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==========================================================
Hello Everyone,
I'm learning R and am trying to get a better sense of what it will and
will not
do. I'm hearing in some places that R may not be able to accomplish all
of the
data manipulation tasks that SAS can. In others, I'm hearing that R can do
pretty much any data manipulation that SAS can but the way in which it
does so
is likely to be quite different.
Below is some SAS syntax that that codes Highly Active Antiretroviral
Therapy
(HAART) regimens in HIV patients by retaining the values of variables.
Interspersed between the bits of code are printouts of data sets that are
created in the process of coding. I'm hoping this will come through
clearly and
that people will be able to see exactly what is being done. Basically,
the code
keeps track of how many drugs people are on and what types of drugs they
are
taking during specific periods of time and decides whether that
constitutes
HAART or not.
To me, this is a pretty tricky data manipulation in SAS. Is there any way
to
get the equivalent result in R?
Thanks,
Paul
**** SAS syntax for coding HAART in HIV patients;
**** Read in test data;
data haart;
input id drug_class $ start_date :mmddyy. stop_date :mmddyy.;
format start_date stop_date mmddyy8.;
cards;
1004 NRTI 07/24/95 01/05/99
1004 NRTI 11/20/95 12/10/95
1004 NRTI 01/10/96 01/05/99
1004 PI 05/09/96 11/16/97
1004 NRTI 06/01/96 02/01/97
1004 NRTI 07/01/96 03/01/97
9999 PI 01/02/03 .
9999 NNRTI 04/05/06 07/08/09
;
run;
proc print data=haart;
run;
drug_ start_ stop_
Obs id class date date
1 1004 NRTI 07/24/95 01/05/99
2 1004 NRTI 11/20/95 12/10/95
3 1004 NRTI 01/10/96 01/05/99
4 1004 PI 05/09/96 11/16/97
5 1004 NRTI 06/01/96 02/01/97
6 1004 NRTI 07/01/96 03/01/97
7 9999 PI 01/02/03 .
8 9999 NNRTI 04/05/06 07/08/09
**** Reshape data into series with 1 date rather than separate starts and
stops;
data changes (drop=start_date stop_date where=(not missing(date)));
set haart;
date = start_date;
change = 1;
output;
date = stop_date;
change = -1;
output;
format date mmddyy10.;
run;
proc sort data=changes;
by id date;
run;
proc print data=changes;
run;
drug_
Obs id class date change
1 1004 NRTI 07/24/1995 1
2 1004 NRTI 11/20/1995 1
3 1004 NRTI 12/10/1995 -1
4 1004 NRTI 01/10/1996 1
5 1004 PI 05/09/1996 1
6 1004 NRTI 06/01/1996 1
7 1004 NRTI 07/01/1996 1
8 1004 NRTI 02/01/1997 -1
9 1004 NRTI 03/01/1997 -1
10 1004 PI 11/16/1997 -1
11 1004 NRTI 01/05/1999 -1
12 1004 NRTI 01/05/1999 -1
13 9999 PI 01/02/2003 1
14 9999 NNRTI 04/05/2006 1
15 9999 NNRTI 07/08/2009 -1
**** Get regimen information plus start and stop dates;
data cumulative(drop=drug_class change stop_date)
stop_dates(keep=id regimen stop_date);
set changes;
by id date;
if first.id then do;
regimen = 0;
NRTI = 0;
NNRTI = 0;
PI = 0;
end;
if drug_class = 'NNRTI' then NNRTI + change;
else if drug_class = 'NRTI' then NRTI + change;
else if drug_class = 'PI ' then PI + change;
if last.date then do;
stop_date = date - 1;
if regimen then output stop_dates;
regimen + 1;
alldrugs = NNRTI + NRTI + PI;
HAART = (NRTI >= 3 AND NNRTI=0 AND PI=0) OR
(NRTI >= 2 AND (NNRTI >= 1 OR PI >= 1)) OR
(NRTI = 1 AND NNRTI >= 1 AND PI >= 1);
output cumulative;
end;
format stop_date mmddyy10.;
run;
proc print data=cumulative;
run;
Obs id date regimen NRTI NNRTI PI alldrugs
HAART
1 1004 07/24/1995 1 1 0 0 1
0
2 1004 11/20/1995 2 2 0 0 2
0
3 1004 12/10/1995 3 1 0 0 1
0
4 1004 01/10/1996 4 2 0 0 2
0
5 1004 05/09/1996 5 2 0 1 3
1
6 1004 06/01/1996 6 3 0 1 4
1
7 1004 07/01/1996 7 4 0 1 5
1
8 1004 02/01/1997 8 3 0 1 4
1
9 1004 03/01/1997 9 2 0 1 3
1
10 1004 11/16/1997 10 2 0 0 2
0
11 1004 01/05/1999 11 0 0 0 0
0
12 9999 01/02/2003 1 0 0 1 1
0
13 9999 04/05/2006 2 0 1 1 2
0
14 9999 07/08/2009 3 0 0 1 1
0
proc print data=stop_dates;
run;
Obs id regimen stop_date
1 1004 1 11/19/1995
2 1004 2 12/09/1995
3 1004 3 01/09/1996
4 1004 4 05/08/1996
5 1004 5 05/31/1996
6 1004 6 06/30/1996
7 1004 7 01/31/1997
8 1004 8 02/28/1997
9 1004 9 11/15/1997
10 1004 10 01/04/1999
11 9999 1 04/04/2006
12 9999 2 07/07/2009
**** Merge data to create regimens dataset;
data regimens;
retain id start_date stop_date;
merge cumulative(rename=(date=start_date)) stop_dates;
by id regimen;
if alldrugs;
run;
proc print data=regimens;
run;
Obs id start_date stop_date regimen NRTI NNRTI PI
alldrugs HAART
1 1004 07/24/1995 11/19/1995 1 1 0 0
1 0
2 1004 11/20/1995 12/09/1995 2 2 0 0
2 0
3 1004 12/10/1995 01/09/1996 3 1 0 0
1 0
4 1004 01/10/1996 05/08/1996 4 2 0 0
2 0
5 1004 05/09/1996 05/31/1996 5 2 0 1
3 1
6 1004 06/01/1996 06/30/1996 6 3 0 1
4 1
7 1004 07/01/1996 01/31/1997 7 4 0 1
5 1
8 1004 02/01/1997 02/28/1997 8 3 0 1
4 1
9 1004 03/01/1997 11/15/1997 9 2 0 1
3 1
10 1004 11/16/1997 01/04/1999 10 2 0 0
2 0
11 9999 01/02/2003 04/04/2006 1 0 0 1
1 0
12 9999 04/05/2006 07/07/2009 2 0 1 1
2 0
13 9999 07/08/2009 . 3 0 0 1
1 0
==========================================================
Paul Miller
Paul Miller <[email protected]>
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E-Mail: (Ted Harding) <[email protected]>
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Date: 20-Apr-11 Time: 19:59:21
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