[R] Regression models w/ splines

John Fieberg John.Fieberg at dnr.state.mn.us
Fri Apr 9 22:16:34 CEST 2004

Hi - I am fitting various Cox PH models with spline predictors.  After
fitting the model, I would like to use termplot() to examine the
functional form of the fitted model (e.g., to obtain a plot of the
relative risk (or log r.r.) versus the predictors). 

When there is only 1 predictor in the model, termplot returns a "?". 
In this case, I have not been able to figure out how to create the
desired plot.  Otherwise,termplot is easy to use. 



fit1<-coxph(Surv(time,status)~ns(bili,4)+ns(age,4), data=pbc)
fit2<-coxph(Surv(time,status)~ns(bili,4), data=pbc)

termplot(fit1) # returns two plots (one for bili and one for age)
termplot(fit2) # returns a "?" prompt

Does anyone have any suggestions for obtaining a plot of the log
relative risk as a function of bili in the second example (or for this
type of model in general)?

On a similar note, I would like to be able to obtain predicted values
for "new" subjects.  I tried using:

predict(fit2,newdata=temp, safe=T)

This gives the following error message:
Error in qr(t(const)) : NA/NaN/Inf in foreign function call (arg 1)

Is there a simple method available for obtaining predicted values for
new subjects when using these types of models?

I have encountered similar problems when trying to use smoothing
splines w/ the above examples (i.e., 'pspline' in the survival package).
 I am currently using R version 1.8.1 for windows. Any help would be
greatly appreciated!


John Fieberg, Ph.D.
Wildlife Biometrician, MN DNR
5463-C W. Broadway
Forest Lake, MN 55434
Phone: (651) 296-2704

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