Nothing
## ---- include = FALSE---------------------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----setup--------------------------------------------------------------------
library(dplyr)
library(ggplot2)
library(survival)
library(survParamSim)
set.seed(12345)
## ----prep---------------------------------------------------------------------
# ref for dataset https://vincentarelbundock.github.io/Rdatasets/doc/survival/colon.html
colon2 <-
as_tibble(colon) %>%
# recurrence only and not including Lev alone arm
filter(rx != "Lev",
etype == 1) %>%
# Same definition as Lin et al, 1994
mutate(rx = factor(rx, levels = c("Obs", "Lev+5FU")),
depth = as.numeric(extent <= 2))
## ----plot_raw_data------------------------------------------------------------
survfit.colon <- survfit(Surv(time, status) ~ rx, data = colon2)
survminer::ggsurvplot(survfit.colon)
survfit.colon.censor <- survfit(Surv(time, 1-status) ~ rx, data = colon2)
survminer::ggsurvplot(survfit.colon.censor)
## ----fit----------------------------------------------------------------------
fit.colon <- survreg(Surv(time, status) ~ rx + node4 + depth,
data = colon2, dist = "lognormal")
summary(fit.colon)
## ----sim----------------------------------------------------------------------
sim <-
surv_param_sim(object = fit.colon, newdata = colon2,
# Simulate censoring according to the plot above
censor.dur = c(1800, 3000),
# Simulate only 100 times to make the example go fast
n.rep = 100)
## ----simout-------------------------------------------------------------------
sim
## ----km_pi_calc---------------------------------------------------------------
km.pi <- calc_km_pi(sim, trt = "rx")
km.pi
## ----km_pi_plot---------------------------------------------------------------
plot_km_pi(km.pi) +
theme(legend.position = "bottom") +
labs(y = "Recurrence free rate") +
expand_limits(y = 0)
## ----km_pi_table--------------------------------------------------------------
extract_medsurv_pi(km.pi)
## ----km_pi_group--------------------------------------------------------------
km.pi <- calc_km_pi(sim, trt = "rx", group = c("node4", "depth"))
plot_km_pi(km.pi) +
theme(legend.position = "bottom") +
labs(y = "Recurrence free rate") +
expand_limits(y = 0)
## ----hr_pi--------------------------------------------------------------------
hr.pi <- calc_hr_pi(sim, trt = "rx", group = c("depth"))
hr.pi
plot_hr_pi(hr.pi)
## ----hr_pi_table--------------------------------------------------------------
extract_hr_pi(hr.pi)
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