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 in basehaz(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 - ______________________________________________ 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.
