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Li, Jia

2006-Jun-14 18:14 UTC

[R] A question about stepwise procedures: step function

Dear all,

I tried to use "step"  function to do model selection, but I got an
error massage.  What I don't understand is that data as data.frame worked
well for my other programs, how come I cannot make it run this time. Could you
please tell me how I can fix it?

***************************************************************************************************
>all<-data.frame(z1,z2,z3)
>fit.model.all<- coxph(Surv(t,cen) ~z1+z2+z3,data=all)
> reg.model.all<-step(fit.model.all)Start:  AIC= 689.1 
 Surv(t, cen) ~ z1 + z2 + z3 
Error in as.data.frame.default(data) : cannot coerce class "function"
into a data.frame
***************************************************************************************************
Thanks a lot!
 
Jia

Li, Jia

2006-Jun-15 13:52 UTC

head link

[R] A question about stepwise procedures: step function

Hi,
 
Step works for a Cox model. And I got the same error massage using
stepAIC.
 
Jia

  _____  

From: Ritwik Sinha [mailto:ritwik.sinha@gmail.com] 
Sent: Thursday, June 15, 2006 12:12 AM
To: Li, Jia
Subject: Re: [R] A question about stepwise procedures: step function


Hi,

The step documentation says 

"object: an object representing a model of an appropriate class
          (mainly '"lm"' and '"glm"'). This
is used as the initial
          model in the stepwise search. 
"
I wonder if it will work for a cox proportional hazard model. You could
try stepAIC in MASS.




On 6/14/06, Li, Jia < LI@nsabp.pitt.edu <mailto:LI@nsabp.pitt.edu> >
wrote: 

	Dear all,
	
	I tried to use "step"  function to do model selection, but I got
an error massage.  What I don't understand is that data as data.frame
worked well for my other programs, how come I cannot make it run this
time. Could you please tell me how I can fix it?
	
	
************************************************************************
*************************** 
	
	>all<-data.frame(z1,z2,z3)
	
	>fit.model.all<- coxph(Surv(t,cen) ~z1+z2+z3,data=all)
	
	> reg.model.all<-step(fit.model.all)
	Start:  AIC= 689.1
	Surv(t, cen) ~ z1 + z2 + z3
	Error in as.data.frame.default(data) : cannot coerce class
"function" into a data.frame
	
************************************************************************
***************************
	Thanks a lot!
	
	Jia
	
	______________________________________________
	R-help@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
	




-- 
Ritwik Sinha
Graduate Student 
Epidemiology and Biostatistics
Case Western Reserve University

http://darwin.cwru.edu/~rsinha 

	[[alternative HTML version deleted]]

Li, Jia

2006-Jun-15 15:44 UTC

head link

[R] A question about stepwise procedures: step function

Sorry, I still cannot find what's wrong with it. And it seems that
nothing is wrong with t.
 
Jia
 > z1<-rnorm(N,0,1)
> z2<-rnorm(N,3,5)
> z3<-rbinom(N,1,0.6)
> 
> prop.cens<-0.45                   
> cen<-rbinom(N,1,1-prop.cens)     #<-- censor indicator:45% censor in
the data.> t<- rexp(N)
> all<-data.frame(z1,z2,z3)
> fit.model.all<- coxph(Surv(t,cen) ~z1+z2+z3,data=all)
> fit.model.allCall:
coxph(formula = Surv(t, cen) ~ z1 + z2 + z3, data = all)
 

        coef exp(coef) se(coef)       z    p
z1  0.057466     1.059   0.1377  0.4173 0.68
z2  0.000907     1.001   0.0332  0.0273 0.98
z3 -0.349273     0.705   0.2867 -1.2184 0.22
 
Likelihood ratio test=1.81  on 3 df, p=0.613  n= 100 > reg.model.all<-step(fit.model.all)Start:  AIC= 376.39 
 Surv(t, cen) ~ z1 + z2 + z3 
 
Error in as.data.frame.default(data) : cannot coerce class "function"
into a data.frame


  _____  

From: Hong Ooi [mailto:Hong.Ooi@iag.com.au] 
Sent: Thursday, June 15, 2006 10:53 AM
To: Li, Jia
Subject: RE: [R] A question about stepwise procedures: step function



Note: This e-mail is subject to the disclaimer contained at the bottom
of this message.

  _____  

t is the name of a function. If you have a variable called t in your
dataset, try renaming it.
 

  _____  

From: r-help-bounces@stat.math.ethz.ch on behalf of Li, Jia
Sent: Thu 15/06/2006 11:52 PM
To: r-help@stat.math.ethz.ch; ritwik.sinha@gmail.com
Subject: Re: [R] A question about stepwise procedures: step function



Hi,

Step works for a Cox model. And I got the same error massage using
stepAIC.

Jia

  _____ 

From: Ritwik Sinha [mailto:ritwik.sinha@gmail.com]
Sent: Thursday, June 15, 2006 12:12 AM
To: Li, Jia
Subject: Re: [R] A question about stepwise procedures: step function


Hi,

The step documentation says

"object: an object representing a model of an appropriate class
          (mainly '"lm"' and '"glm"'). This
is used as the initial
          model in the stepwise search.
"
I wonder if it will work for a cox proportional hazard model. You could
try stepAIC in MASS.




On 6/14/06, Li, Jia < LI@nsabp.pitt.edu <mailto:LI@nsabp.pitt.edu> >
wrote:

        Dear all,
       
        I tried to use "step"  function to do model selection, but I
got
an error massage.  What I don't understand is that data as data.frame
worked well for my other programs, how come I cannot make it run this
time. Could you please tell me how I can fix it?
       
       
************************************************************************
***************************
       
        >all<-data.frame(z1,z2,z3)
       
        >fit.model.all<- coxph(Surv(t,cen) ~z1+z2+z3,data=all)
       
        > reg.model.all<-step(fit.model.all)
        Start:  AIC= 689.1
        Surv(t, cen) ~ z1 + z2 + z3
        Error in as.data.frame.default(data) : cannot coerce class
"function" into a data.frame
       
************************************************************************
***************************
        Thanks a lot!
       
        Jia
       
        ______________________________________________
        R-help@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
       




--
Ritwik Sinha
Graduate Student
Epidemiology and Biostatistics
Case Western Reserve University

http://darwin.cwru.edu/~rsinha

        [[alternative HTML version deleted]]

______________________________________________
R-help@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


  _____  

The information transmitted in this message and its attachme...{{dropped}}

Frede Aakmann Tøgersen

2006-Jun-16 06:34 UTC

head link

[R] A question about stepwise procedures: step function

Well Jia, you use 'all' as a name for your dataframe, but this is also a
function, see ?all. If I try it with

mydata <- data.frame(z1,z2,z3) 

all goes well.


Med venlig hilsen
Frede Aakmann T?gersen
 

 
> -----Oprindelig meddelelse-----
> Fra: r-help-bounces at stat.math.ethz.ch 
> [mailto:r-help-bounces at stat.math.ethz.ch] P? vegne af Li, Jia
> Sendt: 15. juni 2006 17:45
> Til: Hong Ooi; r-help at stat.math.ethz.ch
> Emne: Re: [R] A question about stepwise procedures: step function
> 
> Sorry, I still cannot find what's wrong with it. And it seems 
> that nothing is wrong with t.
>  
> Jia
>  
> > z1<-rnorm(N,0,1)
> > z2<-rnorm(N,3,5)
> > z3<-rbinom(N,1,0.6)
> > 
> > prop.cens<-0.45                   
> > cen<-rbinom(N,1,1-prop.cens)     #<-- censor indicator:45%
censor in
> the data.
> > t<- rexp(N)
> 
> > all<-data.frame(z1,z2,z3)
> > fit.model.all<- coxph(Surv(t,cen) ~z1+z2+z3,data=all) fit.model.all
> Call:
> coxph(formula = Surv(t, cen) ~ z1 + z2 + z3, data = all)
>  
> 
>         coef exp(coef) se(coef)       z    p
> z1  0.057466     1.059   0.1377  0.4173 0.68
> z2  0.000907     1.001   0.0332  0.0273 0.98
> z3 -0.349273     0.705   0.2867 -1.2184 0.22
>  
> Likelihood ratio test=1.81  on 3 df, p=0.613  n= 100 
> > reg.model.all<-step(fit.model.all)
> Start:  AIC= 376.39
>  Surv(t, cen) ~ z1 + z2 + z3 
>  
> Error in as.data.frame.default(data) : cannot coerce class
"function"
> into a data.frame
> 
> 
>   _____  
> 
> From: Hong Ooi [mailto:Hong.Ooi at iag.com.au]
> Sent: Thursday, June 15, 2006 10:53 AM
> To: Li, Jia
> Subject: RE: [R] A question about stepwise procedures: step function
> 
> 
> 
> Note: This e-mail is subject to the disclaimer contained at the bottom
> of this message.
> 
>   _____  
> 
> t is the name of a function. If you have a variable called t in your
> dataset, try renaming it.
>  
> 
>   _____  
> 
> From: r-help-bounces at stat.math.ethz.ch on behalf of Li, Jia
> Sent: Thu 15/06/2006 11:52 PM
> To: r-help at stat.math.ethz.ch; ritwik.sinha at gmail.com
> Subject: Re: [R] A question about stepwise procedures: step function
> 
> 
> 
> Hi,
> 
> Step works for a Cox model. And I got the same error massage using
> stepAIC.
> 
> Jia
> 
>   _____ 
> 
> From: Ritwik Sinha [mailto:ritwik.sinha at gmail.com]
> Sent: Thursday, June 15, 2006 12:12 AM
> To: Li, Jia
> Subject: Re: [R] A question about stepwise procedures: step function
> 
> 
> Hi,
> 
> The step documentation says
> 
> "object: an object representing a model of an appropriate class
>           (mainly '"lm"' and '"glm"').
This is used as the initial
>           model in the stepwise search.
> "
> I wonder if it will work for a cox proportional hazard model. 
> You could
> try stepAIC in MASS.
> 
> 
> 
> 
> On 6/14/06, Li, Jia < LI at nsabp.pitt.edu <mailto:LI at
nsabp.pitt.edu> >
> wrote:
> 
>         Dear all,
>        
>         I tried to use "step"  function to do model 
> selection, but I got
> an error massage.  What I don't understand is that data as data.frame
> worked well for my other programs, how come I cannot make it run this
> time. Could you please tell me how I can fix it?
>        
>        
> **************************************************************
> **********
> ***************************
>        
>         >all<-data.frame(z1,z2,z3)
>        
>         >fit.model.all<- coxph(Surv(t,cen) ~z1+z2+z3,data=all)
>        
>         > reg.model.all<-step(fit.model.all)
>         Start:  AIC= 689.1
>         Surv(t, cen) ~ z1 + z2 + z3
>         Error in as.data.frame.default(data) : cannot coerce class
> "function" into a data.frame
>        
> **************************************************************
> **********
> ***************************
>         Thanks a lot!
>        
>         Jia
>        
>         ______________________________________________
>         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
>        
> 
> 
> 
> 
> --
> Ritwik Sinha
> Graduate Student
> Epidemiology and Biostatistics
> Case Western Reserve University
> 
> http://darwin.cwru.edu/~rsinha
> 
>         [[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
> 
> 
>   _____  
> 
> The information transmitted in this message and its 
> attachme...{{dropped}}
> 
> ______________________________________________
> 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
>

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