On Fri, 4 Dec 2009, David Winsemius wrote:
On Dec 4, 2009, at 5:49 PM, Hien Nguyen wrote:
Dear Dr. Winsemius,
Thank you very much for your reply.
I have tried many possible combinations (even with the model of
only 2 predictors) but it produces the same message. With more
than 4000 observations, I think 14 predictors might not be too many.
It is what happens in the factor combinations that concern me. I am
guessing that some of those predictors are factors. You really
should not ask r-help questions without providing better
descriptions of both the outcomes and the predictor variables.
Although my dependent variable (Pin) is not discrete (it ranges
from 0 to 1), I do not think it will create problems to the
estimation but I'm not sure
I would think it _would_ cause problems. As I understand it,
conditional methods create contingency tables. Why are you using an
outcome type that is not consistent with the fundamental regression
assumptions of the clogit function?
I do not get that particular error when I munge the infert dataset
to have case be a random uniform value, but I do get an error.
infert$case <- runif(nrow(infert))
clogit(case~spontaneous+induced+strata(stratum),data=infert)
Error in Surv(rep(1, 248L), case) : Invalid status value
David, I think you were on the right track. I get this:
-----------
clogit(I(case*runif(length(case)))~spontaneous+induced+strata(ifelse(stratum>40,NA,stratum)),data=infert)
Error in fitter(X, Y, strats, offset, init, control, weights =
weights, :
NA/NaN/Inf in foreign function call (arg 6)
In addition: Warning messages:
1: In Surv(rep(1, 248L), I(case * runif(length(case)))) :
Invalid status value, converted to NA
2: In fitter(X, Y, strats, offset, init, control, weights = weights, :
Ran out of iterations and did not converge
------------
which looks pretty much the same as Hien's error msg
So Hien needs to create a logical status value.
Chuck
p.s.
sessionInfo()
R version 2.10.0 (2009-10-26)
i386-pc-mingw32
locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] splines stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] survival_2.35-7
loaded via a namespace (and not attached):
[1] tools_2.10.0
So I certainly would not have proceeded to submit a full analysis
to clogit if I could not get a test case to run under the situation
you propose.
--
David
I have checked the collinearity among predictors and they are all
< 0.5 (which I think is OK). Do you know what else could make this
errors?
Thanks a lot
Hien Nguyen
David Winsemius wrote:
> > On Dec 4, 2009, at 9:22 AM, Hien Nguyen wrote:
> > > Dear R-helpers,
> > > > I am very new to R and trying to run the conditional logit
model using
> > "clogit " command.
> > I have more than 4000 observations in my dataset and try to
predict the
> > dependent variable from 14 independent variables. My command
is as > > follows
> > > > clmtest1 <-
> >
clogit(Pin~Income+Bus+Pop+Urbpro+Health+Student+Grad+NE+NW+NCC+SCC+CH+SE+MRD+strata(IDD),data=clmdata)
> > > > > > However, it produces the following errors:
> > > > Error in fitter(X, Y, strats, offset, init, control,
weights = weights, > > :
> > NA/NaN/Inf in foreign function call (arg 6)
> > In addition: Warning messages:
> > 1: In Surv(rep(1, 4096L), Pinmig) : Invalid status value,
converted to > > NA
> > 2: In fitter(X, Y, strats, offset, init, control, weights =
weights, :
> > Ran out of iterations and did not converge
> > > > I search the error message from R forums but it does not
say anything
> > for Conditional Logit Model.
> > With that many predictors in a small dataset, you may have
created matrix > singularities. Perhaps you created a stratum
where all of the subjects > experience the event and others where
none did so. The coefficients might > be driven to infinities. Try
simplifying the model.
> > > > > > Please check for me what it says and what should I do
to solve it.
> >
David Winsemius, MD
Heritage Laboratories
West Hartford, CT
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