Hello everyone,
I got an issue with calling predict.coxph.penal inside a function.
Regarding the context: My original problem is that I wrote a function that
uses predict.coxph and survfit(model) to predict
a lot of survival-curves using only the basis-curves for the strata (as
delivered by survfit(model) ) and then adapts them with
the predicted risk-scores. Because there are cases where my new data has
strata which didn't exist in the original model I exclude
them, using a Boolean vector inside the function.
I end up with a call like this: predict (coxph_model,
newdata[subscript_vector,] )
This works fine for coxph.model, but when I fit a model with a spline
(class coxph.penal), I get an error:
"Error in `[.data.frame`(newdata, [subscript_vector, ) : object
'[subscript_vector ' not found"
I suppose this is because of NextMethod, but I am not sure how to work
around it. I also read a little bit about all those
matching-and-frame-issues,
But must confess I am not really into it.
I attach a reproducible example.
Any help or suggestions of work-arounds will be appreciated.
Thanks
Julian
> version
_
platform x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, mingw32
status
major 3
minor 0.1
year 2013
month 05
day 16
svn rev 62743
language R
version.string R version 3.0.1 (2013-05-16)
nickname Good Sport
##TEST-DATA
# Create the simplest test data set
test1 <- data.frame(time=c(4,3,1,1,2,2,3),
status=c(1,1,1,0,1,1,0),
x=c(0,2,1,1,1,0,0),
sex=c(0,0,0,0,1,1,1))
# Fit a stratified model
fit1 <- coxph(Surv(time, status) ~ x + strata(sex), test1)
summary(fit1)
#fit stratified wih spline
fit2 <- coxph(Surv(time, status) ~ pspline(x, df=2) + strata(sex), test1)
summary(fit2)
#function to predict within
predicting_function <- function(model, newdata){
subs <-vector(mode='logical', length=nrow(newdata))
subs[1:length(subs)]<- TRUE
ret <- predict (model, newdata=newdata[subs,])
return(ret)
}
predicting_function(fit1, test1) # works
predicting_function(fit2,test1) #doesnt work - Error in
`[.data.frame`(newdata, subs, ) : object 'subs' not found
# probably because of NextMethod
#--------
> traceback()
#12: `[.data.frame`(newdata, subs, )
#11: newdata[subs, ]
#10: is.data.frame(data)
#9: model.frame.default(data = newdata[subs, ], formula = ~pspline(x,
# df = 2) + strata(sex), na.action = function (object, ...)
# object)
#8: model.frame(data = newdata[subs, ], formula = ~pspline(x, df = 2) +
# strata(sex), na.action = function (object, ...)
# object)
#7: eval(expr, envir, enclos)
#6: eval(tcall, parent.frame())
#5: predict.coxph(model, newdata = newdata[subs, ])
#4: NextMethod("predict", object, ...)
#3: predict.coxph.penal(model, newdata = newdata[subs, ])
#2: predict(model, newdata = newdata[subs, ]) at #5
#1: predicting_function(fit2, test1)
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