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Kaplan-Meier frames for halftone survival plots

Source: R/km.R
km_steps.Rd

Convert a survival::survfit object into data frames for with_halftone(geom_ribbon()) and with_halo(geom_step()). km_steps() returns the step outline with one row per corner (time, surv, lo, hi, strata), starting at (0, 1), so that a ribbon between lo and hi follows the steps exactly. km_censor() returns the censor marks (time, surv, strata). km_risk() returns the number at risk at times. Strata labels are the level values without the variable name; "ph.ecog=1" becomes "1".

Usage

km_steps(fit, conf = TRUE)

km_censor(fit)

km_risk(fit, times)

Arguments

fit

A survfit object.

conf

Include the confidence limits (lo, hi); otherwise both equal surv.

times

Times at which to report the number at risk.

Value

A data frame.

References

Loprinzi, C. L., Laurie, J. A., Wieand, H. S., et al. (1994). Prospective evaluation of prognostic variables from patient-completed questionnaires. North Central Cancer Treatment Group. Journal of Clinical Oncology, 12(3), 601-607. doi:10.1200/JCO.1994.12.3.601 . Distributed as survival::lung.

Examples

if (requireNamespace("survival", quietly = TRUE)) {
  fit <- survival::survfit(survival::Surv(time, status) ~ sex, data = survival::lung)
  s <- km_steps(fit)
  ggplot2::ggplot(s, ggplot2::aes(time, group = strata)) +
    with_halftone(ggplot2::geom_ribbon(ggplot2::aes(ymin = lo, ymax = hi, fill = strata))) +
      with_halo(ggplot2::geom_step(ggplot2::aes(y = surv, colour = strata))) +
  ggplot2::theme_classic() + theme_halftone()
}