Warning trying to plot -log(log(survival))
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:jsorkin at grecc.umaryland.edu] Sent: Monday, May 11, 2009 8:53 PM To: Steven McKinney; r-help at 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 <smckinney at 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: smckinney at 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-bounces at r-project.org [mailto:r-help-bounces at r- project.org] On Behalf Of John Sorkin Sent: Monday, May 11, 2009 12:19 PM To: r-help at 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)
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