mstate: plot.Cuminc – R documentation

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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 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

Details

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

Value

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

Author(s)

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

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 
)

mstate

Data Preparation, Estimation and Prediction in Multi-State Models

v0.3.1

GPL (>= 2)

Authors

Hein Putter [aut, cre], Liesbeth C. de Wreede [aut], Marta Fiocco [aut], Ronald B. Geskus [ctb], Edouard F. Bonneville [ctb], Damjan Manevski [ctb]

Initial release

2020-12-17