ciplot: 'cuminc2' plotting method

In raredd/cmprsk2: cmprsk2

cuminc2 plotting method

Description

Plot a cuminc2 object with optional cumulative events or estimate table, Gray's test results, and other features.

Usage

ciplot(
  x,
  col.ci = seq_along(xx),
  lty.ci = par("lty"),
  lwd.ci = par("lwd"),
  conf.int = FALSE,
  alpha.conf = 0.05,
  col.conf = NULL,
  lty.conf = 2L,
  lwd.conf = lwd.ci,
  conf.band = FALSE,
  alpha.band = 0.5,
  events = TRUE,
  atrisk = TRUE,
  events.total = TRUE,
  wh.events = c("events", "est", "est.sd", "est.ci", "atrisk", "percent", "percent.ci"),
  events.lab = NULL,
  events.pad = 0.5,
  events.digits = ifelse(grepl("percent", wh.events), 0L, 3L),
  events.lines = TRUE,
  events.col = FALSE,
  include_censored = FALSE,
  main = NULL,
  xlab = "Time",
  ylab = "Probability",
  groups.lab = names(xx),
  xlim = NULL,
  ylim = NULL,
  cex.lab = par("cex.lab"),
  cex.main = par("cex.main"),
  cex.axis = par("cex.axis"),
  cex.events = cex.axis,
  gy_test = TRUE,
  test_details = TRUE,
  legend.args = list(),
  split = FALSE,
  xaxis.at = pretty(xlim),
  yaxis.at = pretty(ylim),
  xaxis.lab = xaxis.at,
  yaxis.lab = yaxis.at,
  events.at = xaxis.at,
  groups.order = seq_along(xx),
  extra.margin = 5L,
  mar = NULL,
  add = FALSE,
  panel.first = NULL,
  panel.last = NULL,
  ...
)

## S3 method for class 'cuminc2'
plot(
  x,
  col.ci = seq_along(xx),
  lty.ci = par("lty"),
  lwd.ci = par("lwd"),
  conf.int = FALSE,
  alpha.conf = 0.05,
  col.conf = NULL,
  lty.conf = 2L,
  lwd.conf = lwd.ci,
  conf.band = FALSE,
  alpha.band = 0.5,
  events = TRUE,
  atrisk = TRUE,
  events.total = TRUE,
  wh.events = c("events", "est", "est.sd", "est.ci", "atrisk", "percent", "percent.ci"),
  events.lab = NULL,
  events.pad = 0.5,
  events.digits = ifelse(grepl("percent", wh.events), 0L, 3L),
  events.lines = TRUE,
  events.col = FALSE,
  include_censored = FALSE,
  main = NULL,
  xlab = "Time",
  ylab = "Probability",
  groups.lab = names(xx),
  xlim = NULL,
  ylim = NULL,
  cex.lab = par("cex.lab"),
  cex.main = par("cex.main"),
  cex.axis = par("cex.axis"),
  cex.events = cex.axis,
  gy_test = TRUE,
  test_details = TRUE,
  legend.args = list(),
  split = FALSE,
  xaxis.at = pretty(xlim),
  yaxis.at = pretty(ylim),
  xaxis.lab = xaxis.at,
  yaxis.lab = yaxis.at,
  events.at = xaxis.at,
  groups.order = seq_along(xx),
  extra.margin = 5L,
  mar = NULL,
  add = FALSE,
  panel.first = NULL,
  panel.last = NULL,
  ...
)

Arguments

x	an object of class cuminc2
col.ci, lty.ci, lwd.ci	line color, type, and width for each curve
conf.int	logical; if TRUE, adds a confidence interval for each curve
alpha.conf	the confidence level for conf.int
col.conf, lty.conf, lwd.conf	line color, type, and width for each confidence interval line
conf.band	logical; if TRUE, a band is draw for confidence intervals
alpha.band	alpha transparency (in [0, 1]) of the band
events	logical; if TRUE, a cumulative events table is drawn
atrisk	logical; if TRUE, the number at risk is added to the events table
events.total	logical or numeric; if TRUE, cumulative events for each group is added to events table at a calculated position; for more control, use a specific x-coordinate
wh.events	a character string giving the type of events table to show; one of "events" (cumulative number of events), "est" (estimates, see timepoints), "est.sd" (estimate +/- standard deviation), "est.ci" (estimate with confidence interval), "atrisk" (event at-risk table with censored), "percent" (percent), or "percent.ci" (pecent with confidence interval)
events.lab	heading for events table
events.pad	extra padding between plot and events table; alternatively, a vector of padding for each line in the events table, recycled as needed
events.digits	when estimates are shown in events table (see wh.events), number of digits past the decimal to show
events.lines	logical; draw lines next to groups in events table
events.col	logical or a vector with colors for events table text; if TRUE, col.ci will be used
include_censored	logical; if TRUE, censored patients are included in at-risk counts (may not be desired); the default (FALSE) will only sum the at-risk table rows
main	title of plot
xlab, ylab	x- and y-axis labels
groups.lab	labels for each line in events table
xlim, ylim	x- and y-axis limits
cex.lab, cex.main	text size for axis and main titles
cex.axis	text size for axis labels and gy_testevents table
cex.events	text size for events table
gy_test	logical; if TRUE the tests of group equality will be shown
test_details	logical; if TRUE (default), all test details (test statistic, degrees of freedom, p-value) are shown; if FALSE, only the p-value is shown
legend.args	an optional named list of legend arguments controlling the annotations when gy_test = TRUE
split	optionally split plot by unique competing risks or group; one of FALSE (default, no splitting), "group", or "event"
xaxis.at, yaxis.at	positions for x- and y-axis labels and ticks
xaxis.lab, yaxis.lab	x- and y-axis tick labels
events.at	x-coordinates to show events table (default is xaxis.at)
groups.order	order of groups in events table
extra.margin	increase left margin when groups labels in events table are long (note that this will be overridden by mar)
mar	margins; see mar section in par
add	logical; if TRUE, pars are not reset; allows for multiple panels, e.g., when using par(mfrow = c(1, 2))
panel.first	an expression to be evaluated after the plot axes are set up but before any plotting takes place
panel.last	an expression to be evaluated after plotting but before returning from the function
...	additional parameters (font, mfrow, bty, tcl, cex.lab, xaxs, etc) passed to par

See Also

ciplot_by; cuminc2; summary.cuminc2; cuminc

Examples

tp <- within(transplant, {
  futime <- futime + 1e-8
  age50 <- factor(+(age > 50))
  age_cat <- cut(age, c(0, 40, 60, Inf), c('<40', '40-60', '60+'))
})

## basic usage
ci1 <- cuminc2(Surv(futime, event(censored)) ~ 1, tp)
plot(ci1)
plot(ci1, groups.lab = paste('1', names(ci1$cuminc))) ## testing
plot(ci1, conf.int = TRUE, lty.conf = 3)
plot(ci1, conf.band = TRUE)

ci1 <- cuminc2(Surv(futime, event(censored)) ~ age_cat, tp)
plot(ci1)
plot(ci1, split = 'event')
plot(ci1, split = 'event', events = FALSE, test_details = FALSE,
     legend.args = list(x = 'topright', cex = 1.5, text.col = 2,
                        title = "Gray\'s test p-value for"))

## also plots "cuminc" objects but without extra features
plot(ci1$cuminc)

ci1 <- cuminc2(Surv(futime, event(censored) == death) ~ age50, tp)
plot(ci1, lty.ci = c(1, 1, 2, 2, 3, 3), col.ci = 1:2)

ci2 <- cuminc2(Surv(futime, event(censored) == death) ~ 1, tp)
plot(ci2, wh.events = 'est', events.digits = 2, groups.order = c(2, 1, 3))

raredd/cmprsk2 documentation built on Dec. 7, 2024, 10:11 p.m.