[R] Warning trying to plot -log(log(survival))

[John Sorkin]

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:
> This email message, including any attachments, is for\...{{dropped:17}}