ggcuminc: Lisa's Cumulative Incidence Plots

In lisaerein/nicesurv: This package creates a nice summary tables and plots for survival analysis

Lisa's Cumulative Incidence Plots

Description

This function creates cumulative incidence plots from a survfit object of type "mstate" using gglot2 graphics. It returns a ggplot2 object and prints the resulting plot.

Usage

ggcuminc(
  msfit,
  groups = NA,
  grlabs = NA,
  grname = " ",
  events = NA,
  evlabs = NA,
  evtitle = "Event",
  perc = FALSE,
  xlab = "Time",
  ylab = "Probability",
  xlim = NA,
  ylim = c(0, 1),
  xby = NA,
  yby = 0.1,
  xbrlabs = NA,
  stack = "events",
  state0 = "state_0",
  cuminc.col = NA,
  cuminc.lty = NA,
  cuminc.size = 1.5,
  step = TRUE,
  main = "",
  graystest = FALSE,
  df = NA,
  timevar = NA,
  eventvar = NA
)

Arguments

msfit	survfit object of type "mstate" (REQUIRED).
groups	Character vector for groups as listed in dataset. Default = NA (no groups).
grlabs	Character vector for group names, must be in same order as groups. Default = NA (no groups or use group levels from dataset).
grname	Character label for group legend. Default = " ".
events	Character vector for event names (do not include 0 level).
evlabs	Character vector for event labels (do not include 0 level).
evtitle	Character label for event legend. Default = "Events".
perc	Logical indicator to show y axis as percentages. Default = FALSE.
xlab	Character label for x axis. Default = "Time".
ylab	Character label for y axis. Default = "Probability".
xlim	Numeric vector of length 2 for x axis min and max. Default = NA, using 0 to data maximum.
ylim	Numeric vector of length 2 for y axis min and max. Default = c(0, 1).
xby	Number for x axis major tick marks. Default = NA (ggplot selected).
yby	Numeric for y axis major tick marks. Default = 0.1.
xbrlabs	Vector for alternative x axis labels. Default = NA.
stack	Character to indicate stacking events "events" or groups "groups". Default = "events".
state0	Character label for state 0. Default = "state_0".
cuminc.col	Character vector for color of shaded cumulative incidence bands (do not include 0 level). Default = default colors.
cuminc.lty	Numeric vector for line type of cumulative incidence lines. Default = 1.
cuminc.size	Number for size of cumulative incidence lines. Default = 1.
step	Logical indicator to use step function or not. Default = TRUE.
main	Character label for plot title. Default = " ".
graystest	Logical indicator to provide Gray's test p-values (Default = FALSE). If TRUE, you must provide df, timevar, and eventvar.
df	Dataframe to use for Gray's test. Default = NA.
timevar	Character name of time to event variable. Default = NA.
eventvar	Character nane of event variable. Default = NA.

lisaerein/nicesurv documentation built on Dec. 9, 2024, 12:17 a.m.