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Re: st: RE: Complex Medical Data


From   Tom Trikalinos <ttrikalin@gmail.com>
To   statalist@hsphsun2.harvard.edu
Subject   Re: st: RE: Complex Medical Data
Date   Sun, 15 Feb 2009 18:55:07 -0500

Pete, sorry for being cryptic. Eva finished the job for me. Thanks to Eva.

TAT

On Sun, Feb 15, 2009 at 8:46 AM, TA Stat <tastat@gmail.com> wrote:
> Thanks
>
> Pete
>
> On Sun, Feb 15, 2009 at 5:32 PM, Eva Poen <eva.poen@gmail.com> wrote:
>> TA,
>>
>> -reshape- does work for you. You simply need to fiddle a bit with the
>> id variable.
>> See here:
>>
>> egen namevisit = group(name visit)
>> bys name visit (drug) : gen drugID = _n
>>
>> reshape wide drug, i(namevisit) j(drugID)
>> gen str drug = drug1 + " " + drug2 + " " + drug3 + " " + drug4
>> gen GMMT = 0
>>
>> replace GMMT = 1 if strpos(drug,"A") > 0 & strpos(drug,"C") > 0
>> replace GMMT = 1 if strpos(drug,"A") > 0 & strpos(drug,"D") > 0
>> replace GMMT = 1 if strpos(drug,"B") > 0 & strpos(drug,"C") > 0
>> replace GMMT = 1 if strpos(drug,"A") > 0 & strpos(drug,"B") > 0 &
>> strpos(drug,"A4") == 0 & strpos(drug,"B3") == 0
>> replace GMMT = 1 if strpos(drug,"A") > 0 & strpos(drug,"B") > 0 &
>> strpos(drug,"C") > 0
>>
>> And the result is
>>
>> . list name visit drug GMMT
>>
>>     +-----------------------------------+
>>     | name   visit          drug   GMMT |
>>     |-----------------------------------|
>>  1. |  Jen       1     B3 C3 D4       1 |
>>  2. |  Jen       2   A4 B3 C3 D4      1 |
>>  3. |  Jen       3       A4 B3        0 |
>>  4. |  Jen       4     A4 B3 C4       1 |
>>  5. | John       1     A1 B1 C1       1 |
>>     |-----------------------------------|
>>  6. | John       2       A1 B1        1 |
>>  7. | John       3       C1 D1        0 |
>>  8. | John       4     B2 C2 D1       1 |
>>     +-----------------------------------+
>>
>> HTH,
>> Eva
>>
>>
>>
>> 2009/2/15 TA Stat <tastat@gmail.com>:
>>> If reshape wide is used, that means "visit" is ignored.  However, but
>>> both visit and drug are important in this case.  Look at each clinic
>>> visit of John, he received GMMT at visit 1, visit 2 and visit 3, but
>>> not visit 4.  GMMT can't be determined by one drug, but it is a
>>> combination of some drugs.  In other words, I want to conclude that at
>>> each visit, each patient received GMMT or not.
>>>
>>> I can do Table 2 to Table 3, but not Table 1 to Table 2.
>>>
>>> TA
>>>
>>>
>>> On Sun, Feb 15, 2009 at 4:01 AM, Tom Trikalinos <ttrikalin@gmail.com> wrote:
>>>> TA, see
>>>>
>>>> help reshape wide
>>>>
>>>> in reshaping, j will be your drug
>>>>
>>>> hth,
>>>>
>>>> TAT
>>>>
>>>>
>>>> On Sat, Feb 14, 2009 at 12:22 AM, TA Stat <tastat@gmail.com> wrote:
>>>>> For example, from table 1 to table 2, create a variable name "GMMT"
>>>>> with the conditions explain earlier.  John received GMMT for visit 1,
>>>>> visit 2, visit 4, but not visit 3.  Jen received GMMT at visit 1,
>>>>> visit 2, visit 4, but not visit 3.
>>>>>
>>>>> Although at visit 4 for Jen, a combination of A4 and B3 is not GMMT,
>>>>> but she also received C4. So she received GMMT.  At visit 3 for John,
>>>>> he received C1 and D1 (any combination of drug from Class C and Class
>>>>> D), so he received GMMT.
>>>>>
>>>>> I want to know how to get Table 2 from Table 1.
>>>>>
>>>>> ***************************************************************************************
>>>>>
>>>>> Table 1
>>>>>
>>>>> Name       Visit      Drug
>>>>>
>>>>> John           1           A1
>>>>> John           1           B1
>>>>> John           1           C1
>>>>> John           2           A1
>>>>> John           2           B1
>>>>> John           3           C1
>>>>> John           3           D1
>>>>> John           4           B2
>>>>> John           4           C2
>>>>> John           4           D1
>>>>> Jen             1           B3
>>>>> Jen             1           C3
>>>>> Jen             1           D4
>>>>> Jen             2           A4
>>>>> Jen             2           B3
>>>>> Jen             2           C3
>>>>> Jen             2           D4
>>>>> Jen             3           A4
>>>>> Jen             3           B3
>>>>> Jen             4           A4
>>>>> Jen             4           B3
>>>>> Jen             4           C4
>>>>>
>>>>> ***************************************************************************************
>>>>>
>>>>> Table 2
>>>>>
>>>>> Name       Visit      Drug        GMMT (Y=Yes, N=No)
>>>>>
>>>>> John           1           A1            Y
>>>>> John           1           B1            Y
>>>>> John           1           C1            Y
>>>>> John           2           A1            Y
>>>>> John           2           B1            Y
>>>>> John           3           C1            N
>>>>> John           3           D1            N
>>>>> John           4           B2            Y
>>>>> John           4           C2            Y
>>>>> John           4           D1            Y
>>>>> Jen             1           B3            Y
>>>>> Jen             1           C3            Y
>>>>> Jen             1           D4            Y
>>>>> Jen             2           A4            Y
>>>>> Jen             2           B3            Y
>>>>> Jen             2           C3            Y
>>>>> Jen             2           D4            Y
>>>>> Jen             3           A4            N
>>>>> Jen             3           B3            N
>>>>> Jen             4           A4            Y
>>>>> Jen             4           B3            Y
>>>>> Jen             4           C4            Y
>>>>>
>>>>>
>>>>> ***************************************************************************************
>>>>>
>>>>> Table 3
>>>>>
>>>>> Name       Visit      Drug        GMMT (Y=Yes, N=No)
>>>>>
>>>>> John           1           A1            Y
>>>>> John           2           A1            Y
>>>>> John           3           C1            N
>>>>> John           4           B2            Y
>>>>> Jen             1           B3            Y
>>>>> Jen             2           A4            Y
>>>>> Jen             3           A4            N
>>>>> Jen             4           A4            Y
>>>>>
>>>>>
>>>>> On Sat, Feb 14, 2009 at 2:29 AM, Nick Cox <n.j.cox@durham.ac.uk> wrote:
>>>>>> <>
>>>>>>
>>>>>> An example of data would help make this clearer.
>>>>>>
>>>>>> Nick
>>>>>> n.j.cox@durham.ac.uk
>>>>>>
>>>>>> TA Stat
>>>>>>
>>>>>> I have data arranged in the format that each row represents one drug
>>>>>> for clinic visit. So, one patient may have more than one drug (row)
>>>>>> for each visit. Each patient also have several clinic visits.
>>>>>>
>>>>>> There are 4 classes of drugs, called Class A, Class B, Class C and
>>>>>> Class D. Class A has four drugs, called A1, A2, A3 and A4. Class B has
>>>>>> 3 drugs, called B1, B2, B3. so as Class C and Class D (as presented
>>>>>> below). Some combination of drugs is called GMMT, other is not. I
>>>>>> would like to find if each patient has received GMMT at each clinic
>>>>>> visit or not. Basically, I want to identify whether patient receive
>>>>>> GMMT for each visit or not.
>>>>>>
>>>>>> Class A: A1, A2, A3, A4
>>>>>>
>>>>>> Class B: B1, B2, B3
>>>>>>
>>>>>> Class C: C1, C2, C3
>>>>>>
>>>>>> Class D: D1, D2, D3, D4
>>>>>>
>>>>>> a combination of drug is called GMMT if
>>>>>>
>>>>>> Class A and Class B
>>>>>>
>>>>>> Class A and Class C
>>>>>>
>>>>>> Class A and Class D
>>>>>>
>>>>>> Class B and Class C
>>>>>>
>>>>>> Class A and Class B and Class C
>>>>>>
>>>>>> (However, there are some exception)
>>>>>>
>>>>>> but not for Class C and Class D
>>>>>>
>>>>>> but not for A4 and B3
>>>>>>
>>>>>>
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