Yes, Thank you. I did not separate the arguments for basehaz from those for survfit in the documentation. I had been hoping the tedious alignment of the baseline curve with the value of the variables in the new data set would be [somehow] handled for me.
On Apr 7, 12:27 pm, "Austin, Matt" <[EMAIL PROTECTED]> wrote: > I don't believebasehaztakes a newdata argument. > > > args(basehaz) > > function (fit, centered = TRUE) > NULL > > It simply extracts info from the fitted object. I think you want to use > survfit method for coxph objects and then derive/extract what you need. > > --Matt > > Matt Austin > Global Statistical Leader, denosumab PMO > Biostatistics Director > Amgen, Inc > > > > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] On Behalf Of mah > Sent: Monday, April 07, 2008 10:01 AM > To: [EMAIL PROTECTED] > Subject: Re: [R]basehazand newdata > > Thanks Roland, but using data frames does not resolve the issue. See revised > code and output below: > > > test1 <- data.frame( > + time= c(4, 3,1,1,2,2,3), > + status=c(1,NA,1,0,1,1,0), > + x= c(0, 2,1,1,1,0,0), > + sex= c(0, 0,0,0,1,1,1) > + ) > > f1 <- coxph( Surv(time, status) ~ x + strata(sex), data=test1) > > #stratified model > > > test2 <- data.frame( > + time= c(4, 3,1,1,2,2,3), > + status=c(1,NA,1,0,1,1,0), > + x= c(1, 2,1,1,1,0,0), > + sex= c(0, 0,0,0,1,1,1) > + ) > > f2 <- coxph( Surv(time, status) ~ x + strata(sex), data=test2) > > #stratified model > > > f1 > Call: > coxph(formula = Surv(time, status) ~ x + strata(sex), data = test1) > > coef exp(coef) se(coef) z p > x 1.17 3.22 1.29 0.907 0.36 > > Likelihood ratio test=0.87 on 1 df, p=0.351 n=6 (1 observation deleted due > to missingness) > > f2 > Call: > coxph(formula = Surv(time, status) ~ x + strata(sex), data = test2) > > coef exp(coef) se(coef) z p > x 0.896 2.45 1.42 0.63 0.53 > > Likelihood ratio test=0.38 on 1 df, p=0.535 n=6 (1 observation deleted due > to missingness) > > basehaz(f1, newdata=test2) > Error inbasehaz(f1, newdata = test2) : > unused argument(s) (newdata = list(time = c(4, 3, 1, 1, 2, 2, 3), status = > c(1, NA, 1, 0, 1, 1, 0), x = c(1, 2, 1, 1, 1, 0, 0), sex = c(0, 0, 0, 0, 1, > 1, 1))) > > Mike > > On Apr 7, 11:43 am, Roland Rau <[EMAIL PROTECTED]> wrote: > > Hi, > > > just looked at it briefly and I don't know if it is the real cause for > > your problems. But 'data' as well as 'newdata' require a data.frame > > and not a list as input. > > > Does this help? > > > Best, > > Roland > > > mah wrote: > > > I am unable to get thebasehazfunction to apply a proportional > > > hazards model to a new data frame. I replicated my specific > > > situation with the example for coxph in the help, where I changed > > > the x value of the first record from 0 to 1. Is there something > > > incorrect in the syntax that I am using? Thanks in advance! > > > > test1 <- list(time= c(4, 3,1,1,2,2,3), > > > status=c(1,NA,1,0,1,1,0), > > > x= c(0, 2,1,1,1,0,0), > > > sex= c(0, 0,0,0,1,1,1)) > > > test2 <- list(time= c(4, 3,1,1,2,2,3), > > > status=c(1,NA,1,0,1,1,0), > > > x= c(1, 2,1,1,1,0,0), > > > sex= c(0, 0,0,0,1,1,1)) > > > f1 <- coxph( Surv(time, status) ~ x + strata(sex), data=test1) > > > #stratified model > > > f2 <- coxph( Surv(time, status) ~ x + strata(sex), data=test2) > > > #stratified model > > > f1 > > > Call: > > > coxph(formula = Surv(time, status) ~ x + strata(sex), data = test1) > > > > coef exp(coef) se(coef) z p > > > x 1.17 3.22 1.29 0.907 0.36 > > > > Likelihood ratio test=0.87 on 1 df, p=0.351 n=6 (1 observation > > > deleted due to missingness) > > >> f2 > > > Call: > > > coxph(formula = Surv(time, status) ~ x + strata(sex), data = test2) > > > > coef exp(coef) se(coef) z p > > > x 0.896 2.45 1.42 0.63 0.53 > > > > Likelihood ratio test=0.38 on 1 df, p=0.535 n=6 (1 observation > > > deleted due to missingness) > > >>basehaz(f1, newdata=test2) > > > Error inbasehaz(f1, newdata = test2) : > > > unused argument(s) (newdata = list(time = c(4, 3, 1, 1, 2, 2, 3), > > > status = c(1, NA, 1, 0, 1, 1, 0), x = c(1, 2, 1, 1, 1, 0, 0), sex = > > > c(0, 0, 0, 0, 1, 1, 1))) > > > > ______________________________________________ > > > [EMAIL PROTECTED] mailing list > > >https://stat.ethz.ch/mailman/listinfo/r-help > > > PLEASE do read the posting > > >guidehttp://www.R-project.org/posting-guide.html > > > and provide commented, minimal, self-contained, reproducible code. > > > ______________________________________________ > > [EMAIL PROTECTED] mailing > > listhttps://stat.ethz.ch/mailman/listinfo/r-help > > PLEASE do read the posting > > guidehttp://www.R-project.org/posting-guide.html > > and provide commented, minimal, self-contained, reproducible code.- > > Hide quoted text - > > > - Show quoted text - > > ______________________________________________ > [EMAIL PROTECTED] mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. > > ______________________________________________ > [EMAIL PROTECTED] mailing listhttps://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guidehttp://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code.- Hide > quoted text - > > - Show quoted text - ______________________________________________ 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.
