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### R code from vignette source 'Ch_survival_analysis.Rnw'
###################################################
### code chunk number 1: setup
###################################################
rm(list = ls())
s <- search()[-1]
s <- s[-match(c("package:base", "package:stats", "package:graphics", "package:grDevices",
"package:utils", "package:datasets", "package:methods", "Autoloads"), s)]
if (length(s) > 0) sapply(s, detach, character.only = TRUE)
if (!file.exists("tables")) dir.create("tables")
if (!file.exists("figures")) dir.create("figures")
set.seed(290875)
options(prompt = "R> ", continue = "+ ",
width = 63, # digits = 4,
show.signif.stars = FALSE,
SweaveHooks = list(leftpar = function()
par(mai = par("mai") * c(1, 1.05, 1, 1)),
bigleftpar = function()
par(mai = par("mai") * c(1, 1.7, 1, 1))))
HSAURpkg <- require("HSAUR2")
if (!HSAURpkg) stop("cannot load package ", sQuote("HSAUR2"))
rm(HSAURpkg)
### </FIXME> hm, R-2.4.0 --vanilla seems to need this
a <- Sys.setlocale("LC_ALL", "C")
### </FIXME>
book <- TRUE
refs <- cbind(c("AItR", "DAGD", "SI", "CI", "ANOVA", "MLR", "GLM",
"DE", "RP", "GAM", "SA", "ALDI", "ALDII", "SIMC", "MA", "PCA",
"MDS", "CA"), 1:18)
ch <- function(x) {
ch <- refs[which(refs[,1] == x),]
if (book) {
return(paste("Chapter~\\\\ref{", ch[1], "}", sep = ""))
} else {
return(paste("Chapter~", ch[2], sep = ""))
}
}
if (file.exists("deparse.R"))
source("deparse.R")
setHook(packageEvent("lattice", "attach"), function(...) {
lattice.options(default.theme =
function()
standard.theme("pdf", color = FALSE))
})
###################################################
### code chunk number 2: singlebook
###################################################
book <- FALSE
###################################################
### code chunk number 3: SA-setup
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x <- library("survival")
x <- library("coin")
x <- library("party")
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### code chunk number 4: SA-glioma-KM
###################################################
data("glioma", package = "coin")
library("survival")
layout(matrix(1:2, ncol = 2))
g3 <- subset(glioma, histology == "Grade3")
plot(survfit(Surv(time, event) ~ group, data = g3),
main = "Grade III Glioma", lty = c(2, 1),
ylab = "Probability", xlab = "Survival Time in Month",
legend.text = c("Control", "Treated"),
legend.bty = "n")
g4 <- subset(glioma, histology == "GBM")
plot(survfit(Surv(time, event) ~ group, data = g4),
main = "Grade IV Glioma", ylab = "Probability",
lty = c(2, 1), xlab = "Survival Time in Month",
xlim = c(0, max(glioma$time) * 1.05))
###################################################
### code chunk number 5: SA-glioma-logrank
###################################################
survdiff(Surv(time, event) ~ group, data = g3)
###################################################
### code chunk number 6: SA-glioma-exact
###################################################
library("coin")
logrank_test(Surv(time, event) ~ group, data = g3,
distribution = "exact")
###################################################
### code chunk number 7: SA-glioma-g4
###################################################
logrank_test(Surv(time, event) ~ group, data = g4,
distribution = "exact")
###################################################
### code chunk number 8: SA-glioma-hist
###################################################
logrank_test(Surv(time, event) ~ group | histology,
data = glioma, distribution = approximate(B = 10000))
###################################################
### code chunk number 9: SA-GBSG2-plot
###################################################
data("GBSG2", package = "TH.data")
plot(survfit(Surv(time, cens) ~ horTh, data = GBSG2),
lty = 1:2, mark.time = FALSE, ylab = "Probability",
xlab = "Survival Time in Days")
legend(250, 0.2, legend = c("yes", "no"), lty = c(2, 1),
title = "Hormonal Therapy", bty = "n")
###################################################
### code chunk number 10: SA-GBSG2-coxph
###################################################
GBSG2_coxph <- coxph(Surv(time, cens) ~ ., data = GBSG2)
###################################################
### code chunk number 11: SA-GBSG2-coxph-ci
###################################################
ci <- confint(GBSG2_coxph)
exp(cbind(coef(GBSG2_coxph), ci))["horThyes",]
###################################################
### code chunk number 12: GBSG2-coxph-summary
###################################################
summary(GBSG2_coxph)
###################################################
### code chunk number 13: SA-GBSG2-zph
###################################################
GBSG2_zph <- cox.zph(GBSG2_coxph)
GBSG2_zph
###################################################
### code chunk number 14: SA-GBSG2-zph-plot
###################################################
plot(GBSG2_zph, var = "age")
###################################################
### code chunk number 15: SA-GBSG2-Martingal
###################################################
layout(matrix(1:3, ncol = 3))
res <- residuals(GBSG2_coxph)
plot(res ~ age, data = GBSG2, ylim = c(-2.5, 1.5),
pch = ".", ylab = "Martingale Residuals")
abline(h = 0, lty = 3)
plot(res ~ pnodes, data = GBSG2, ylim = c(-2.5, 1.5),
pch = ".", ylab = "")
abline(h = 0, lty = 3)
plot(res ~ log(progrec), data = GBSG2, ylim = c(-2.5, 1.5),
pch = ".", ylab = "")
abline(h = 0, lty = 3)
###################################################
### code chunk number 16: SA-GBSG2-ctree
###################################################
GBSG2_ctree <- ctree(Surv(time, cens) ~ ., data = GBSG2)
###################################################
### code chunk number 17: SA-GBSG2-ctree-plot
###################################################
plot(GBSG2_ctree)
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