R: Plot method for Cuminc objects

plot.Cuminc {mstate} | R Documentation

## 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
    )

[Package mstate version 0.3.2 Index]