On Fri, 16 Jun 2006, Frede Aakmann Tøgersen wrote:
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.
Exactly: 'step' is in the stats namespace and so object 'all' in the base
namespace is preferred to the object you have in the user workspace.
You are advised not to use the names of base R objects for other purposes.
Use conflicts() to find out if you have done so.
(Here R could have figured out that a function was not appropriate, and it
is smarter about that in pre-2.4.0.)
Med venlig hilsen
Frede Aakmann Tøgersen
-----Oprindelig meddelelse-----
Fra: [EMAIL PROTECTED]
[mailto:[EMAIL PROTECTED] På vegne af Li, Jia
Sendt: 15. juni 2006 17:45
Til: Hong Ooi; [email protected]
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:[EMAIL PROTECTED]
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: [EMAIL PROTECTED] on behalf of Li, Jia
Sent: Thu 15/06/2006 11:52 PM
To: [email protected]; [EMAIL PROTECTED]
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:[EMAIL PROTECTED]
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 < [EMAIL PROTECTED] <mailto:[EMAIL PROTECTED]> >
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
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--
Ritwik Sinha
Graduate Student
Epidemiology and Biostatistics
Case Western Reserve University
http://darwin.cwru.edu/~rsinha
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