etm: plot.etmCIF – R documentation

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plot.etmCIF

Plot cumulative incidence functions

Description

Plot function for etmCIF objects. The function plots cumulative incidence curves, possibly with pointwise confidence intervals.

Usage

## S3 method for class 'etmCIF'
plot(x, which.cif, xlim, ylim,
    ylab = "Cumulative Incidence", xlab = "Time", col = 1, lty, lwd = 1,
    ci.type = c("none", "bars", "pointwise"), ci.fun = "cloglog",
    ci.col = col, ci.lty = 3, legend = TRUE, legend.pos, curvlab,
    legend.bty = "n", pos.ci = 27, ci.lwd = 3, ...)

Arguments

`x`	A `etmCIF` object
`which.cif`	A numeric vector indicating which CIFs should be plotted. When missing, only the CIF of interest is plotted (determined through the `failcode` argument in `etmCIF`.)
`xlim`	x-axis limits for the plot. By default, `c(0, max(time))`
`ylim`	y-axis limits. Default is `c(0, 1)`
`ylab`	Label for y-axis. Default is `"Cumulative Incidence"`
`xlab`	Label for x-axis. Default is "Time"
`col`	Vector describing colours used for the CIF curves. Default is black
`lty`	Vector of line type
`lwd`	Thickness of the lines
`ci.type`	One of `c("none", "bars", "pointwise")`. `none` plots no confidence interval, `bars` plots the confidence intervals in the form of a segment for one time point, and `pointwise` draws pointwise confidence intervals for the whole follow-up period.
`ci.fun`	Transformation used for the confidence intervals. Default is "clolog", and is a better choice for cumulative incidences. Other choices are "log" and "log-log"
`ci.col`	Colour for the pointwise confidence interval curves. Default is same as the CIF curves
`ci.lty`	Line type for the confidence intervals. Default is 3
`legend`	Logical. Whether to draw a legend. Default is `TRUE`
`legend.pos`	A vector giving the legend's position. See `legend` for further details
`curvlab`	A character or expression vector to appear in the legend. Default is CIF + event label
`legend.bty`	Box type for the legend. Default is none ("n")
`pos.ci`	If `ci.type = "bars"`, vector of integers indicating at which time point to put the confidence interval bars. Default is 27
`ci.lwd`	Thickness of the confidence interval segment (for `ci.type = "bars"`)
`...`	Further graphical arguments

Details

The function relies on plot.etm and lines.etm with more or less the same options. Exception is the drawing of the confidence intervals, for which several displays are possible.

Value

No value returned

Author(s)

Arthur Allignol arthur.allignol@gmail.com

Examples

data(abortion)

cif.ab <- etmCIF(survival::Surv(entry, exit, cause != 0) ~ group, abortion,
                 etype = cause, failcode = 3)

cif.ab

plot(cif.ab, ci.type = "bars", pos.ci = 24,
     col = c(1, 2), lty = 1, curvlab = c("Control", "Exposed"))

plot(cif.ab, which = c(1, 2))

etm

Empirical Transition Matrix

v1.1.1

MIT + file LICENSE

Authors

Mark Clements [aut, cre], Arthur Allignol [aut]

Initial release