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data-examples.R
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data-examples.R
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# install package CPsurv from GitHub
devtools::install_github("stefkruegel/CPsurv")
library(CPsurv)
################################################################################
### Data set 1: Critically ill patients
################################################################################
load("dataset1.RData")
data1result <- list()
### estimate changepoint (raw estimate)
# 10 days grid length
data1result$raw10 <- cpsurv(dataset1$time, dataset1$event, intwd = 10, cpmax = 300,
censoring = "type1", censpoint = 730,
boot.ci = TRUE, seed = 20160501, cores = 6)
summary(data1result$raw10)
# 20 days grid length
data1result$raw20 <- cpsurv(dataset1$time, dataset1$event, intwd = 20, cpmax = 300,
censoring = "type1", censpoint = 730,
boot.ci = TRUE, seed = 20160501, cores = 6)
summary(data1result$raw20)
### estimate changepoint with nonparametric median bias correction
# (note extended runtime because of bias correction:
# about 30 minutes using 6 cores, Intel i7 processor)
# 10 days grid length
data1result$mbc10 <- cpsurv(dataset1$time, dataset1$event, intwd = 10, cpmax = 300,
censoring = "type1", censpoint = 730, biascorrect = TRUE,
boot.ci = TRUE, opt.start = c(0.8, 2500), seed = 20160501,
cores = 6)
summary(data1result$mbc10)
# 20 days grid length
data1result$mbc20 <- cpsurv(dataset1$time, dataset1$event, intwd = 20, cpmax = 300,
censoring = "type1", censpoint = 730, biascorrect = TRUE,
boot.ci = TRUE, opt.start = c(0.8, 2500), seed = 20160501,
cores = 6)
summary(data1result$mbc20)
# estimate of beta (expectation of p-values for intervals above the changepoint)
data1result$raw10$pv.mean
data1result$raw20$pv.mean
################################################################################
### Data set 2: Patients after severe trauma injury
################################################################################
load("dataset2.RData")
data2result <- list()
### estimate changepoint (raw estimate)
# 10 days grid length
data2result$raw10 <- cpsurv(dataset2$time, dataset2$event, intwd = 10, cpmax = 700,
boot.ci = TRUE, seed = 20160501, cores = 6)
summary(data2result$raw10)
# 20 days grid length
data2result$raw20 <- cpsurv(dataset2$time, dataset2$event, intwd = 20, cpmax = 700,
boot.ci = TRUE, seed = 20160501, cores = 6)
summary(data2result$raw20)
### estimate changepoint with nonparametric median bias correction
# 10 days grid length
data2result$mbc10 <- cpsurv(dataset2$time, dataset2$event, intwd = 10, cpmax = 700,
biascorrect = TRUE, boot.ci = TRUE,
opt.start = c(0.2, 200000000), seed = 20160501,
cores = 6)
summary(data2result$mbc10)
# 20 days grid length
data2result$mbc20 <- cpsurv(dataset2$time, dataset2$event, intwd = 20, cpmax = 700,
biascorrect = TRUE, boot.ci = TRUE,
opt.start = c(0.2, 200000000), seed = 20160501,
cores = 6)
summary(data2result$mbc20)
# estimate of beta (expectation of p-values for intervals above the changepoint)
data2result$raw10$pv.mean
data2result$raw20$pv.mean
################################################################################
### Data set 3: Postoperative survival of patients after a partial hepatectomy
################################################################################
load("dataset3.RData")
data3result <- list()
### estimate changepoint (raw estimate)
# 10 days grid length
data3result$raw10 <- cpsurv(dataset3$time, dataset3$event, intwd = 10, cpmax = 200,
boot.ci = TRUE, seed = 20160501, cores = 6)
summary(data3result$raw10)
# 20 days grid length
data3result$raw20 <- cpsurv(dataset3$time, dataset3$event, intwd = 20, cpmax = 200,
boot.ci = TRUE, seed = 20160501, cores = 6)
summary(data3result$raw20)
### estimate changepoint with nonparametric median bias correction
# 10 days grid length
data3result$mbc10 <- cpsurv(dataset3$time, dataset3$event, intwd = 10, cpmax = 200,
biascorrect = TRUE, boot.ci = TRUE,
opt.start = c(0.8, 2500), seed = 20160501, cores = 6)
summary(data3result$mbc10)
# 20 days grid length
data3result$mbc20 <- cpsurv(dataset3$time, dataset3$event, intwd = 20, cpmax = 200,
biascorrect = TRUE, boot.ci = TRUE,
opt.start = c(0.8, 2500), seed = 20160501, cores = 6)
summary(data3result$mbc20)
# estimate of beta (expectation of p-values for intervals above the changepoint)
data3result$raw10$pv.mean
data3result$raw20$pv.mean