[R] Can R replicate this data manipulation in SAS?
Ista Zahn
izahn at psych.rochester.edu
Wed Apr 20 23:53:18 CEST 2011
Oops, I missed the HAART part. Fortunately that translates straightforwardly:
n.dat$HAART <- with(n.dat, ifelse((NRTI >= 3 & NNRTI==0 & PI==0) |
(NRTI >= 2 & (NNRTI >= 1 | PI >= 1)) |
(NRTI == 1 & NNRTI >= 1 & PI >= 1),
1, 0))
Best,
Ista
On Wed, Apr 20, 2011 at 5:22 PM, Ista Zahn <izahn at psych.rochester.edu> wrote:
> I think this is kind of like asking "will your Land Rover make it up
> my driveway?", but I'll assume the question was asked in all
> seriousness.
>
> Here is one solution:
>
> ## **** Read in test data;
> dat <- read.table(textConnection("id drug start stop
> 1004 NRTI 07/24/95 01/05/99
> 1004 NRTI 11/20/95 12/10/95
> 1004 NRTI 01/10/96 01/05/99
> 1004 PI 05/09/96 11/16/97
> 1004 NRTI 06/01/96 02/01/97
> 1004 NRTI 07/01/96 03/01/97
> 9999 PI 01/02/03 NA
> 9999 NNRTI 04/05/06 07/08/09"), header=TRUE)
> closeAllConnections()
>
> dat$start <- as.Date(dat$start, format = "%m/%d/%y")
> dat$stop <- as.Date(dat$stop, format = "%m/%d/%y")
>
> ## **** Reshape data into series with 1 date rather than separate starts and
> ## stops;
>
> library(reshape)
>
> m.dat <- melt(dat, id = c("id", "drug"))
> m.dat <- m.dat[order(m.dat$id, m.dat$value),]
> m.dat$variable <- ifelse(m.dat$variable == "start", 1, -1)
> names(m.dat) <- c("id", "drug", "value", "date")
> m.dat
>
> ## **** Get regimen information plus start and stop dates;
>
> n.dat <- cast(m.dat, id + date ~ drug, fun.aggregate=sum, margins="grand_col")
> for (i in names(n.dat)[-c(1:2)]) {
> n.dat[i] <- cumsum(n.dat[i])
> }
> n.dat <- ddply(n.dat, .(id), transform,
> regimen = 1:length(id))
> n.dat
>
> ssd.dat <- ddply(n.dat, .(id), summarize,
> id = id[-1],
> regimen = regimen[-length(regimen)],
> start_date = date[-length(date)],
> stop_date = date[-1])
> ssd.dat
>
> ## **** Merge data to create regimens dataset;
> all.dat <- merge(n.dat[-2], ssd.dat)
> all.dat <- all.dat[order(all.dat$id, all.dat$regimen), c("id",
> "start_date", "stop_date", "regimen", "NRTI", "NNRTI", "PI",
> "X.all.")]
> all.dat
>
>
> Best,
> Ista
>
>
>
> On Wed, Apr 20, 2011 at 2:59 PM, Ted Harding <ted.harding at wlandres.net> wrote:
>> [*** PLEASE NOTE: I am sending this message on behalf of
>> Paul Miller:
>> Paul Miller <pjmiller_57 at yahoo.com>
>> (to whom this message has also been copied). He has been
>> trying to send it, but it has never got through. Please
>> do not reply to me, but either to the list and/or to Paul
>> at that address ***]
>> ==========================================================
>> 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 <pjmiller_57 at yahoo.com>
>>
>>
>> --------------------------------------------------------------------
>> E-Mail: (Ted Harding) <ted.harding at wlandres.net>
>> Fax-to-email: +44 (0)870 094 0861
>> Date: 20-Apr-11 Time: 19:59:21
>> ------------------------------ XFMail ------------------------------
>>
>> ______________________________________________
>> 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.
>>
>
>
>
> --
> Ista Zahn
> Graduate student
> University of Rochester
> Department of Clinical and Social Psychology
> http://yourpsyche.org
>
--
Ista Zahn
Graduate student
University of Rochester
Department of Clinical and Social Psychology
http://yourpsyche.org
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