> -----Original Message----- > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > project.org] On Behalf Of ?e???da? ?pa?t?? > Sent: Tuesday, October 27, 2009 3:51 PM > To: r-help@r-project.org > Subject: [R] cox regression extract strata as numeric > > > Hi there, > > I perform a stratified cox and then I need the strata as a numeric > array "straft.ln" > ft.ln <- > coxph(Surv(times,deaths)~ages+chemos+chemos:f1+chemos:f2+horms+horms:f1 > +horms:f2+grades+grades:f1+grades:f2+positives+positives:f1+positives:f > 2+sizes+sizes:f1+sizes:f2+strata(stra),data=ddd) > > basehazzft.ln=basehaz(ft.ln,centered=FALSE) > H0ft.ln=c(basehazzft.ln[,1]) > timeft.ln=c(basehazzft.ln[,2]) > straft.ln=c(basehazzft.ln[,3]) > > I notice that basehazzft.ln[,3] is not the same with straft.ln with > respect to the values i.e.: > > (basehazzft.ln$stra[1]) > [1] stra=1 > 134 Levels: stra=1 stra=10 stra=100 stra=101 stra=102 ... stra=99 > > c(basehazzft.ln$stra[1]) > [1] 1 > > > so far so good but: > > (basehazzft.ln$stra[285]) > [1] stra=2 > 134 Levels: stra=1 stra=10 stra=100 stra=101 stra=102 ... stra=99 > > c(basehazzft.ln$stra[285]) > [1] 47 > > while the desired value is 2, I get a 47. What am I doing wrong? I > tried the as.numeric function but I have the same problem.. > > I just want instead of the [ "stra=1" "stra=1" "stra=1" etc] the > [1,1,1 etc] > > Thanx in advance for any answers!
Here's one way to do it (using the example on coxph help page): > require("survival") Loading required package: survival Loading required package: splines > bladder1 <- bladder[bladder$enum < 5, ] > m1 <- coxph(Surv(stop, event) ~ (rx + size + number) * strata(enum) + > cluster(id), bladder1) > basehazzft.ln=basehaz(m1,centered=FALSE) > (basehazzft.ln$stra[1]) [1] enum=1 Levels: enum=1 enum=2 enum=3 enum=4 > basehazzft.ln$stra [1] enum=1 enum=1 enum=1 enum=1 enum=1 enum=1 enum=1 enum=1 enum=1 enum=1 enum=1 enum=1 enum=1 [14] enum=1 enum=1 enum=1 enum=1 enum=1 enum=1 enum=1 enum=1 enum=2 enum=2 enum=2 enum=2 enum=2 [27] enum=2 enum=2 enum=2 enum=2 enum=2 enum=2 enum=2 enum=2 enum=2 enum=2 enum=2 enum=2 enum=2 [40] enum=2 enum=3 enum=3 enum=3 enum=3 enum=3 enum=3 enum=3 enum=3 enum=3 enum=3 enum=3 enum=3 [53] enum=3 enum=3 enum=3 enum=3 enum=3 enum=4 enum=4 enum=4 enum=4 enum=4 enum=4 enum=4 enum=4 [66] enum=4 enum=4 enum=4 Levels: enum=1 enum=2 enum=3 enum=4 > as.character(basehazzft.ln$stra) [1] "enum=1" "enum=1" "enum=1" "enum=1" "enum=1" "enum=1" "enum=1" "enum=1" "enum=1" "enum=1" [11] "enum=1" "enum=1" "enum=1" "enum=1" "enum=1" "enum=1" "enum=1" "enum=1" "enum=1" "enum=1" [21] "enum=1" "enum=2" "enum=2" "enum=2" "enum=2" "enum=2" "enum=2" "enum=2" "enum=2" "enum=2" [31] "enum=2" "enum=2" "enum=2" "enum=2" "enum=2" "enum=2" "enum=2" "enum=2" "enum=2" "enum=2" [41] "enum=3" "enum=3" "enum=3" "enum=3" "enum=3" "enum=3" "enum=3" "enum=3" "enum=3" "enum=3" [51] "enum=3" "enum=3" "enum=3" "enum=3" "enum=3" "enum=3" "enum=3" "enum=4" "enum=4" "enum=4" [61] "enum=4" "enum=4" "enum=4" "enum=4" "enum=4" "enum=4" "enum=4" "enum=4" > substr(as.character(basehazzft.ln$stra), 6, 999) [1] "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "1" "2" "2" "2" [25] "2" "2" "2" "2" "2" "2" "2" "2" "2" "2" "2" "2" "2" "2" "2" "2" "3" "3" "3" "3" "3" "3" "3" "3" [49] "3" "3" "3" "3" "3" "3" "3" "3" "3" "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" "4" > as.numeric(substr(as.character(basehazzft.ln$stra), 6, 999)) [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 2 3 3 3 3 3 3 3 3 [49] 3 3 3 3 3 3 3 3 3 4 4 4 4 4 4 4 4 4 4 4 > HTH Steven McKinney Statistician Molecular Oncology and Breast Cancer Program British Columbia Cancer Research Centre > > > > > > ___________________________________________________________ > ×ñçóéìïðïéåßôå Yahoo!; > ÂáñåèÞêáôå ôá åíï÷ëçôéêÜ ìçíýìáôá (spam); Ôï Yahoo! Mail > äéáèÝôåé ôçí êáëýôåñç äõíáôÞ ðñïóôáóßá êáôÜ ôùí åíï÷ëçôéêþí > ìçíõìÜôùí http://login.yahoo.com/config/mail?.intl=gr > > [[alternative HTML version deleted]] ______________________________________________ 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.