Paul Johnson wrote: > On Fri, Apr 18, 2008 at 3:06 AM, Kåre Edvardsen <[EMAIL PROTECTED]> wrote: >> Hi all. >> >> If I run the simple regression when x is a categorical variable ( x <- >> factor(x) ): >> >> > MyFit <-coxph( Surv(start, stop, event) ~ x ) >> >> How can I get the overall p-value on x other than for each dummy >> variable? >> >> > anova(MyFit) >> >> does NOT provide that information as previously suggested on the list. >> > > It "should" work... Here's a self contained example showing that > anova does give the desired significance test for an lm model. > >> y <- rnorm(100) >> x <- gl(5,20) >> mod <- lm(y~x) >> anova(mod) > Analysis of Variance Table > > Response: y > Df Sum Sq Mean Sq F value Pr(>F) > x 4 6.575 1.644 1.5125 0.2047 > Residuals 95 103.237 1.087 > > If you provide a similar self contained example leading up to a coxph, > I would be glad to investigate your question. You don't give enough > information for me to tell which version of coxph you are running, and > from what package. > > Suppose I "guess" that you are using the coxph from the package > "survival". If so, it appears to me there is a bug in that package at > the moment. The methods anova.coxph and drop1.coxph did exist at one > time, until very recently. There is a thread in r-help (which I found > by typing "RSiteSearch("anova.coxph")" ) discussing recent troubles > with anova.coxph. > > http://finzi.psych.upenn.edu/R/Rhelp02a/archive/118481.html > > As you see from the discussion in that thread, there used to be an > anova method for coxph, and in the version of survival I have now, > there is no such method. The version I have is 2.34-1, Date: > 2008-03-31. > > Here's what I see after I run "example(coxph)" in order to create some > coxph objects, on which I can test the diagnostics: > >> drop1(test2) > Error in terms.default(terms1) : no terms component >> anova(test2) > Error in UseMethod("anova") : no applicable method for "anova" > > In that survival package, I do find anova.survreg, but not > anova.coxph. If you are using the survival package, I'd suggest you > contact Thomas Lumley directly, since he maintains it. > > I think if you had reported the exact error you saw, it would have > been easier for me to diagnose the trouble. > > HTH > pj >
In the meantime you can do library(Design) f <- cph( . . . ) anova(f) # multiple d.f. Wald statistics including tests of nonlinearity cph uses coxph but anova.Design is separate from the survival package. Frank -- Frank E Harrell Jr Professor and Chair School of Medicine Department of Biostatistics Vanderbilt University ______________________________________________ R-help@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.