knitr::opts_chunk$set( collapse = TRUE, comment = "#>" )
library(dplyr) library(ggplot2) library(survival) library(survParamSim) set.seed(12345)
Fit model with
Before running a parametric survival simulation, you need to fit a model to your data using
survreg() function of
In this vignette, we will be using
colon dataset available in
survival package, where the treatment effect of adjuvant Levamisole+5-FU for colon cancer over placebo is evaluated.
First, we load the data and do some data wrangling.
# 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))
Generating Kaplan-Meier curves for visually checking the data.
The second plot is looking at how many censoring we have over time.
Looks like we have a fairly uniform censoring between 1800 to 3000 days.
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)
Next we fit a lognormal parametric model for the data.
Here we are using
depth as additional covariates in addition to treatment (
You can see that all of the factor has strong association with the outcome.
fit.colon <- survreg(Surv(time, status) ~ rx + node4 + depth, data = colon2, dist = "lognormal") summary(fit.colon)
surv_param_sim() is the main function of the package that takes
survreg object as described above.
It also require you to supply
newdata, which is required even if it is not new - i.e. the same data was used for both
What it does is:
- Re-sample all the coefficients in the parametric survival model from variance-covariance matrix for
- Perform survival time for all subjects in
newdatawith the corresponding covariates, using one of the resampled coefficients. Also generate censoring time according to
censor.dur(if not NULL), and replace the simulated survival time above if censoring time is earlier.
- Repeat the steps 2. for
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)
After the simulation is performed, you can either extract raw simulation results or further calculate Kaplan-Meier estimates or hazard ratio of treatment effect, as you see when you type
sim in the console.
Survival time profile
To calculate survival curves for each simulated dataset,
calc_km_pi() can be used on the simulated object above.
km.pi <- calc_km_pi(sim, trt = "rx") km.pi
Similar to the raw simulated object, you can have a few options for further processing - one of them is plotting prediction intervals with
km.pi plot_km_pi(km.pi) + theme(legend.position = "bottom") + labs(y = "Recurrence free rate") + expand_limits(y = 0)
Plot can also be made for subgroups.
You can see that prediction interval is wide for (depth: 1 & nodes4: 1) group, mainly due to small number of subjects
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)
Hazard ratios (HRs)
To calculate prediction intervals of HRs,
calc_hr_pi() can be used on the simulated object above.
Here I only generated subgroups based on "depth", since the very small N in (depth: 1 & nodes4: 1) can cause issue with calculating HRs.
hr.pi <- calc_hr_pi(sim, trt = "rx", group = c("depth")) hr.pi plot_hr_pi(hr.pi)