[R] coxph() - unexpected result using Crawley's seedlings data (The R Book)

[Jacob Brogren]

All,

I rerun once again and managed to reproduce the results from the text book. Made no changes to the code. Could it be some problem with convergence?

Anyhow, now it works!

Cheers

Jacob

ps. I find "The R Book" very useful ds.

28 jun 2011 kl. 15.48 skrev Robert A LaBudde:

> Did you create the 'status' variable the way indicated on p. 797?
> 
> Frequently with Surv() it pays to use syntax such as Surv(death, status==1) to make a clear logical statement of what is an event (status==1) vs. censored.
> 
> PS. Next time include head(seedlings) and str(seedlings) to make clear what you are using as data.
> 
> 
> At 06:51 AM 6/28/2011, Jacob Brogren wrote:
>> Hi,
>> 
>> I ran the example on pp. 799-800 from Machael Crawley's "The R Book" using package survival v. 2.36-5, R 2.13.0 and RStudio 0.94.83. The model is a Cox's Proportional Hazards model. The result was quite different compared to the R Book. I have compared my code to the code in the book but can not find any differences in the function call. My results are attached as well as a link to the results presented in the book (link to Google Books).
>> 
>> When running the examples on pp. 797-799 I can't detect any differences in results so I don't think there are errors in the data set or in the creation of the status variable.
>> 
>> ---------------------------------
>> Original from the R Book:
>> http://books.google.com/books?id=8D4HVx0apZQC&lpg=PA799&ots=rQgd_8ofeS&dq=r%20coxph%20crawley&pg=PA799#v=onepage&q&f=false
>> 
>> ---------------------------------
>> My result:
>> > summary(model1)
>> Call:
>> coxph(formula = Surv(death, status) ~ strata(cohort) * gapsize,
>>    data = seedlings)
>> 
>>  n= 60, number of events= 60
>> 
>>                                            coef exp(coef)  se(coef)      z Pr(>|z|)
>> gapsize                                -0.001893  0.998109  0.593372 -0.003    0.997
>> gapsize:strata(cohort)cohort=September  0.717407  2.049112  0.860807  0.833    0.405
>> 
>>                                       exp(coef) exp(-coef) lower .95 upper .95
>> gapsize                                   0.9981      1.002 0.3120     3.193
>> gapsize:strata(cohort)cohort=September    2.0491      0.488 0.3792    11.074
>> 
>> Rsquare= 0.022   (max possible= 0.993 )
>> Likelihood ratio test= 1.35  on 2 df,   p=0.5097
>> Wald test            = 1.32  on 2 df,   p=0.5178
>> Score (logrank) test = 1.33  on 2 df,   p=0.514
>> 
>> Anyone have an idea why this is occurring?
>> 
>> Kind Regards
>> 
>> Jacob
>> ______________________________________________
>> R-help at 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.
> 
> ================================================================
> Robert A. LaBudde, PhD, PAS, Dpl. ACAFS  e-mail: ral at lcfltd.com
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