CODEWITHSUNDEEP
rpredictsurvival
Nick O
Nick O

Reputation: 21

Cannot use coxph.predict for type="expected" with newdata in Competing Risks context

I'm using a Cox Proportional Hazards (survival::coxph) model in a competing risks context- i.e. multiple event types with one endpoint for each observation. I'm having a hard time using the coxph.predict function to show an estimate of expected number of events given a supplied set of covariates and follow-up time. Here is an example using the mgus2 dataset in the survival package:

library(survival)

#Modify data so each subject transitions only once to a state.
crdata <- mgus2
crdata$etime <- pmin(crdata$ptime, crdata$futime)
crdata$event <- ifelse(crdata$pstat==1, 1, 2*crdata$death)
crdata$event <- factor(crdata$event, 0:2, c("censor", "PCM", "death"))

cfit <- coxph(Surv(etime, event) ~ I(age/10) + sex + mspike,
              id = id, crdata)

Once I fit a model, and create a "newdata" data frame, R throws an error.

I tried using a from-scratch dataframe but this results in an error suggesting that the column size or the number of rows does not mesh:

#providing both follow-up time and covariates
nd=data.frame(etime=81 ,sex= "M", age=60, mspike=1.2)
predict(cfit, newdata=nd ,type="expected")

> Data is not the same size as it was in the original fit

I get the same issue Using model.frame when extracting the same data.frame used fitting the model.

nd=model.frame(cfit)
predict(cfit,newdata=nd,type="expected")

> Data is not the same size as it was in the original fit

This results in the same error. Trying to use the original data frame to make predictions doesn't work either:

nd=crdata[1,]
predict(cfit,newdata=nd,type="expected")

> Data is not the same size as it was in the original fit

I'm wondering what I'm missing here. Thanks in advance!

Upvotes: 1

Views: 497

Answers (1)

Nick O
Nick O

Reputation: 21

I've updated my survival package from 2.7 to 3.1 and the error thrown states that "expected" predict type is not available for multistate coxph.

> predict(fit,type="expected",newdata=newdat)
Error in predict.coxphms(fit, type = "expected", newdata = newdat) : 
  predict method not yet available for multistate coxph

Upvotes: 0

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