R: Plot method for an msfit object

plot.msfit {mstate} | R Documentation

## Plot method for an msfit object

### Description

Plot method for an object of class `"msfit"`. It plots the estimated cumulative transition intensities in the multi-state model.

### Usage

    ## S3 method for class 'msfit'
    plot(
      x,
      type = c("single", "separate"),
      cols,
      xlab = "Time",
      ylab = "Cumulative hazard",
      ylim,
      lwd,
      lty,
      legend,
      legend.pos = "right",
      bty = "n",
      use.ggplot = FALSE,
      xlim,
      scale_type = "fixed",
      conf.int = 0.95,
      conf.type = "none",
      ...
    )

### Arguments

`x` | Object of class `"msfit"`, containing estimated cumulative transition intensities for all transitions in a multi-state model
`type` | One of `"single"` (default) or `"separate"`; in case of `"single"`, all estimated cumulative hazards are drawn in a single plot, in case of `"separate"`, separate plots are shown for the estimated transition intensities
`cols` | A vector specifying colors for the different transitions; default is 1:K (K no of transitions), when type=`"single"`, and 1 (black), when type=`"separate"`
`xlab` | A title for the x-axis; default is `"Time"`
`ylab` | A title for the y-axis; default is `"Cumulative hazard"`
`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
`lwd` | The line width, see `par`; default is 1
`lty` | The line type, see `par`; default is 1
`legend` | Character vector of length equal to the number of transitions, to be used in a legend; if missing, these will be taken from the row- and column-names of the transition matrix contained in `x$trans`. Also used as titles of plots for type=`"separate"`
`legend.pos` | The position of the legend, see `legend`; default is `"topleft"`
`bty` | The box type of the legend, see `legend`
`use.ggplot` | Default FALSE, set TRUE for ggplot version of plot
`xlim` | Limits of x axis, relevant if use_ggplot = T
`scale_type` | "fixed", "free", "free_x" or "free_y", see scales argument of facet_wrap(). Only relevant for use_ggplot = T.
`conf.int` | Confidence level (%) from 0-1 for the cumulative hazard, default is 0.95. Only relevant for use_ggplot = T
`conf.type` | Type of confidence interval - either "log" or "plain" . See function details of `plot.probtrans` for details
`...` | Further arguments to plot

### Value

No return value

### Author(s)

Hein Putter H.Putter@lumc.nl

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

### See Also

`msfit`

### Examples

    # transition matrix for illness-death model
    tmat <- trans.illdeath()
    # data in wide format, for transition 1 this is dataset E1 of
    # Therneau & Grambsch (2000)
    tg <- data.frame(illt=c(1,1,6,6,8,9),ills=c(1,0,1,1,0,1),
            dt=c(5,1,9,7,8,12),ds=c(1,1,1,1,1,1),
            x1=c(1,1,1,0,0,0),x2=c(6:1))
    # data in long format using msprep
    tglong <- msprep(time=c(NA,"illt","dt"),status=c(NA,"ills","ds"),
    		data=tg,keep=c("x1","x2"),trans=tmat)
    # events
    events(tglong)
    table(tglong$status,tglong$to,tglong$from)
    # expanded covariates
    tglong <- expand.covs(tglong,c("x1","x2"))
    # Cox model with different covariate
    cx <- coxph(Surv(Tstart,Tstop,status)~x1.1+x2.2+strata(trans),
    	data=tglong,method="breslow")
    summary(cx)
    # new data, to check whether results are the same for transition 1 as
    # those in appendix E.1 of Therneau & Grambsch (2000)
    newdata <- data.frame(trans=1:3,x1.1=c(0,0,0),x2.2=c(0,1,0),strata=1:3)
    msf <- msfit(cx,newdata,trans=tmat)
    # standard plot
    plot(msf)
    # specifying line width, color, and legend
    plot(msf,lwd=2,col=c("darkgreen","darkblue","darkred"),legend=c("1->2","1->3","2->3"))
    # separate plots
    par(mfrow=c(2,2))
    plot(msf,type="separate",lwd=2)
    par(mfrow=c(1,1))

    # ggplot version - see vignette for details
    library(ggplot2)
    plot(msf, use.ggplot = TRUE)

[Package mstate version 0.3.2 Index]