From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>

Date: Sat 27 Aug 2005 - 21:20:40 EST

Date: Sat 27 Aug 2005 - 21:20:40 EST

The survival package is a recommended package in R and contains survreg() which uses the AFT definitions for Weibull survival. This is well documented, and MASS (the book) has comparisons of PH and AFT parametrization for a Weibull example.

I think you mean Frank Harrell's `Design' package. As far as I am aware that has a function psm() (not PSM) which is based on survreg(), so the interpretation should be the same.

On Fri, 26 Aug 2005, denis lalountas wrote:

> Hi to all,

*> I am working on design package using survival function.
**> First using PSM and adopting a weibull specification for the baseline hazard , I have got the following results(since weibull has both PH and AFT propreties ,in addition I have used the PPHSm command):
**>
**> Value Std. Error z p
**>
**> (Intercept) 1.768 1.0007 1.77 7.73e-02
**>
**> SIZE -0.707 0.0895 -7.90 2.80e-15
**>
**> REtoTA -0.896 0.4208 -2.13 3.33e-02
**>
**> D1toEQ 0.281 0.0330 8.51 1.81e-17
**>
**> EBTtoTA -6.706 1.0807 -6.21 5.46e-10
**>
**> SALtoTA -3.943 0.3575 -11.03 2.78e-28
**>
**> fishes 2.619 0.4194 6.24 4.26e-10
**>
**> computers 2.781 0.2105 13.21 7.35e-40
**>
**> Log(scale) -0.945 0.1514 -6.24 4.25e-10
**>
**> and the loglikelihood -82.0
**>
**> I dont know the specification of the weibull that Desing package uses so
**> I can't evaluate the result.
**>
**> For comparison reasons I have estimated the same model using another
**> spftware EasyReg
**>
**> wich gave the following results( the weibull specification has the form
**> a(1).a(2).t^(a(2)-1):
**>
**> parameters ML estimate t-value p-value Covariates
**>
**> beta(1) 2.411460 2.136 0.03265 fishes
**>
**> beta(2) 2.710115 3.322 0.00089 computers
**>
**> beta(3) -7.539632 -2.646 0.00815 EBTtoTA
**>
**> beta(4) -3.720231 -2.547 0.01086 SALtoTA
**>
**> beta(5) 0.262115 1.982 0.04751 D1toEQ
**>
**> beta(6) -0.710535 -0.515 0.60684 REtoTA
**>
**> beta(7) -0.493369 -1.938 0.05262 LOG(SIZE)
**>
**> alpha(1) 0.485828 0.392 0.69491
**>
**> alpha(2) 2.597073 5.516 0.00000
**>
**> log(L)=-83,4
**>
**> First observe that the results are almost the same but the weibull parameters are not.
**>
**> acooring to the weibull specification that easyreg uses a(2)>0 so the baseline hazard is monotonically increases ,acording to my expectations :(the empirical uncoditional hazard increases monotonically from t=1,12 and then decreases to zero)
**>
**> My question is what is the weibull specification that R-design package uses for the baseline hazard. Second ,it is possible to plot the baseline hazard in R , in order to "see" the accelerating-decelerating effect in the AFT case.
**>
**> In addition how can simulate a model in the AFT case ( some examples of simulation are given in the design manual for the COX-PH case.
**>
**> I hope that my questions are not borring, if so sory I am a new user of R package.
**>
**> Best regards
**>
**> D.Lalountas
**>
**> University of Patras , Greece
**>
**>
**>
**> ---------------------------------
**>
**>
**> [[alternative HTML version deleted]]
**>
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**>
*

-- 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 ______________________________________________ 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.htmlReceived on Sat Aug 27 21:29:33 2005

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