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Plot method for Cuminc objects

Source: R/plot.Cuminc.R
plot.Cuminc.Rd

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 class '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,
  ...
)

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

Value

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

Details

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

Author

Edouard F. Bonneville e.f.bonneville@lumc.nl

Examples

library(ggplot2)

data("aidssi")
head(aidssi)
#>   patnr   time status      cause ccr5
#> 1     1  9.106      1       AIDS   WW
#> 2     2 11.039      0 event-free   WM
#> 3     3  2.234      1       AIDS   WW
#> 4     4  9.878      2         SI   WM
#> 5     5  3.819      1       AIDS   WW
#> 6     6  6.801      1       AIDS   WW
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 
)