R help - Sep 2006 - Textmate project drawer: is there a Windows alternative?

I was reading about the project drawer feature in Textmate, which is Mac
only.

Is there a similar feature in a Windows based text editor that works with R.
This feature sounds really useful.

Thanks,

Graham

	[[alternative HTML version deleted]]

Dear R users,

 

I am calculating several cox proportional hazard models after each other (I know
this is unusual, but I am just exploring the data). For the purpose of multiple
testing correction I need to construct an array of these p-values. However since
the output is not an array in itself, I cannot find a way to obtain the p-value
only.

 
> attach(tms)      
> 
> goal<-rep(0.7*FREQUENC[1:13],6)
> event<- Surv(TIJD,FREQUENC<goal)
> results<-coxph(event~ TYPETREA)
> summary(results)
 

Call:

coxph(formula = event ~ TYPETREA)

 

  n=76 (2 observations deleted due to missing)

                     coef exp(coef) se(coef)     z     p

TYPETREAnon-guided -0.826     0.438    0.484 -1.71 0.088

 

                   exp(coef) exp(-coef) lower .95 upper .95

TYPETREAnon-guided     0.438       2.28     0.169      1.13

 

Rsquare= 0.041   (max possible= 0.829 )

Likelihood ratio test= 3.2  on 1 df,   p=0.0737

Wald test            = 2.91  on 1 df,   p=0.088

Score (logrank) test = 3.08  on 1 df,   p=0.0794

 

Does anyone now how to extract the p-value?

Many thanks!,

Marco

On 9/30/2006 8:38 AM, Graham Smith wrote:
> I was reading about the project drawer feature in Textmate, which is Mac
> only.
> 
> Is there a similar feature in a Windows based text editor that works with
R.
> This feature sounds really useful.
If you don't get an answer, it would probably be a good idea to describe 
what a "project drawer" is.  The population of people who know
Textmate
and Windows text editors is probably pretty small.

Duncan Murdoch
> 
> Thanks,
> 
> Graham
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-help at stat.math.ethz.ch 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.

This is how you go about doing this.

summary(results)$coefficients[1,5]

You will have to check this for you code. But the idea is that
summary(results) is a list (?) and one of its components is called
"coefficients", which is a matrix. So the problem is just to extract
one element of this matrix.

I am not well versed with coxph so there may be some minor details I
am missing, but that is the general idea (same as with lm, glm etc.).

Ritwik.

On 9/30/06, Boks, M.P.M. <M.P.M.Boks at umcutrecht.nl>
wrote:
>
>
> Dear R users,
>
>
>
> I am calculating several cox proportional hazard models after each other (I
know this is unusual, but I am just exploring the data). For the purpose of
multiple testing correction I need to construct an array of these p-values.
However since the output is not an array in itself, I cannot find a way to
obtain the p-value only.
>
>
>
> > attach(tms)
>
> >
>
> > goal<-rep(0.7*FREQUENC[1:13],6)
>
> > event<- Surv(TIJD,FREQUENC<goal)
>
> > results<-coxph(event~ TYPETREA)
>
> > summary(results)
>
>
>
> Call:
>
> coxph(formula = event ~ TYPETREA)
>
>
>
>   n=76 (2 observations deleted due to missing)
>
>                      coef exp(coef) se(coef)     z     p
>
> TYPETREAnon-guided -0.826     0.438    0.484 -1.71 0.088
>
>
>
>                    exp(coef) exp(-coef) lower .95 upper .95
>
> TYPETREAnon-guided     0.438       2.28     0.169      1.13
>
>
>
> Rsquare= 0.041   (max possible= 0.829 )
>
> Likelihood ratio test= 3.2  on 1 df,   p=0.0737
>
> Wald test            = 2.91  on 1 df,   p=0.088
>
> Score (logrank) test = 3.08  on 1 df,   p=0.0794
>
>
>
> Does anyone now how to extract the p-value?
>
> Many thanks!,
>
> Marco
>
> ______________________________________________
> R-help at stat.math.ethz.ch 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.
>

-- 
Ritwik Sinha
Graduate Student
Epidemiology and Biostatistics
Case Western Reserve University
ritwik.sinha at gmail.com | +12163682366 | http://darwin.cwru.edu/~rsinha