Thanks for this, which is good news for me because it explains why the code I was seeing looked as it did.
In terms of moving forward, I have a few vague suggestions.
0. Spells. See the suggestions on reading and software in the thread started by Jakob Petersen yesterday.
<http://www.hsph.harvard.edu/cgi-bin/lwgate/STATALIST/archives/statalist.0902/date/article-1122.html>
1. One is more of style or taste than technique. I prefer to think in terms of tagging observations I want to keep or work on with 1 and those I don't with 0. Then you can do almost anything later
... if tag
or
... if !tag
as the case may be.
An advantage of that style: it is reversible, both within an algorithm and generally.
(If you really want to -drop- observations, -drop- them in one go when the selection is final.)
2. One strategy might be
loop over individuals {
-expand- each individual to a block of observations with one observation per day
<magic bit>
reduce each individual back again
}
3. This problem reminds me loosely of one tackled with -panelthin- on SSC. The code for that may suggest some technique.
Nick
[email protected]
Ilona Carneiro
Many thanks to Nick & Martin for pointing out my error using "if" -
you are correct and that's why it wasn't working. However, I'm still
unable to do what I wanted to. Apologies for posting code which I
tried to simplify, but just made incomprehensible! The snippet was
part of a much larger programme in which the other local macros are
all defined.
I'll try to clarify. Here is an example of the problem I have. These
are consecutive periods of observations for an individual - the end
denoted by a clinic visit which may or may not be defined as a case
(depending on diagnostic result), or by exit from the study.
id start end case tx
1 10 20 1 1
1 20 35 1 0
1 35 50 1 0
1 50 100 . .
I need to exclude 19 days at risk if the patient received treatment
(tx==1) as this is considered to be prophylaxis, and to avoid counting
the same episode (case==1) twice I also exclude 19 days at risk after
a case is diagnosed. However, as the latter is only to prevent double-
counting it is not necessary if the case has already been disqualified.
What I need to get is the following:
id start end case tx
1 10 20 1 1
1 40 50 1 0
1 50 100 . .
I originally coded the following VERY crudely:
/* To calculate the gaps */
sort id start
by id: gen lagend = end + lag if (tx > 0 & tx < .) | (case > 0 & case
< .) & _n!=_N
/* To drop periods of time that are disqualified - repeated 3 times as
there may be up to 3 consecutively - to be generalisable, it could be
more */
sort id start
by id: drop if lagend[_n-1] > end & lagend[_n-1] < . & _n!=1
sort id start
by id: drop if lagend[_n-1] > end & lagend[_n-1] < . & _n!=1
sort id start
by id: drop if lagend[_n-1] > end & lagend[_n-1] < . & _n!=1
sort id start
by id: drop if lagstart > end & lagstart < . & _n!=1
/* To update the start date */
sort id start
by id: replace start = lagend[_n-1] if lagend[_n-1] < . & _n!=1
sort id start
by id: drop if (end < start | start[_n-1] > end) & end < . & start < .
& _n!=1
This works fine for adding a gap after each treatment, as I need to do
this even if the observation period is dropped from the time at risk.
The code gave the following result, as both the 2nd & 3rd episodes
were disqualified, instead of just the 2nd:
id start end case tx
1 10 20 1 1
1 55 100 . .
I realise that I need to evaluate the generation of the gap after
cases separately for each observation period, incase the observation
is dropped. But can't seem to find a way to do this. I hope this is a
clearer explanation of the problem.
On another point, I subsequently use stgen gap = gaplen() to
calculate how much time to exclude from the time at risk. Stata
appears to count one more than just the actual gap, i.e. it will give
me a gap of 20 days between an observation ending with day 20, and a
subsequent observation starting at day 40, when the actual time
excluded in-between is 19 days. I'm just subtracting 1 from the
calculation at present, but is there a reason for this?
Ilona
On 25 Feb 2009, at 18:27, Martin Weiss wrote:
>
> <>
>
>
> I was desperate to find an SJ tip for Ilona on the difference
> between "if"
> and "if"; turns out it is an FAQ:
> http://www.stata.com/support/faqs/lang/ifqualifier.html
>
>
>
>
> HTH
> Martin
>
>
> -----Ursprüngliche Nachricht-----
> Von: [email protected]
> [mailto:[email protected]] Im Auftrag von Nick Cox
> Gesendet: Mittwoch, 25. Februar 2009 18:22
> An: [email protected]
> Betreff: st: RE: Problem looping over spells for an individual
>
> Unless you are working under the aegis of -by:- _N will always be
> interpreted as the total number of observations. This code doesn't
> satisfy that.
>
> I echo Martin Weiss in suspecting that your -if `touse'- is a bug. You
> are almost certainly confusing the two flavours of -if-.
>
> Otherwise, your code still looks very confused and based on a
> variety of
> misunderstandings. Apart from `touse', which is defined by -
> marksample-,
> all of the local macros you refer to will be treated as empty strings,
> as none has been defined earlier in the program. I am surprised to
> hear
> that it is running at all.
>
> It does not look as if you need a program anyway. My impression is
> that
> all you need is to use -by:- but I don't understand your problem well
> enough to suggest better code. Someone else may be able to give better
> help. If not, rather than a lengthy word description, you should
> perhaps
> give an example of your data with the intended result.
>
> Nick
> [email protected]
>
> Ilona Carneiro
>
> I am trying to write a programme that will run a command sequentially
> for observations of an individual. For each individual I have multiple
> spells and multiple failures. However, the twist is that I also need
> to exclude a period of time at risk after each treatment (prophylaxis)
> and after each failure (to prevent double-counting of failures that
> may actually be the same episode). I managed to do this without any
> problem for the treatment, but if an episode is disqualified (by a
> prior treatment or episode) I don't want it to disqualify a subsequent
> episode. Therefore I need to run the code sequentially for each spell
> of an individual, but using the marksample touse code to run it "by"
> individual doesn't seem to be working - the "forvalues" seems to
> always interpret _N as the last observation in the whole dataset, not
> the last observation for each individual.
>
> I have the following code:
>
> program define byid, byable(recall, noheader)
> marksample touse
> sort `id' `start'
> if `touse' {
> forvalues i = 1(1)`=_N' {
> replace lagend = (`end' + `lag') if ((`tx' > 0 & `tx' <
> .) | (`case'
>> 0 & `case' < .))
> drop if lagend[`i'-1]>`end' & `id'[`i'-1]==`id'
> }
> }
> end
>
> gen lagend=.
> qui by id: byid
>
> but I get the error:
> 2nd by group not found
> r(111);
>
> And the programme isn't doing what I need it to.
>
>
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>
>
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