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List:       r-help
Subject:    Re: [R] Calculate survival function for AFT model
From:       David Winsemius <dwinsemius () comcast ! net>
Date:       2011-12-31 2:42:33
Message-ID: 45F3C6BA-BF12-47BB-9297-5BB0CAE790C4 () comcast ! net
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On Dec 30, 2011, at 6:19 PM, Milan Bouchet-Valat wrote:

> Le vendredi 30 d=E9cembre 2011 =E0 12:46 -0800, thebennjammin a =E9crit :
>> I have fit an accelerated failure time model using coxph, and have  =

>> what seems
>> to be a simple question that I can't figure out.
> Please specify the exact package, functions and actual code you use.
> coxph(), as the name says, runs a Cox *proportional hazards* model,
> which is different from an accelerated failure time model.

I had the same puzzlement. I do think it is possible to construct some  =

AFT models with survival::coxph using time in the rhs of the formula,  =

but I do not think it is the recommended way, and I would feel much  =

more comfortable using survreg as well.

> You should
> use survreg (package survival) if you want to run the later family.
>
>> Given a vector of predictor values X, the survival time S[t|X] is the
>> probability the entity will survive longer than some time t.  Now,  =

>> how do I
>> calculate this for a specific value of t?
> Package rms offers convenience functions to compute and plot this. See
> psm() and predict.psm().

In package survival the survfit function is the way to go if you want  =

to recover S(t|X)

--

David Winsemius, MD
West Hartford, CT

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