topic Re: lab data- repeated tests in SAS Procedures

lab data- repeated tests

TEJ — Tue, 10 May 2016 22:07:25 GMT

Hi,

I am working on a lab data with different test types and corresponding specimen dates. I have included a snapshot of my data in the attachment (only tests included, there's dates for each test like date1, date2, date3 etc. for test1, test2, test3 resp).

there are 4 kinds of tests-

EIA IgM, EIA total, WB IgM and WB IgG.

I want to obtain proportion/counts of of observations who had -

1) WB IgG-

2) EIA (total or IgM) followed by WB IgM within 30 days

3)both combinations (1 AND 2)

4)neither (like those with only EIAs, or EIA followed by WBIgG but not within 30 days).

PLEASE SUGGEST!

Re: lab data- repeated tests

PGStats — Wed, 11 May 2016 02:41:21 GMT

Please post test data in machine readable form.

Re: lab data- repeated tests

RW9 — Wed, 11 May 2016 08:19:03 GMT

For a good response, post some test data, in the form of a datastep (most wont download files or type test data in for you), and an example of what the output should look like. You should be able to do this in multiple ways (proc freq/means/summary, or datastep retain count on sorted dataset, or proc sql).

Re: lab data- repeated tests

TEJ — Wed, 11 May 2016 14:44:46 GMT

CaseID	TEST1	TEST2	TEST3	TEST4	DATE1	DATE2	DATE3	DATE4
1	WB IgG				2/5/2015
2	WB IgG	EIA total	EIA total		3/4/2015	3/4/2015	7/13/2015
3	EIA IgM	WB IgM	WB IgG		3/4/2016	3/4/2016	7/3/2016
4	EIA total	WB IgG	WB IgG	WB IgG	2/4/2015	2/4/2015	7/7/2015	12/2/2015
5	WB IgM	EIA total			7/11/2015	9/11/2015
6	WB IgM	WB IgG	EIA total		12/12/2015	12/12/2015	3/12/2016
7	WB IgM	WB IgG	EIA total	WB IgM	10/8/2015	10/8/2015	11/2/2015	11/2/2015

And re:output- as outlined in my first post, I am looking at different combinations of tests (used to “confirm” a case’s disease status) for each observations.

If WB IgG (regardless of other tests performed on that ID) say cat=1

If EIA total/EIA IgM and is followed by WB IgM within 30 days, cat=2

If cat=1 is true AND cat=2 is true, cat=3

If neither (only EIA total, EIA IgM, WB IgM but not within 30 days), cat=4.

Output I want will be a basic proc freq of “cat”.

hope this helps understand what i need

Thanks a lot!

Re: lab data- repeated tests

ballardw — Wed, 11 May 2016 15:49:32 GMT

Is the case of WB IgM preceding EIA total or EIA IgM to be considered category 4?

This is a poorly worded description of assigning a single category variable as the first line contradicts the second when the

"regardless of other tests" is used in the definition.

If WB IgG (regardless of other tests performed on that ID) say cat=1

If cat=1 is true AND cat=2 is true, cat=3

You need to clarify which combinations of other tests will yield a cat=1

For this one:

If EIA total/EIA IgM and is followed by WB IgM within 30 days, cat=2

What happens if you have both EIA total and EIA IgM but the WB lgm is within 30 days of only one of them?

Re: lab data- repeated tests

PGStats — Wed, 11 May 2016 15:58:16 GMT

Converting your data to a long structure help a lot:

data have;
infile datalines dsd;
input CaseID	(TEST1	TEST2	TEST3	TEST4) (:$8.)	(DATE1	DATE2	DATE3	DATE4)(:mmddyy.);
datalines;
1,WB IgG, , , ,2/5/2015, , , 
2,WB IgG,EIA total,EIA total, ,3/4/2015,3/4/2015,7/13/2015, 
3,EIA IgM,WB IgM,WB IgG, ,3/4/2016,3/4/2016,7/3/2016, 
4,EIA total,WB IgG,WB IgG,WB IgG,2/4/2015,2/4/2015,7/7/2015,12/2/2015
5,WB IgM,EIA total, , ,7/11/2015,9/11/2015, , 
6,WB IgM,WB IgG,EIA total, ,12/12/2015,12/12/2015,3/12/2016, 
7,WB IgM,WB IgG,EIA total,WB IgM,10/8/2015,10/8/2015,11/2/2015,11/2/2015
;

data long;
set have;
array t test:;
array d date:;
do i = 1 to dim(t);
    if not missing(t{i}) then do;
        test = t{i}; date = d{i}; output;
        end;
    end;
keep caseId test date;
run;

proc sql;

create table cat1 as
select unique caseId 
from long where test="WB IgG";

create table cat2 as
select unique a.caseId 
from long as a inner join long as b 
on a.caseId=b.caseId and intck("DAY", a.date, b.date) <= 30
where a.test in ("EIA total", "EIA IgM") and b.test = "WB IgM";

create table cat3 as
select * from cat1
intersect
select * from cat2;

create table cat4 as
select unique caseId from long
except
select * from cat1
except
select * from cat2;

create table cat as
select unique 
    caseId,
    caseId in (select * from cat1) as cat1,
    caseId in (select * from cat2) as cat2,
    caseId in (select * from cat3) as cat3,
    caseId in (select * from cat4) as cat4
from long
order by caseId;

select * from cat;

quit;