Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----setup, warning = FALSE---------------------------------------------------
library(BayesSurvival)
library(survival)
library(ggplot2)
## -----------------------------------------------------------------------------
cancer$status[cancer$status == 1] <- 0 #censored
cancer$status[cancer$status == 2] <- 1 #died
table(cancer$status)
## -----------------------------------------------------------------------------
res <- BayesSurv(df = cancer, #our data frame
time = "time", #name of column with survival/censoring times
event = "status", #name of column with status indicator
prior = "Dependent", #use dependent Gamma prior
)
## ---- warning = FALSE, fig.width = 5------------------------------------------
PlotBayesSurv(bayes.surv.object = res,
object = "survival")
## ---- warning = FALSE, fig.width = 5------------------------------------------
PlotBayesSurv(bayes.surv.object = res,
object = "survival",
color = "orange",
plot.title = "Survival function")
## ---- warning = FALSE, fig.width = 5------------------------------------------
gg <- PlotBayesSurv(bayes.surv.object = res,
object = "survival")
km <- survfit( Surv(time, status) ~ 1, data = cancer ) #Kaplan-Meier
df.km <- data.frame(t = km$time, km = km$surv)
gg <- gg + geom_line(data = df.km, aes(x = t, y = km), colour = "black", size = 1, lty = 6)
gg <- gg + labs(title = "With Kaplan-Meier + CI's")
gg
## ---- warning = FALSE, fig.width = 5------------------------------------------
PlotBayesSurv(bayes.surv.object = res,
object = "cumhaz",
plot.title = "Cumulative hazard")
## ---- warning = FALSE, fig.width = 5------------------------------------------
PlotBayesSurv(bayes.surv.object = res,
object = "hazard",
plot.title = "Hazard")
## -----------------------------------------------------------------------------
res <- BayesSurv(df = cancer, #our data frame
time = "time", #name of column with survival/censoring times
event = "status", #name of column with status indicator
prior = "Independent", #use independent Gamma prior
)
## ---- warning = FALSE, fig.width = 5------------------------------------------
PlotBayesSurv(bayes.surv.object = res,
object = "survival",
plot.title = "Survival")
PlotBayesSurv(bayes.surv.object = res,
object = "cumhaz",
plot.title = "Cumulative hazard")
PlotBayesSurv(bayes.surv.object = res,
object = "hazard",
plot.title = "Hazard")
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