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Basic Kaplan Meier (KM) plot function

Source: R/plot_km.R
basic_kmplot.Rd

This function can generate a basic KM plot with or without risk set table appended at the bottom. In a single plot, it can include up to 4 KM curves. This depends on number of levels in 'treatment' column in the input data.frame kmdat

Usage

basic_kmplot(
  kmdat,
  endpoint_name = "Time to Event Endpoint",
  time_scale = NULL,
  time_grid = NULL,
  show_risk_set = TRUE,
  main_title = "Kaplan-Meier Curves",
  subplot_heights = NULL,
  suppress_plot_layout = FALSE,
  use_colors = NULL,
  use_line_types = NULL,
  use_pch_cex = 0.65,
  use_pch_alpha = 100
)

Arguments

kmdat

a data.frame, must consist treatment, time (unit in days), n.risk, censor, surv, similar to an output from maicplus:::survfit_makeup

endpoint_name

a string, name of time to event endpoint, to be show in the last line of title

time_scale

a string, time unit of median survival time, taking a value of 'years', 'months', 'weeks' or 'days'

time_grid

a numeric vector in the unit of time_scale, risk set table and x axis of the km plot will be defined based on this time grid

show_risk_set

logical, show risk set table or not, TRUE by default

main_title

a string, main title of the KM plot

subplot_heights

a numeric vector, heights argument to graphic::layout(),NULL by default which means user will use the default setting

suppress_plot_layout

logical, suppress the layout setting in this function so that user can specify layout outside of the function, FALSE by default

use_colors

a character vector of length up to 4, colors to the KM curves, it will be passed to col of lines()

use_line_types

a numeric vector of length up to 4, line type to the KM curves, it will be passed to lty of lines()

use_pch_cex

a scalar between 0 and 1, point size to indicate censored individuals on the KM curves, it will be passed to cex of points()

use_pch_alpha

a scalar between 0 and 255, degree of color transparency of points to indicate censored individuals on the KM curves, it will be passed to cex of points()

Value

a KM plot with or without risk set table appended at the bottom, with up to 4 KM curves

Examples

library(survival)
data(adtte_sat)
data(pseudo_ipd_sat)

combined_data <- rbind(adtte_sat[, c("TIME", "EVENT", "ARM")], pseudo_ipd_sat)
kmobj <- survfit(Surv(TIME, EVENT) ~ ARM, combined_data, conf.type = "log-log")
kmdat <- do.call(rbind, survfit_makeup(kmobj))
kmdat$treatment <- factor(kmdat$treatment)

# without risk set table
basic_kmplot(kmdat,
  time_scale = "month",
  time_grid = seq(0, 20, by = 2),
  show_risk_set = FALSE,
  main_title = "Kaplan-Meier Curves",
  subplot_heights = NULL,
  suppress_plot_layout = FALSE,
  use_colors = NULL,
  use_line_types = NULL
)


# with risk set table
basic_kmplot(kmdat,
  time_scale = "month",
  time_grid = seq(0, 20, by = 2),
  show_risk_set = TRUE,
  main_title = "Kaplan-Meier Curves",
  subplot_heights = NULL,
  suppress_plot_layout = FALSE,
  use_colors = NULL,
  use_line_types = NULL
)