mjp-methods: Format a MJP for pretty printing.

In CharlotteJana/pdmpsim: Simulate Piecewise Deterministic Markov Processes

Format a MJP for pretty printing.

Description

Give important information about a mjpModel in one character string. This method is used internally to generate default filenames or plot titles.

This is method plots single simulations of markov jump processes defined as mjpModel. There are also other plot methods available that use ggplot2.

Usage

## S4 method for signature 'mjpModel'
format(
  x,
  begin = NULL,
  end = NULL,
  short = TRUE,
  slots = c("parms", "init", "times"),
  sep,
  collapse
)

## S4 method for signature 'mjpModel,missing'
plot(x, y, ...)

Arguments

x	an object of class mjpModel with a simulation stored in slot out
begin	a character string that is pasted at the beginning.
end	a character string that is pasted at the end.
short	logical. If TRUE, a shorter version without space characters will be returned (useful to generate filenames). Defaults to TRUE.
slots	a vector specifying the names of all slots that shall be pasted to the string. ' The default is c("parms", "init", "times"). Supported slots are "descr", "parms", "init", and "times".
sep	a character string to separate the names and values of slots that are vectors or lists (e. g. "times" or "parms"). It defaults to "=" if short is TRUE and to " = " if short is FALSE.
collapse	a character string to separate the slots. It defaults to "___" if short is TRUE and to ". " if short is FALSE.
y	ignored
...	optional plotting parameters

See Also

plotSeeds for another plot function to plot single simulations

Examples

data("KendallBD")
format(KendallBD, begin = "ToggleSwitch__", end = ".rda")
format(KendallBD, begin = paste0(descr(toggleSwitch), ": "), short=FALSE)
parms(KendallBD) <- list()
cat(format(KendallBD, short = FALSE, collapse = ".\n",
           slots = c("init", "times","parms"),
           begin = "Kendalls birth-death-process:\n"))
data("SIRstoch")
sim <- sim(SIRstoch, seed = 1)
plot(sim, col = "red", lwd = 2)

# Alternative: plotSeeds
msim <- multSim(SIRstoch, seeds = 1)
plot <- plotSeeds(msim)
plot + ggplot2::facet_grid(variable ~ seed)

CharlotteJana/pdmpsim documentation built on Oct. 21, 2024, 4:54 p.m.