R: Tidy a(n) survfit object

tidy.survfit {broom}

R Documentation

Tidy a(n) survfit object

Description

Tidy summarizes information about the components of a model. A model component might be a single term in a regression, a single hypothesis, a cluster, or a class. Exactly what tidy considers to be a model component varies cross models but is usually self-evident. If a model has several distinct types of components, you will need to specify which components to return.

Usage

## S3 method for class 'survfit'
tidy(x, ...)

Arguments

x

An survfit object returned from survival::survfit().

...

Additional arguments. Not used. Needed to match generic signature only. Cautionary note: Misspelled arguments will be absorbed in ..., where they will be ignored. If the misspelled argument has a default value, the default value will be used. For example, if you pass conf.lvel = 0.9, all computation will proceed using conf.level = 0.95. Additionally, if you pass newdata = my_tibble to an augment() method that does not accept a newdata argument, it will use the default value for the data argument.

Value

A tibble::tibble with one row for each time point and columns:

`time`	timepoint
`n.risk`	number of subjects at risk at time t0
`n.event`	number of events at time t
`n.censor`	number of censored events
`estimate`	estimate of survival or cumulative incidence rate when multistate
`std.error`	standard error of estimate
`conf.high`	upper end of confidence interval
`conf.low`	lower end of confidence interval
`state`	state if multistate survfit object inputted
`strata`	strata if stratified survfit object inputted

Examples


library(survival)
cfit <- coxph(Surv(time, status) ~ age + sex, lung)
sfit <- survfit(cfit)

tidy(sfit)
glance(sfit)

library(ggplot2)
ggplot(tidy(sfit), aes(time, estimate)) + geom_line() +
    geom_ribbon(aes(ymin=conf.low, ymax=conf.high), alpha=.25)

# multi-state
fitCI <- survfit(Surv(stop, status * as.numeric(event), type = "mstate") ~ 1,
              data = mgus1, subset = (start == 0))
td_multi <- tidy(fitCI)
td_multi

ggplot(td_multi, aes(time, estimate, group = state)) +
    geom_line(aes(color = state)) +
    geom_ribbon(aes(ymin = conf.low, ymax = conf.high), alpha = .25)