Plot the estimated cumulative incidence function (CIF)

This function plots the estimated potential cumulative incidence function, along with pointwise confidence intervals.

plot_inc(
  fit,
  decrease = FALSE,
  conf.int = 0.95,
  nboot = 0,
  seed = 0,
  xlab = "Time",
  xlim = NULL,
  ylim = c(0, 1),
  plot.configs = list(ylab = NULL, main = NULL, cex = 0.9, lty = 1, lwd = 2, ci.lty = 5,
    ci.lwd = 1.5, legend = c("Treated", "Control"), col = c("brown", "darkcyan"),
    legend.cex = 0.9, show.p.value = TRUE),
  ...
)

Arguments

fit

A fitted object returned by the function surv.tteICE or scr.tteICE.

decrease

A logical variable indicating the type of curve to display. If decrease = FALSE (default), the function displays the cumulative incidence functions (CIFs). If decrease = TRUE, the function instead displays the survival functions.

conf.int

Confidence level for the interval. If conf.int = NULL, no confidence interval is provided.

nboot

Number of resampling in bootstrapping. By default, nboot = 0, meaning no bootstrap is performed and the standard error is computed using the explicit analytical formula.

seed

Sets the random seed used when generating bootstrap samples.

xlab

Label for x-axis.

xlim

A numeric vector of length 2 giving the limits of the x-axis. If xlim=NULL (default), the range is determined automatically from the data.

ylim

A numeric vector of length 2 giving the limits of the y-axis. Defaults to ylim=c(-1, 1).

plot.configs

A named list of additional plot configurations. Common entries include:

ylab: character, label for the y-axis (default: ylab=NULL, use the default label).
main: character, title for the plot (default: main=NULL, use the default label).
lty: line type for the curve (default: 1).
lwd: line width for the curve (default: 2).
ci.lty: line type for confidence interval curves (default: 5).
ci.lwd: line width for confidence interval curves (default: 1.5).
legend.cex: font size for the legend (default: 0.9).

...

Additional graphical arguments passed to function plot.default or function curve

Value

Plot the cumulative incidence function results from a tteICE object

Examples

## load data and fit the model
data(bmt)
bmt = transform(bmt, d4=d2+d3)
A = as.numeric(bmt$group>1)
## Model with competing risk data
fit1 = surv.tteICE(A, bmt$t2, bmt$d4, 'treatment')
## plot asymptotic confidence intervals based on explicit formulas
plot_inc(fit1, ylim=c(0,1),
         plot.configs=list(legend=c('AML','ALL'), show.p.value=FALSE) )
#> Warning: `seed` is supplied but `nboot = 0`; seed will be ignored.

# \donttest{
## plot bootstrap confidence intervals (may take some seconds)
plot_inc(fit1, nboot=200, ylim=c(0,1),
         plot.configs=list(legend=c('AML','ALL')) )

# }
## Model with semicompeting risk data
fit2 = scr.tteICE(A, bmt$t1, bmt$d1, bmt$t2, bmt$d2, "composite")
## plot asymptotic confidence intervals based on explicit formulas
plot_inc(fit2, ylim=c(0,1), plot.configs=list(add.null.line=FALSE))
#> Warning: `seed` is supplied but `nboot = 0`; seed will be ignored.

## plot bootstrap confidence intervals
plot_inc(fit2, nboot=200, ylim=c(0,1),
         plot.configs=list(lty=2, lwd=3,main="Title"))

Plot the estimated cumulative incidence function (CIF)

Arguments

Value

See also

Examples