Nothing
## ---- include = FALSE----------------------------------------------------
knitr::opts_chunk$set(collapse = TRUE, warning = FALSE, message = FALSE,
fig.height = 5, fig.width = 10,
dpi = 200)
library(knitr)
library(cr17)
library(dplyr)
## ---- echo = FALSE-------------------------------------------------------
sampleTable <- data.frame('Patient' = numeric(5),
'Time' = numeric(5),
'Status' = numeric(5))
sampleTable$Patient <- 1:5
sampleTable$Time <- c(5,1,4,5,2)
sampleTable$Status <- c(1,0,1,2,2)
kable(sampleTable)
## ------------------------------------------------------------------------
survivalCurves <- fitSurvival(time = LUAD$time,
risk = LUAD$event,
group = LUAD$gender,
cens = "alive")
## ------------------------------------------------------------------------
names(survivalCurves)
## ------------------------------------------------------------------------
SC <- survivalCurves$death[c("time",
"n.risk",
"n.event",
"n.censor",
"surv",
"strata",
"std.err",
"lower",
"upper")]
SC <- as.data.frame(SC)
SC <- filter(SC, strata == "male")
kable(head(SC, n = 10))
## ---- out.width=700, fig.align='center'----------------------------------
plotSurvival(fit = survivalCurves,
target = 1500,
ggtheme = theme_gray(),
legendtitle = "Gender")
## ------------------------------------------------------------------------
testSurvival(time = LUAD$time,
risk = LUAD$event,
group = LUAD$gender,
cens = "alive",
rho = 0)
## ------------------------------------------------------------------------
coxModel <- fitCox(time = LUAD$time,
risk = LUAD$event,
group = LUAD$gender,
cens = "alive",
conf.int = 0.95)
## ------------------------------------------------------------------------
names(coxModel)
## ------------------------------------------------------------------------
coxModel$death$coefficients
## ------------------------------------------------------------------------
kable(testCox(fitCox = coxModel))
## ------------------------------------------------------------------------
cuminc <- fitCuminc(time = LUAD$time,
risk = LUAD$event,
group = LUAD$gender,
cens = "alive")
## ------------------------------------------------------------------------
names(cuminc)
## ------------------------------------------------------------------------
femaleDeathCuminc <- cuminc[["female death"]]
femaleDeathCuminc <- as.data.frame(femaleDeathCuminc)
kable(head(femaleDeathCuminc))
## ---- out.width=700, fig.align='center'----------------------------------
plotCuminc(ci = cuminc,
cens = "alive",
target = 1500,
ggtheme = theme_gray(),
legendtitle = "Gender")
## ------------------------------------------------------------------------
testCuminc(cuminc)
## ------------------------------------------------------------------------
reg <- fitReg(time = LUAD$time,
risk = LUAD$event,
group = LUAD$gender,
cens = "alive")
## ------------------------------------------------------------------------
reg$death$coef
## ------------------------------------------------------------------------
testReg(reg)
## ---- eval=FALSE---------------------------------------------------------
# riskTab(time = LUAD$time,
# risk = LUAD$event,
# group = LUAD$gender,
# cens = "alive",
# title = "Number at risk")
#
## ---- eval=FALSE---------------------------------------------------------
# eventTab(time = LUAD$time,
# risk = LUAD$event,
# group = LUAD$gender,
# cens = "alive",
# title = "Number of events")
#
## ---- eval = FALSE-------------------------------------------------------
# summarizeCR(time = LUAD$time,
# risk = LUAD$event,
# group = LUAD$gender, cens = "alive")
## ---- eval = FALSE-------------------------------------------------------
# summarizeCR(time = LUAD$time,
# risk = LUAD$event,
# group = LUAD$gender,
# cens = "alive",
# rho = 1,
# target = 800,
# type = "kaplan-meier",
# ggtheme = theme_gray(),
# titleSurv = "Survival analysis",
# titleCuminc = "Competing risks models",
# xtitle = "Days",
# ytitleSurv = "Survival curves",
# ytitleCuminc = "Cumulative incidence functions",
# legendtitle = "Gender")
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