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Re: st: AW: RE: Problem looping over spells for an individual


From   Ilona Carneiro <ilonac@orange.es>
To   statalist@hsphsun2.harvard.edu
Subject   Re: st: AW: RE: Problem looping over spells for an individual
Date   Wed, 25 Feb 2009 23:06:14 +0100

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: owner-statalist@hsphsun2.harvard.edu
[mailto:owner-statalist@hsphsun2.harvard.edu] Im Auftrag von Nick Cox
Gesendet: Mittwoch, 25. Februar 2009 18:22
An: statalist@hsphsun2.harvard.edu
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
n.j.cox@durham.ac.uk

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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