Re: [R] Survival dummy variables and some questions

From: Stephen <szlevine_at_nana.co.il>
Date: Tue 19 Jul 2005 - 02:43:05 EST

Hi 1. Right perhaps this should clarify. I would like to extract coefficeints for different levels of the IVs (covariate). So for instance, age of onset I would want Hazards etc for every 5 years and so on... The approach I took was to categorize the variables (e.g., age of onset) and then turn the resultant categorical variable into a factor as opposed to a variable... that is when the problems began.... An alternative approach to pulling out different values at different levels of the variable is what I seek. 2. I looked for the link, but can't locate it. Will update. Many thanks S ----- Original Message ----- From: "Prof Brian Ripley" To: "Stephen" Cc: "Frank E Harrell Jr" ; Sent: Monday, July 18, 2005 4:46 PM Subject: Re: [R] Survival dummy variables and some questions > This is almost unreadable. > > On Mon, 18 Jul 2005, Stephen wrote: > >> Hi 1. To clarify: There is a posting saying that dummy regression using >> the coxph function is not possible... That posting may be outdated.... > > Clarification needs > > 1) an explanation of what you mean by `dummy regression' and > > 2) a link to the URL of that posting in the archives. > > I would normally use RSiteSearch for the latter, but it is temporarily > unavailable. > >> 2. Q. You say 'Make sure that eventbefore is a "pre time zero" >> measurement' please explain: Do you mean that if someone who is not left
>> censored and has no eventbefore then their value is zero? So John is
in >> my study from 1978 to 1992 and has no events prior to 1980 then John's >> eventbefore is 0 prior to 1980. 3. .... just kidding... Thanks S ----- >> Original Message ----- From: "Frank E Harrell Jr" To: "Stephen" Cc: >> Sent: Monday, July 18, 2005 2:46 PM Subject: Re: [R] Survival dummy >> variables and some questions > Stephen wrote: >> Hi

All, >> >> I am >> currently conducting some survival analyses. I would
like to >> extract >> coefficients at each level of the IVs. I read on a
previous >> posting >> that dummy regression using coxph was not >>
possible. > > I'm not sure >> what that means. > >> >> Therefore I though, hey why not categorize the >> variables (I realize some >> folks object to categorization but the >> paper I am >> replicating appears to have done so ...) > > The fact that >> some people murder doesn't mean we should copy them. And > murdering >> data, though not as serious, should also be avoided. > > Make sure that >> eventbefore is a "pre time zero" measurement. > > Frank > >> >> and turn >> the variables into factors and then try the analysis. >> >> E.g., >> Dataset <- read.table("categ.dat", header=TRUE) >> >> >> Dataset$eventbefore2c <- factor(Dataset$eventbefore) >> >> .. other IVs >> here >> >> ... >> >> surv.mod1 <- coxph(Surv(start, stop, event) ~ sex2 >> + ageonset2c + >> eventbefore2c + daysbefore2c, data=Dataset) >> >> >> Strangely enough, I receive a warning message when the variables are >> >> treated in this way: X matrix deemed to be singular; variable 11 in: >> >> coxph(Surv(start, stop, event) ~ sex2 + ageonset2c + eventbefore2c + I
>>>> don't receive any warnings just treating the variables in their >>

>> initial continuous format. >> >> I am currently using version >> >>
>> platform i386-pc-mingw32 >> >> arch i386 os mingw32 system i386,
mingw32 >>>> status major 2 minor 1.1 >> year 2005 month 06 day 20 >> language R >> Is this approach to dummy variable using coxph erroneous?
>> >> Is there >> another way to conduct dummy variable regression with
coxph? >> >> Also, >> if I include frailty (id) does anyone know of a useful way to >> >> investigate frailty? >> >> If one were to plot recurrent events does >> anyone know of a way of >> interpreting them?
>> >> References & code >> appreciated. >> >> BTW. not too familiar with
R, less so with survival >> analysis .... but >> well worth the effort.
>> >> Many thanks in >> advance... >> >> Regards >> >> Stephen >> >> >>
???? ?"? ???? ???? >> >> http://mail.nana.co.il >> >> [[alternative HTML version deleted]] >> >> >>>>>> >>
>>>>>> ______________________________________________ >> >>
R-help@stat.math.ethz.ch mailing list >> >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the >> posting guide! >> http://www.R-project.org/posting-guide.html > > > -- >
>> Frank E Harrell Jr Professor and Chair School of Medicine >
Department >> of Biostatistics Vanderbilt University > >> >> ???? ?"?
???? ???? >> http://mail.nana.co.il >> >> [[alternative HTML version
deleted]] >> >> ______________________________________________ >>
R-help@stat.math.ethz.ch mailing list >> https://stat.ethz.ch/mailman/listinfo/r-help >> PLEASE do read the posting guide! >> http://www.R-project.org/posting-guide.html >> > > -- > Brian D. Ripley, ripley@stats.ox.ac.uk > Professor of Applied Statistics, http://www.stats.ox.ac.uk/~ripley/ > University of Oxford, Tel: +44 1865 272861 (self) > 1 South Parks Road, +44 1865 272866 (PA) > Oxford OX1 3TG, UK Fax: +44 1865 272595 >

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http://mail.nana.co.il

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https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide! http://www.R-project.org/posting-guide.html Received on Tue Jul 19 01:46:12 2005

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