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

[David Winsemius]

On Jun 28, 2011, at 6:51 AM, 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).

Shouldn't this instead go to Mr Crawley? Despite his unfortunately  
successful efforts to give the impression that his book is  
authoritative and somehow official, it is neither. I have never seen a  
contribution to the R effort from Mr. Crawley.

-- 
David.


>
> 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
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David Winsemius, MD
West Hartford, CT