Nothing
## ---- echo = FALSE, message = FALSE-------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----setup--------------------------------------------------------------------
library(WR)
head(non_ischemic)
## -----------------------------------------------------------------------------
colnames(non_ischemic)[4:16]=c(
"Training vs Usual","Age (year)","Male vs Female","Black vs White",
"Other vs White", "BMI","LVEF","Hypertension","COPD","Diabetes",
"ACE Inhibitor","Beta Blocker", "Smoker"
)
## -----------------------------------------------------------------------------
# sample size
length(unique(non_ischemic$ID))
# median length of follow-up time
median(non_ischemic$time[non_ischemic$status<2])/30.5
## -----------------------------------------------------------------------------
# get the number of rows and number of covariates.
nr <- nrow(non_ischemic)
p <- ncol(non_ischemic)-3
# extract ID, time, status and covariates matrix Z from the data.
# note that: ID, time and status should be column vector.
# covariatesZ should be (nr, p) matrix.
ID <- non_ischemic[,"ID"]
time <- non_ischemic[,"time"]
status <- non_ischemic[,"status"]
Z <- as.matrix(non_ischemic[,4:(3+p)],nr,p)
# pass the parameters into the function
pwreg.obj <- pwreg(time=time,status=status,Z=Z,ID=ID)
print(pwreg.obj)
## -----------------------------------------------------------------------------
#extract estimates of (\beta_4,\beta_5)
beta <- matrix(pwreg.obj$beta[4:5])
#extract estimated covariance matrix for (\beta_4,\beta_5)
Sigma <- pwreg.obj$Var[4:5,4:5]
#compute chisq statistic in quadratic form
chistats <- t(beta) %*% solve(Sigma) %*% beta
#compare the Wald statistic with the reference
# distribution of chisq(2) to obtain the p-value
1 - pchisq(chistats, df=2)
## ---- fig.height = 8, fig.width=7.5-------------------------------------------
score.obj <- score.proc(pwreg.obj)
print(score.obj)
oldpar <- par(mfrow = par("mfrow"))
par(mfrow = c(4,4))
for(i in c(1:13)){
plot(score.obj, k = i)
}
par(oldpar)
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