I keep getting the same error in my survival analysis. I have access to a
very large database but am just using small subsets to get some results. In
this particular subset there is 50 explanatory variables(both factors of
many levels and covariates) and 117 data pieces with some of the data being
censored. I am using the stepAIC command to find my model. My initial
model is built from all variables that are solely significant in the cox PH
model. Well, the stepAIC command works for this particular dataset but it
crashes when I bootstrap and I come up with a different model set. I get
another dataset in the following way:
samp = sample(1:117, 117, replace =T)
newdataset = dataset[samp,]
The error I get is
Error in fitter(X, Y, strats, offset, init, control, weights =
weights, :
NA/NaN/Inf in foreign function call (arg 6)
The dataset that is inputted into the model is itself rid from all NA
values. The initial model put into the stepAIC function is comprised of
about 20 different variables. When solely modeled by a coxph using:
coxph(Surv(time, censored)~ var1, data = dataset)
a satisfactory result is ouputted. But when running an additive model with
many more variables, I get something to the following effect:
coef exp(coef) se(coef) z p
var1Unknown 0.000 1.00e+00 0.0000 NaN NaN
varlevel2 -3.242 3.91e-02 2.5701 -1.262 2.1e-01
var2level3 4.730 1.13e+02 3.7318 1.267 2.1e-01
varr2level4 0.314 1.37e+00 2.9936 0.105 9.2e-01
var2level5 0.000 1.00e+00 0.0000 NaN NaN
This is just cut from the output. Even though it seems the data I am working
with is not the best, I am still confused as to why the stepAIC function is
crashing. It appears to be with the variables that have an NaN for their
p-values. But when the variables are modeled separately the model produces
nice results.
thanks for any help
