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From |
Ilona Carneiro <ilonac@orange.es> |

To |
statalist@hsphsun2.harvard.edu |

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

Date |
Sun, 1 Mar 2009 16:07:16 +0100 |

Thanks Martin Here is a sample of the data that requires this fix: pin start end case tx 1 10 20 1 1 1 20 35 1 0 1 35 50 1 0 1 50 100 .

- tempvar T t - sort `_byvars' start = sort pin start - by `_byvars': gen `t' = _n = by pin: gen __000004 = _n - sort `_byvars' start = sort pin start - by `_byvars': gen `T' = _N * `touse' = by pin: gen __000003 = _N * __000002 - sort `_byvars' start = sort pin start - sum `T', meanonly = sum __000003, meanonly - local tmax = r(max) - drop `T' = drop __000003 - replace lagend = (end + 19 + 1) if (anmal > 0 & anmal < .) - sort `_byvars' start = sort pin start - forvalues i = 1(1)`tmax' { = forvalues i = 1(1)2 { - noi di "T=" `tmax' = noi di "T=" 2 T=2 - noi di "t=" `t' = noi di "t=" __000004 t=1 - noi di "i=" `i' = noi di "i=" 1 i=1 - drop if end < lagend[`i'-1] & lagend[`i'-1] < . & `t'==`i' & `i'!=1 = drop if end < lagend[1-1] & lagend[1-1] < . & __000004==1 & 1!=1

- } - noi di "T=" `tmax' = noi di "T=" 2 T=2 - noi di "t=" `t' = noi di "t=" __000004 t=1 - noi di "i=" `i' = noi di "i=" 2 i=2 - drop if end < lagend[`i'-1] & lagend[`i'-1] < . & `t'==`i' & `i'!=1 = drop if end < lagend[2-1] & lagend[2-1] < . & __000004==2 & 2!=1

- } - } Ilona On 27 Feb 2009, at 22:04, Martin Weiss wrote:

<>It is difficult for an outsider to make up data for your specificproblem;therefore either frame the prob in terms of a dataset shipped withStata or-set trace on- and report the area around the error... HTH Martin -----Ursprüngliche Nachricht----- Von: owner-statalist@hsphsun2.harvard.edu[mailto:owner-statalist@hsphsun2.harvard.edu] Im Auftrag von IlonaCarneiroGesendet: Freitag, 27. Februar 2009 19:09 An: statalist@hsphsun2.harvard.edu Betreff: Re: st: AW: RE: Problem looping over spells for an individual Thanks for these suggestions, Nick. Some of them seem to require "tsset"ing the data. However, I am trying to adapt the code from panelthin.ado, but can't quite get it to work for me. I've been battling with this for a couple of days now and I can't seem to find a way to loop over consecutive observations for an individual. I see that in panelthin, it automatically works separately on each panel because it is tsset, but how can I do this for survival time "stset" data? I've written a little sub-programme to see if I can get this to work. Generation of a local for _N now works and does give the correct count of observations per individual. However, my generation of the tempvar `t' to define the sequential observations (_n) for each individual doesn't work. Any suggestions? capture program drop temp program define temp, byable(recall, noheader) sortpreserve qui{ marksample touse count if `touse' if r(N) == 0 error 2000 tempvar T t sort `_byvars' start by `_byvars': gen `t' = _n * `touse' sort `_byvars' start by `_byvars': gen `T' = _N * `touse' sort `_byvars' start sum `T', meanonly local tmax = r(max) drop `T' replace lagend = (end + 19 + 1) if (anmal > 0 & anmal < .) sort pin start forvalues i = 1(1)`tmax' { drop if end < lagend[`i'-1] & lagend[`i'-1] < . & `t'==`i' & `i'!=1 replace lagend = (end + 21 + 1) if (mal0 > 0 & mal0 < .) & lagend==. & `i'<`tmax' } } end bysort id: temp regards Ilona On 26 Feb 2009, at 13:20, Nick Cox wrote: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.090 2/date/article-1122.html1. 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 n.j.cox@durham.ac.uk 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 avoidcountingthe same episode (case==1) twice I also exclude 19 days at riskaftera case is diagnosed. However, as the latter is only to preventdouble-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 timesasthere 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 startby id: drop if (end < start | start[_n-1] > end) & end < . & start< .& _n!=1This works fine for adding a gap after each treatment, as I need todothis 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 NickCoxGesendet: 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 thatall you need is to use -by:- but I don't understand your problemwellenough 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 CarneiroI am trying to write a programme that will run a commandsequentiallyfor 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 subsequentepisode. Therefore I need to run the code sequentially for eachspellof an individual, but using the marksample touse code to run it "by" individual doesn't seem to be working - the "forvalues" seems toalways interpret _N as the last observation in the whole dataset,notthe 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. * * For searches and help try: * http://www.stata.com/help.cgi?search * http://www.stata.com/support/statalist/faq * http://www.ats.ucla.edu/stat/stata/ * * For searches and help try: * http://www.stata.com/help.cgi?search * http://www.stata.com/support/statalist/faq * http://www.ats.ucla.edu/stat/stata/* * For searches and help try: * http://www.stata.com/help.cgi?search * http://www.stata.com/support/statalist/faq * http://www.ats.ucla.edu/stat/stata/ * * For searches and help try: * http://www.stata.com/help.cgi?search * http://www.stata.com/support/statalist/faq * http://www.ats.ucla.edu/stat/stata/* * For searches and help try: * http://www.stata.com/help.cgi?search * http://www.stata.com/support/statalist/faq * http://www.ats.ucla.edu/stat/stata/ * * For searches and help try: * http://www.stata.com/help.cgi?search * http://www.stata.com/support/statalist/faq * http://www.ats.ucla.edu/stat/stata/

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**Follow-Ups**:**RE: AW: st: AW: RE: Problem looping over spells for an individual***From:*"Nick Cox" <n.j.cox@durham.ac.uk>

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