predict.ah.2ph: Prediction Based on the Additive Hazards Model Fitted from...

In addhazard: Fit Additive Hazards Models for Survival Analysis

Description

This function predicts a subject's overall hazard rates at given time points based on this subject's covariate values. The prediction function is an object from ah.2ph. The estimating procedures follow Hu (2014).

Usage

## S3 method for class 'ah.2ph'
predict(object, newdata, newtime, ...)

Arguments

object	an object of class inhering from 'ah.2ph'.
newdata	a dataframe of an individual's predictors.
newtime	a given sequence of time points at which the prediction is performed.
...	further arguments passed to or from other methods.

Value

A dataframe including the given time points, predicted hazards, their standard errors, their variances, the phase I component of the variance for predicted hazards and the phase II component of the variance.

References

Jie Hu (2014) A Z-estimation System for Two-phase Sampling with Applications to Additive Hazards Models and Epidemiologic Studies. Dissertation, University of Washington.

See Also

ah.2ph for fitting the additive hazards model with two-phase

Examples

library(survival)
### load data
nwts <- nwtsco[1:100,]

### create strata based on  institutional histology and disease status
nwts$strt <- 1+nwts$instit
### add a stratum containing all (relapsed) cases
nwts$strt[nwts$relaps==1] <- 3

### assign phase II subsampling probabilities
### oversample unfavorable histology (instit =1) and cases
### Pi = 0.5 for instit =0, Pi =1 for instit =1 and relaps =1
nwts$Pi<-  0.5 * (nwts$strt == 1) + 1 * (nwts$strt == 2) + 1 * (nwts$strt == 3)

### generate phase II sampling indicators
N <- dim(nwts)[1]
nwts$in.ph2 <-  rbinom(N, 1, nwts$Pi)

### fit an additive hazards model to  two-phase sampling data without calibration
fit1 <- ah.2ph(Surv(trel,relaps) ~ age + histol,
               data = nwts,
               ties = FALSE,
               R = in.ph2, Pi = Pi,
               robust = FALSE)

###  input the new data for prediction
newdata <- nwtsco[101,]
###  based on the fitted model fit1, perform prediction at time points t =3 and t= 5
predict(fit1, newdata, newtime = c(3,5))

### fit an additve hazards model to  two-phase sampling data with calibration
### The calibration variable is stage
fit2 <- ah.2ph(Surv(trel,relaps) ~ age + histol, data = nwts, R = in.ph2, Pi = Pi,
                                   ties = FALSE, robust = FALSE, calibration.variables = "stage")

### based on the fitted model fit2, perform prediction at time points t =3 and t= 5
predict(fit2, newdata, newtime = c(3,5))

## Not run: 
### The calibration variable is stage, when set robust = TRUE
fit3 <- ah.2ph(Surv(trel,relaps) ~ age + histol, data = nwts, R = in.ph2, Pi = Pi,
                                   ties = FALSE, robust = TRUE, calibration.variables = "stage")

### based on the fitted model fit2, perform prediction at time points t =3 and t= 5
predict(fit3, newdata, newtime = c(3,5))

## End(Not run)

addhazard documentation built on May 2, 2019, 9:40 a.m.