Hi John, Thanks for the data. I put your data in a plain text file and read it in without any problems.
> jsdf <- read.csv("js.csv") > jsdf Time Time30 Died Age Rx 1 3 0.1000000 0 40 2 2 8 0.2666667 1 21 2 3 10 0.3333333 1 18 2 4 12 0.4000000 0 42 2 5 16 0.5333333 1 23 2 ... I can fit the model you specified and obtain the plot without problem. So this looks like an issue with R 2.8.1 and whatever survival package version you have. I have R 2.9.0 and survival_2.35-4. Can you update your versions? HTH > fit0 <- coxph(Surv(Time30, Died) ~ strata(Rx) + Age, data = jsdf) > fit0 Call: coxph(formula = Surv(Time30, Died) ~ strata(Rx) + Age, data = jsdf) coef exp(coef) se(coef) z p Age 0.0611 1.06 0.0257 2.38 0.017 Likelihood ratio test=5.84 on 1 df, p=0.0156 n= 64 > plot(survfit(fit0),fun="cloglog") ### No warning, two curves plotted. > sessionInfo() R version 2.9.0 (2009-04-17) i386-pc-mingw32 locale: LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252 attached base packages: [1] splines stats graphics grDevices utils datasets methods [8] base other attached packages: [1] survival_2.35-4 > Steven McKinney > -----Original Message----- > From: John Sorkin [mailto:jsor...@grecc.umaryland.edu] > Sent: Monday, May 11, 2009 8:53 PM > To: Steven McKinney; r-h...@stat.math.ethz.ch > Subject: RE: [R] Warning trying to plot -log(log(survival)) > > Time30 is simply Time/30 and reflects months of follow-up. > A copy of my data follows: > Time,Time30,Died,Age,Rx > 3,0.1,0,40,2 > 8,0.266666667,1,21,2 > 10,0.333333333,1,18,2 > 12,0.4,0,42,2 > 16,0.533333333,1,23,2 > 17,0.566666667,1,21,2 > 22,0.733333333,1,13,2 > 64,2.133333333,0,20,2 > 65,2.166666667,0,15,2 > 77,2.566666667,0,34,2 > 82,2.733333333,0,14,2 > 98,3.266666667,0,10,2 > 155,5.166666667,0,27,2 > 189,6.3,0,9,2 > 199,6.633333333,0,19,2 > 247,8.233333333,0,14,2 > 324,10.8,0,23,2 > 356,11.86666667,0,13,2 > 378,12.6,0,34,2 > 408,13.6,0,27,2 > 411,13.7,0,5,2 > 420,14,0,23,2 > 449,14.96666667,0,37,2 > 490,16.33333333,0,37,2 > 528,17.6,0,32,2 > 547,18.23333333,0,32,2 > 691,23.03333333,0,38,2 > 769,25.63333333,0,18,2 > 1111,37.03333333,0,20,2 > 1173,39.1,0,12,2 > 1213,40.43333333,0,12,2 > 1357,45.23333333,0,29,2 > 9,0.3,1,35,1 > 11,0.366666667,1,27,1 > 12,0.4,1,22,1 > 20,0.666666667,1,21,1 > 20,0.666666667,1,30,1 > 22,0.733333333,1,7,1 > 25,0.833333333,1,36,1 > 25,0.833333333,1,38,1 > 25,0.833333333,0,20,1 > 28,0.933333333,1,25,1 > 28,0.933333333,1,28,1 > 31,1.033333333,1,17,1 > 35,1.166666667,1,21,1 > 35,1.166666667,1,25,1 > 46,1.533333333,1,35,1 > 49,1.633333333,1,19,1 > 104,3.466666667,0,27,1 > 106,3.533333333,0,19,1 > 156,5.2,0,15,1 > 218,7.266666667,0,26,1 > 230,7.666666667,0,11,1 > 231,7.7,0,14,1 > 316,10.53333333,0,15,1 > 393,13.1,0,27,1 > 395,13.16666667,0,2,1 > 428,14.26666667,0,3,1 > 469,15.63333333,0,14,1 > 602,20.06666667,0,18,1 > 681,22.7,0,23,1 > 690,23,0,9,1 > 1112,37.06666667,0,11,1 > 1180,39.33333333,0,11,1 > > > > > John David Sorkin M.D., Ph.D. > Chief, Biostatistics and Informatics > University of Maryland School of Medicine Division of Gerontology > Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) > Baltimore, MD 21201-1524 > (Phone) 410-605-7119 > (Fax) 410-605-7913 (Please call phone number above prior to faxing) > > >>> Steven McKinney <smckin...@bccrc.ca> 5/11/2009 10:04 PM >>> > Hi John, > > I can't reproduce your case with built-in data sets. > > Your data set is small. Can you show the data for the variables > involved in your example? > (Time30, Died, Rx, Age) > > > > > > Steven McKinney, Ph.D. > > Statistician > Molecular Oncology and Breast Cancer Program British Columbia Cancer > Research Centre > > email: smckin...@bccrc.ca > tel: 604-675-8000 x7561 > > BCCRC > Molecular Oncology > 675 West 10th Ave, Floor 4 > Vancouver B.C. > V5Z 1L3 > > Canada > > > > > > > > > -----Original Message----- > > From: r-help-boun...@r-project.org [mailto:r-help-boun...@r- > > project.org] On Behalf Of John Sorkin > > Sent: Monday, May 11, 2009 12:19 PM > > To: r-h...@stat.math.ethz.ch > > Subject: [R] Warning trying to plot -log(log(survival)) > > > > windows xp > > R 2.8.1 > > > > I am trying to plot the -log(log(survival)) to visually test the > > proportional hazards assumption of a Cox regression. The plot, which > > should give two lines (one for each treatment) gives only one line > and > > a warning message. I would appreciate help getting two lines, and an > > explanation of the warning message. My problem may the that I have > very > > few events in one of my strata, but I don't know. > > Thanks, > > John > > > > fit0<-coxph(Surv(Time30,Died)~strata(Rx)+Age,data=GVHDdata) > > plot(survfit(fit0),fun="cloglog") > > > > > > WARNING: Warning in xy.coords (x, y, xlabel, ylabel, log) : > > 2 x values <=0 omitted from logarithmic plot > > > > > > > > > print(survfit(fit0),fun="cloglog") > > Call: survfit.coxph(object = fit0) > > > > n events median 0.95LCL 0.95UCL > > Rx=0 31 5 Inf Inf Inf > > Rx=1 32 15 Inf 1.17 Inf > > > > John David Sorkin M.D., Ph.D. > > Chief, Biostatistics and Informatics > > University of Maryland School of Medicine Division of Gerontology > > Baltimore VA Medical Center 10 North Greene Street GRECC (BT/18/GR) > > Baltimore, MD 21201-1524 > > (Phone) 410-605-7119 > > (Fax) 410-605-7913 (Please call phone number above prior to faxing) > > > > Confidentiality Statement: > > This email message, including any attachments, is for > > th...{{dropped:6}} > > > > ______________________________________________ > > 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. > > Confidentiality Statement: > This email message, including any attachments, is for ...{{dropped:6}} ______________________________________________ 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.