Plot general survival models

Usage

# S3 method for class 'surv_object'
plot(
  x,
  times = seq.int(0, 30),
  type = c("surv", "prob"),
  psa,
  Nrep = 100,
  join_opts = list(join_col = "red", join_pch = 20, join_size = 3),
  ...
)

Arguments

x: a survival object of class surv_aft, surv_add_haz, surv_ph, surv_po, surv_model, surv_pooled, or surv_projection.
times: Times at which to evaluate and plot the survival object.
type: either surv (the default) or prob, depending on whether you want to plot survival from the start or conditional probabilities.
psa: a define_psa object
Nrep: The number of replications to estimate the variability of x
join_opts: A list of 3 graphical parameters for points at which different survival functions are joined: join_col, join_pch and join_size.
...: additional arguments to pass to compute_surv functions.

Value

a ggplot2::ggplot() object.

Details

The function currently only highlights join points that are at the top level; that is, for objects with class surv_projection. To avoid plotting the join points, set join_size to a negative number.

Examples

## Evaluation of the variability of the survival distribution
# \donttest{
surv1 <- define_surv_dist("exp", rate = 0.1)
psa <- define_psa(surv1 ~ resample_surv(n = 100))
plot(surv1, psa=psa)
#> Error in eval(rhs, envir = getOption("heemod.env")): object 'surv1' not found

## plot surv_projection object
surv2 <- define_surv_dist("exp", rate = 0.5)
plot(join(surv1, surv2, at = 2), psa = psa, Nrep = 50)


## surv_fit object
library(survival)
km <- define_surv_fit(survfit(formula = Surv(time, status) ~ 1, data = aml))
fs <- flexsurv::flexsurvreg(formula = Surv(time, status) ~ 1, 
                        data = aml, 
                        dist = "weibull") |>
  define_surv_fit()

psa2 <- define_psa(km ~ resample_surv(),
                   fs ~ resample_surv(),
                   surv1 ~ resample_surv(100))
plot(km, psa = psa2)
#> No covariates provided, returning aggregate survival across all subjects.
#> Error in eval(rhs, envir = getOption("heemod.env")): object 'km' not found

plot(join(km, surv1, at = 6), psa = psa2)
#> No covariates provided, returning aggregate survival across all subjects.
#> No covariates provided, returning aggregate survival across all subjects.
#> Error in eval(rhs, envir = getOption("heemod.env")): object 'fs' not found
plot(join(fs, surv1, at = 6), psa = psa2)

# }