Skip to contents

Kaplan-Meier curves stratified by PHS percentile

Source: R/phs_km_curve.R
phs_km_curve.Rd

Compute Kaplan-Meier survival curves stratified by PHS percentile groups. Returns either a ggplot object (output = "plot") or a tidy data frame (output = "data"). Preset strata and custom cutpoints are supported; percentiles are computed from ref_data when supplied so a training->validation workflow is possible.

Usage

phs_km_curve(
  data,
  phs = "phs",
  time = "age",
  event = "status",
  intervals = list(c(0.95, 1), c(0.8, 1), c(0.3, 0.7), c(0, 0.2)),
  breaks = NULL,
  ref_data = NULL,
  output = "plot",
  conf_int = TRUE,
  conf_int_alpha = 0.15,
  palette = "hazrd",
  risk_table = FALSE,
  ...
)

Arguments

data

data.frame with columns specified by phs, time, event

phs

string or numeric vector; column name or vector of PHS values

time

string or numeric vector; column name or vector of event time

event

string or numeric vector; column name or vector of event indicator (0/1)

intervals

list of c(lo, hi) pairs defining percentile bands, e.g. list(c(0.80, 1), c(0, 0.20)). Bands may overlap. Takes precedence over breaks when non-NULL. Default produces four bands: top 5 (0.95-1), top 20 (0.80-1), middle 40 (0.30-0.70), and bottom 20 (0-0.20).

breaks

numeric vector of percentile cutpoints strictly in (0, 1) used to form exclusive bands (legacy); ignored when intervals is non-NULL. Retained for backward compatibility.

ref_data

optional data.frame used to compute percentile cutpoints (training reference)

output

'plot' (default) or 'data'

conf_int

logical; include confidence intervals in output/plot

conf_int_alpha

numeric; alpha for confidence ribbons when plotting

palette

string; name of color palette to use for plots (default: 'hazrd')

risk_table

logical; if TRUE returns numbers-at-risk in the data output (experimental)

...

additional args (reserved)

Value

ggplot object (when output = 'plot') or data.frame (when output = 'data')