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)
Confidentiality Statement:
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