etm: etmCIF – R documentation

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etmCIF

Cumulative incidence functions of competing risks

Description

etmCIF is a wrapper around the etm function for facilitating the computation of the cumulative incidence functions in the competing risks framework.

Usage

etmCIF(formula, data, etype, subset, na.action, failcode = 1)

Arguments

`formula`	A `formula` object, that must have a `Surv` object on the left of ~ operator, and a discrete covariate (or 1) on the right. The status indicator should be 1 (or TRUE) for an event (whatever the type of this event, 0 (or FALSE) for censored observations.)
`data`	A data.frame in which to interpret the terms of the formula
`etype`	Competing risks event indicator. When the status indicator is 1 (or TRUE) in the formula, `etype` describes the type of event, otherwise, for censored observation, the value of `etype` is ignored
`subset`	Expression saying that only a subset of the data should be used.
`na.action`	Missing-data filter function. Default is `options()$na.action`.
`failcode`	Indicates the failure type of interest. Default is one. This option is only relevant for some options of the `plot` function.

Details

This function computes the cumulative incidence functions in a competing risks setting using the etm machinery, without having to specify the matrix of possible transitions and using the more usual formula specification with Surv

Value

Returns a list of etm objects (1 per covariate level) plus additional informations:

`failcode`	As in function call
`call`	Function call
`X`	A matrix giving the name of the covariate (if present) and the levels of this covariate.

Author(s)

Arthur Allignol arthur.alignol@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"))

etm

Empirical Transition Matrix

v1.1.1

MIT + file LICENSE

Authors

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

Initial release