to dsread in the coming weeks so you may want to
hold off with your helper function in case my changes break it (the
formatting of the variable metadata listing may well change).  Re: the
metadata, feel free to suggest an alternate output format that would make
this a cleaner process.  For example, I have in mind to allow the -c
(contents) and -v (CSV) flags together, in which case the dataset metadata
will be output in CSV format.

Any other suggestions or comments are welcomed.

Chris.


Thanks very much for your note Chris.  Having an option to output the 
metadata in a standard csv format as well as the nice table format you 
provide already (either one or the other) will be good.  If you allow 
flags (one could be -o) to specify the names of 2 different output files 
when STDOUT is not being used, that will expedite things.


As sas7bdat files are unbelievably inefficient storage-wise (I'm looking 
at an example where the file is 525K and the bzip2'd version is 29K) it 
will be great if you can handled compressed sas7bdat files too.


Thanks for the excellent work,
Frank


--
Frank E Harrell Jr   Professor and ChairmanSchool of Medicine
 Department of Biostatistics   Vanderbilt University

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Re: [R] Reading sas7bdat files directly

[Chris Long]

No problem, Frank, I'm glad that you think it will be useful.

I will be making changes to dsread in the coming weeks so you may want to
hold off with your helper function in case my changes break it (the
formatting of the variable metadata listing may well change).  Re: the
metadata, feel free to suggest an alternate output format that would make
this a cleaner process.  For example, I have in mind to allow the -c
(contents) and -v (CSV) flags together, in which case the dataset metadata
will be output in CSV format.

Any other suggestions or comments are welcomed.

Chris.
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Re: [R] Reading sas7bdat files directly

[Frank E Harrell Jr]

Chris Long wrote:

I suppose a link would have added usefulness:

http://www.oview.co.uk/dsread

Chris.


As dsread seems to work perfectly under wine on Ubuntu linux (and quite 
quickly), it could be quite valuable to many of us.  Thanks for posting 
this and for developing dsread!  If time allows I'll write a function to 
add to the Hmisc package that runs dsread to output the SAS dataset 
metadata, then runs dsread again to read the data, adding back metadata 
such as variable labels.

Frank

--
Frank E Harrell Jr   Professor and ChairmanSchool of Medicine
 Department of Biostatistics   Vanderbilt University

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Re: [R] Reading sas7bdat files directly

[Chris Long]

I suppose a link would have added usefulness:

http://www.oview.co.uk/dsread

Chris.
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Re: [R] Reading sas7bdat files directly

[Chris Long]

Hi Alex,

'm not an R user but I found your question during a general Google search
re: SAS7BDAT files.  You might like to try my free 'dsread' utility which
will convert most Windows-format SAS7BDAT files to CSV.  It's command-line
based so can easily be called from other code with relevant parameters.

I'd be keen to hear any feedback on this utility from you and other R users
(I'm a SAS guy myself).

Cheers,

Chris.
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Re: [R] Reading sas7bdat files directly

[Annoyia Mouse]

If you don't have SAS and still need to read or write sas7bdat files: there
is the "World Programming System" (WPS) (commercial software). 
http://www.teamwpc.co.uk/home/
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Re: [R] Reading sas7bdat files directly

[Frank E Harrell Jr]

David Winsemius wrote:


On Feb 4, 2010, at 5:31 PM, Alex Bryant wrote:

Hi,   I have a need to process (in real-time) a large number of 
.sas7bdat files from within R.  The problem is I don't want to convert 
these files to .xpt (transport) every time.  So just checking if 
anyone has a (viable) way to read .sas7bdat files directly into R?


I believe (on the basis of what is written on the NCHS/NHANESwebsite) 
that if you are a Windows user, which I am only under duress, you can 
get at such data with a free product that SAS makes available:


http://www.sas.com/apps/demosdownloads/sassysview_PROD_8.2_sysdep.jsp?packageID=000176 



Whether that product can be called as a system()  executable with 
arguments, I have no idea.




The SAS viewer has a pretty pathetic data export feature that won't even 
 produce valid csv files if you have any unmatched quotes in character 
variables.  I don't think it's very good about exporting metadata either.


Frank

--
Frank E Harrell Jr   Professor and ChairmanSchool of Medicine
 Department of Biostatistics   Vanderbilt University

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Re: [R] Reading sas7bdat files directly

[David Winsemius]

On Feb 4, 2010, at 5:31 PM, Alex Bryant wrote:

Hi,   I have a need to process (in real-time) a large number  
of .sas7bdat files from within R.  The problem is I don't want to  
convert these files to .xpt (transport) every time.  So just  
checking if anyone has a (viable) way to read .sas7bdat files  
directly into R?


I believe (on the basis of what is written on the NCHS/NHANESwebsite)  
that if you are a Windows user, which I am only under duress, you can  
get at such data with a free product that SAS makes available:


http://www.sas.com/apps/demosdownloads/sassysview_PROD_8.2_sysdep.jsp?packageID=000176

Whether that product can be called as a system()  executable with  
arguments, I have no idea.


--
David Winsemius, MD
Heritage Laboratories
West Hartford, CT

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Re: [R] Reading sas7bdat files directly

[Duncan Murdoch]

Alex Bryant wrote:

Hi,   I have a need to process (in real-time) a large number of .sas7bdat files 
from within R.  The problem is I don't want to convert these files to .xpt 
(transport) every time.  So just checking if anyone has a (viable) way to read 
.sas7bdat files directly into R?


SAS now advertises some sort of R support (see 
http://support.sas.com/rnd/app/studio/Rinterface2.html), so maybe you 
could get SAS to convert them to a native R format. I think you won't 
find a way for R to read a SAS proprietary format.


Duncan Murdoch

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Re: [R] Reading sas7bdat files directly

[Jorge Ivan Velez]

Hi Alex,

Perhaps the read.ssd function in the foreign package might do what you want.
See [1] for details.

HTH,
Jorge

[1]  http://cran.r-project.org/web/packages/foreign/index.html


On Thu, Feb 4, 2010 at 5:31 PM, Alex Bryant <> wrote:

> Hi,   I have a need to process (in real-time) a large number of .sas7bdat
> files from within R.  The problem is I don't want to convert these files to
> .xpt (transport) every time.  So just checking if anyone has a (viable) way
> to read .sas7bdat files directly into R?
>
> Thank You.
>
> //--
> // Alex Bryant
> // Software Developer
> // Integrated Clinical systems
> // 908-996-7208
>
>
> 
> Confidentiality Note: This e-mail, and any attachment to...{{dropped:13}}
>
> __
> R-help@r-project.org mailing list
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> http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

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__
R-help@r-project.org mailing list
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[R] Reading sas7bdat files directly

[Alex Bryant]

Hi,   I have a need to process (in real-time) a large number of .sas7bdat files 
from within R.  The problem is I don't want to convert these files to .xpt 
(transport) every time.  So just checking if anyone has a (viable) way to read 
.sas7bdat files directly into R?

Thank You.

//--
// Alex Bryant
// Software Developer
// Integrated Clinical systems
// 908-996-7208



Confidentiality Note: This e-mail, and any attachment to...{{dropped:13}}

__
R-help@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.