PPD {SemiCompRisks} | R Documentation |
Function to predict the joint probability involving two event times in Bayesian illness-death models
Description
PPD
is a function to predict the joint probability involving two event times in Bayesian illness-death models.
Usage
PPD(fit, x1, x2, x3, t1, t2)
Arguments
fit |
an object of class |
x1 |
a vector of covariates for |
x2 |
a vector of covariates for |
x3 |
a vector of covariates for |
t1 |
time to non-terminal event for which the joint probability is calculated. |
t2 |
time to terminal event for which the joint probability is calculated. |
Details
Using the posterior predictive density, given (x_1
, x_2
, x_3
), one can predict any joint probability involving the two event times such as P(T_1<t_1, T_2<t_2| x_1, x_2, x_3)
for 0<t_1\le t_2
and P(T_1=\infty, T_2<t_2| x_1, x_2, x_3)
for t_2>0
.
Value
F_u |
Predicted |
F_l |
Predicted |
Author(s)
Kyu Ha Lee and Sebastien Haneuse
Maintainer: Kyu Ha Lee <klee15239@gmail.com>
References
Lee, K. H., Haneuse, S., Schrag, D., and Dominici, F. (2015),
Bayesian semiparametric analysis of semicompeting risks data:
investigating hospital readmission after a pancreatic cancer diagnosis, Journal of the Royal Statistical Society: Series C, 64, 2, 253-273.
See Also
Examples
## Not run:
# loading a data set
data(scrData)
id=scrData$cluster
form <- Formula(time1 + event1 | time2 + event2 ~ x1 + x2 | x1 + x2 | x1 + x2)
#####################
## Hyperparameters ##
#####################
## Subject-specific frailty variance component
## - prior parameters for 1/theta
##
theta.ab <- c(0.7, 0.7)
## PEM baseline hazard function
##
PEM.ab1 <- c(0.7, 0.7) # prior parameters for 1/sigma_1^2
PEM.ab2 <- c(0.7, 0.7) # prior parameters for 1/sigma_2^2
PEM.ab3 <- c(0.7, 0.7) # prior parameters for 1/sigma_3^2
##
PEM.alpha1 <- 10 # prior parameters for K1
PEM.alpha2 <- 10 # prior parameters for K2
PEM.alpha3 <- 10 # prior parameters for K3
##
hyperParams <- list(theta=theta.ab,
PEM=list(PEM.ab1=PEM.ab1, PEM.ab2=PEM.ab2, PEM.ab3=PEM.ab3,
PEM.alpha1=PEM.alpha1, PEM.alpha2=PEM.alpha2,
PEM.alpha3=PEM.alpha3))
###################
## MCMC SETTINGS ##
###################
## Setting for the overall run
##
numReps <- 2000
thin <- 10
burninPerc <- 0.5
## Settings for storage
##
nGam_save <- 0
## Tuning parameters for specific updates
##
## - those common to all models
mhProp_theta_var <- 0.05
##
## - those specific to the Weibull specification of the baseline hazard functions
mhProp_alphag_var <- c(0.01, 0.01, 0.01)
##
## - those specific to the PEM specification of the baseline hazard functions
Cg <- c(0.2, 0.2, 0.2)
delPertg <- c(0.5, 0.5, 0.5)
rj.scheme <- 1
Kg_max <- c(50, 50, 50)
sg_max <- c(max(scrData$time1[scrData$event1 == 1]),
max(scrData$time2[scrData$event1 == 0 & scrData$event2 == 1]),
max(scrData$time2[scrData$event1 == 1 & scrData$event2 == 1]))
time_lambda1 <- seq(1, sg_max[1], 1)
time_lambda2 <- seq(1, sg_max[2], 1)
time_lambda3 <- seq(1, sg_max[3], 1)
##
mcmc.PEM <- list(run=list(numReps=numReps, thin=thin, burninPerc=burninPerc),
storage=list(nGam_save=nGam_save),
tuning=list(mhProp_theta_var=mhProp_theta_var,
Cg=Cg, delPertg=delPertg,
rj.scheme=rj.scheme, Kg_max=Kg_max,
time_lambda1=time_lambda1, time_lambda2=time_lambda2,
time_lambda3=time_lambda3))
##
myModel <- c("semi-Markov", "PEM")
myPath <- "Output/02-Results-PEM/"
startValues <- initiate.startValues_HReg(form, scrData, model=myModel, nChain=2)
##
fit_PEM <- BayesID_HReg(form, scrData, id=NULL, model=myModel,
hyperParams, startValues, mcmc.PEM, path=myPath)
PPD(fit_PEM, x1=c(1,1), x2=c(1,1), x3=c(1,1), t1=3, t2=6)
## End(Not run)