etm: plot.etm – R documentation

Pricing

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

Get Started for Free

Documentation

etm

plot.etm

Plot method for an etm object

Description

Plot method for an object of class 'etm'. It draws the estimated transition probabilities in a basic scatterplot.

Usage

## S3 method for class 'etm'
plot(x, tr.choice, xlab = "Time",
     ylab = "Transition Probability", col = 1, lty, xlim, ylim,
     conf.int = FALSE, level = 0.95, ci.fun = "linear",
     ci.col = col, ci.lty = 3,
     legend = TRUE, legend.pos, curvlab, legend.bty = "n", ...)

Arguments

`x`	An object of class 'etm'
`tr.choice`	character vector of the form 'c("from to","from to")' specifying which transitions should be plotted. Default, all the transition probabilities are plotted
`xlab`	x-axis label. Default is "Time"
`ylab`	y-axis label. Default is "Transition Probability"
`col`	Vector of colour. Default is black
`lty`	Vector of line type. Default is 1:number of transitions
`xlim`	Limits of x-axis for the plot
`ylim`	Limits of y-axis for the plot
`conf.int`	Logical. Whether to display pointwise confidence intervals. Default is FALSE.
`level`	Level of the conficence intervals. Default is 0.95.
`ci.fun`	Transformation applied to the confidence intervals. It could be different for all transition probabilities, though if `length(ci.fun) != number of transitions`, only `ci.fun[1]` will be used. Possible choices are "linear", "log", "log-log" and "cloglog". Default is "linear".
`ci.col`	Colour of the confidence intervals. Default is `col`.
`ci.lty`	Line type of the confidence intervals. Default is 3.
`legend`	A logical specifying if a legend should be added
`legend.pos`	A vector giving the legend's position. See `legend` for further details
`curvlab`	A character or expression vector to appear in the legend. Default is the name of the transitions
`legend.bty`	Box type for the legend
`...`	Further arguments for plot

Details

By default, if the argument strata was used for creating the etm object, the first transition probability for all strata will be plotted. If there is no strata, all transition probabilities are plotted by default.

In any case, a legend with be created by the labels are likely to be ugly. Please use the curvlab argument to control the test or use legend = FALSE and build your own legend.

Value

No value returned

Author(s)

Arthur Allignol, arthur.allignol@gmail.com

Examples

data(sir.cont)

# Modification for patients entering and leaving a state
# at the same date
sir.cont <- sir.cont[order(sir.cont$id, sir.cont$time), ]
for (i in 2:nrow(sir.cont)) {
  if (sir.cont$id[i]==sir.cont$id[i-1]) {
    if (sir.cont$time[i]==sir.cont$time[i-1]) {
      sir.cont$time[i-1] <- sir.cont$time[i-1] - 0.5
    }
  }
}

tra <- matrix(ncol=3,nrow=3,FALSE)
tra[1, 2:3] <- TRUE
tra[2, c(1, 3)] <- TRUE

my.etm <- etm(sir.cont,c("0","1","2"),tra,"cens", s = 0)

plot(my.etm, tr.choice = c("0 0"))

etm

Empirical Transition Matrix

v1.1.1

MIT + file LICENSE

Authors

Mark Clements [aut, cre], Arthur Allignol [aut]

Initial release