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Numbers-at-risk table for PHS percentile-stratified groups

Source: R/phs_risk_table.R
phs_risk_table.Rd

Builds a ggplot2 numbers-at-risk strip intended for combining with a phs_abs_risk() or phs_km_curve() plot using patchwork. Accepts the same data and interval arguments as those functions and computes the survival data internally.

Usage

phs_risk_table(
  data,
  phs = "phs",
  time = "age",
  event = "status",
  competing_event = NULL,
  intervals = list(c(0.95, 1), c(0.8, 1), c(0.3, 0.7), c(0, 0.2)),
  ref_data = NULL,
  method = "km",
  palette = "hazrd",
  time_points = NULL,
  ...
)

Arguments

data

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

phs

string; column name of the continuous PHS values

time

string; column name of the time-to-event variable

event

string; column name of the event indicator (0 = censored, 1 = event of interest)

competing_event

string or NULL; column name of the competing event indicator. Required when method = "aalen_johansen".

intervals

list of c(lo, hi) pairs defining percentile bands. Should match the intervals used in the accompanying phs_abs_risk() or phs_km_curve() call.

ref_data

optional data.frame used as the reference population for computing percentile cutpoints.

method

string; "km" (default) or "aalen_johansen". Should match the method used in the accompanying curve function.

palette

string; color palette name. Should match the palette used in the accompanying curve plot (default "hazrd").

time_points

numeric vector or NULL; time values at which to display numbers at risk. For example, c(50, 60, 70, 80, 90). When NULL (default), values are chosen automatically using pretty().

...

additional arguments (reserved for future use).

Value

A ggplot2 object displaying the numbers at risk over time for each stratum. Combine with the output of phs_abs_risk() or phs_km_curve() using patchwork, e.g.: p / phs_risk_table(data) + patchwork::plot_layout(heights = c(3, 1)).

Examples

data(test_data)

p  <- phs_abs_risk(test_data)
rt <- phs_risk_table(test_data)

# Specify exact ages for the at-risk columns:
rt <- phs_risk_table(test_data, time_points = c(50, 60, 70, 80))

# Combine with patchwork:
# p / rt + patchwork::plot_layout(heights = c(3, 1))