mstate (version 0.3.3)

plot.Cuminc: Plot method for Cuminc objects

Description

Plot the estimates of the non-parametric Aalen-Johansen estimate of the cumulative incidence functions (competing risks data). Note this is a method for mstate::Cuminc and not cmprsk::cuminc. Both return the same estimates, though the former does so in a dataframe, and the latter in the list.

Usage

# S3 method for Cuminc
plot(
  x,
  use.ggplot = FALSE,
  xlab = "Time",
  ylab = "Probability",
  xlim,
  ylim,
  lty,
  legend,
  cols,
  conf.type = c("log", "plain", "none"),
  conf.int = 0.95,
  legend.pos = "right",
  facet = FALSE,
  ...
)

Value

A ggplot object if use.ggplot = T used, otherwise NULL.

Arguments

x

Object of class "Cuminc" to be printed or plotted

use.ggplot

Default FALSE, set TRUE for ggplot version of plot

xlab

A title for the x-axis; default is "Time"

ylab

A title for the y-axis; default is "Probability"

xlim

The x limits of the plot(s), default is range of time

ylim

The y limits of the plot(s); if ylim is specified for type="separate", then all plots use the same ylim for y limits

lty

The line type, see par; default is 1

legend

Character vector corresponding to number of absorbing states. In case of a grouped "Cuminc" object, with facet = FALSE the length of the vector is number absorbing states * group levels. Only relevant when use.ggplot = TRUE

cols

Vector (numeric or character) specifying colours of the lines

conf.type

Type of confidence interval - either "log" or "plain" . See function details for details.

conf.int

Confidence level (%) from 0-1 for probabilities, default is 0.95 (95% CI). Setting to 0 removes the CIs.

legend.pos

The position of the legend, see legend; default is "topleft"

facet

Logical, in case of group used for "Cuminc", facet by it - only relevant when use.ggplot = TRUE

...

Further arguments to plot or print method

Author

Edouard F. Bonneville

Details

Grouped cumulative incidences can be plotted either in the same plot or in facets, see the facet argument.

Examples

library(ggplot2)

data("aidssi")
head(aidssi)
si <- aidssi

# No grouping
cum_incid <- Cuminc(
time = "time",
status = "status",
data = si
)

plot(
x = cum_incid,
use.ggplot = TRUE,
conf.type = "none",
lty = 1:2,
conf.int = 0.95
)

# With grouping
cum_incid_grp <- Cuminc(
time = "time",
status = "status",
group = "ccr5",
data = si
)

plot(
 x = cum_incid_grp,
 use.ggplot = TRUE,
 conf.type = "none",
 lty = 1:4, 
 facet = TRUE 
)