CIFplot: Plotting estimates of the cumulative incidence function

In compeir: Event-specific incidence rates for competing risks data

Description

Function for plotting parametric estimates of the cumulative incidence function based on incidence rates. If individual patient data is available, the function also enables to plot the non-parametric, Aalen-Johansen estimates using etm.

Usage

CIFplot(x, event.code = NULL, covar.code = NULL, indiv.times = NULL, indiv.events = NULL, indiv.covar = NULL, 
xlim = c(0, 30), ylim = NULL, xlab = "Time", ylab = "CIF", legend = TRUE, ...)

Arguments

x	irates object
event.code	A character or numerical value that specifies the respective competing events for which the CIF shall be plotted. If NULL, event.code will be inherited from irates
covar.code	A character or numerical value that specifies the respective covariate vlaues for which the CIF shall be plotted. If NULL, covar.code will be inherited from irates
indiv.times	Timepoints corresponding to event status for each individual (vector or factor). Only relevant if individual patient data is available. Defaults to NULL
indiv.events	Event status for each individual (vector or factor). Only relevant if individual patient data is available. Defaults to NULL
indiv.covar	Event status for each individual (vector or factor). Only relevant if individual patient data is available. Defaults to NULL
xlim	The x limits (x1, x2) of the plot. Defaults to c(0, 30)
ylim	The y limits (y1, y2) of the plot. If NULL, ylim will be determined automatically
xlab	A title for the x axis. Defaults to “Time”
ylab	A title for the y axis. Defaults to “CIF”
legend	Adds a legend to the plot. Defaults to TRUE
...	Further arguments for plot

See Also

cif, etm

Examples

### Example data.frame with aggregated count data
dat <- data.frame(
			times = c(7948,2899), 
			no.event = c(6,8), 
			event.1 = c(589,68), 
			event.2 = c(55,21), 
			row.names = c("covar0","covar1"))  

### Compute irates object from dat
ir <- irates(dat)

### Compute the cumulative incidence function from irates object
### here: timespan is specified by xlim (default: xlim = c(0,30))
CIFplot(x = ir)


### sir.adm: Individual patient data
data(sir.adm)

### aggregate data
agg.sir.adm <- data.reshape(
			times = sir.adm$time, 
			events = sir.adm$status, 
			covar = sir.adm$pneu, 
			no.event.code= "0")

### Plot parametric and non-parametric CIF estimates
CIFplot(
	x = irates(agg.sir.adm), 
	indiv.times = sir.adm$time, 
	indiv.events = sir.adm$status, 
	indiv.covar = sir.adm$pneu)


### okiss: Individual patient data
### here: e.g. just event of interest 1 (infection) is plotted
data(okiss)

### aggregate data
agg.okiss <- data.reshape(
			times = okiss$time, 
			events = okiss$status, 
			covar = okiss$allo, 
			no.event.code= "11")

### Plot parametric and non-parametric CIF estimates
CIFplot(
	x = irates(agg.okiss), 
	event.code = "1",
	indiv.times = okiss$time, 
	indiv.events = okiss$status, 
	indiv.covar = okiss$allo)

compeir documentation built on May 2, 2019, 5:47 a.m.