plot.MizerScan: Plot method for `MizerScan` objects

Description

Draws the result of a scanModel() run: the measured quantity against the quantity that was scanned, with a band showing the range the quantity takes over the attractor wherever that attractor is not a fixed point.

Usage

# S3 method for MizerScan
plot(
  x,
  species = NULL,
  style = c("ribbon", "envelope", "line"),
  highlight = NULL,
  log_x = FALSE,
  log_y = TRUE,
  log = NULL,
  xlim = c(NA, NA),
  ylim = c(NA, NA),
  y_ticks = 6,
  reference_lines = TRUE,
  mark_max = FALSE,
  show_unsettled = TRUE,
  return_data = FALSE,
  ...
)

Value

A ggplot2 object, unless return_data = TRUE, in which case the data frame used for the plot is returned.

Arguments

x: A MizerScan object.
species: The species to show. By default all series in the scan.
style: One of "ribbon" (default: the average as a line inside the band), "envelope" (lines along the edges of the band, no average) or "line" (no band).
highlight: Name or vector of names of the species to be highlighted with a thicker line.
log_x, log_y, log: Whether to use logarithmic axes, see parsePlotLog().
xlim, ylim: Numeric vectors of length two giving the axis limits. Use NA to refer to the existing minimum or maximum.
y_ticks: The approximate number of ticks desired on the y axis.
reference_lines: Whether to draw the reference lines stored in the scan, or a named numeric vector of x positions to draw instead.
mark_max: Whether to mark, for each series, the scanned value at which the measured quantity is largest. See MizerScan().
show_unsettled: Whether to mark the scan values where the model did not settle onto an attractor.
return_data: Whether to return the data frame used for the plot instead of the plot itself.
...: Unused.

Details

A model that settles on a fixed point contributes a single value, so the band has zero width there. A model that settles on a limit cycle contributes the average over one period as the line and the range over that period as the band, so a Hopf bifurcation shows up as the scan value at which the band opens up.

Scan values where the model reached neither a fixed point nor a limit cycle within the time allowed are marked with a cross, because the value plotted there is only an average over the last few years of a run that was still changing.

Examples

Run this code

# \donttest{
scan <- scanModel(NS_params, scan_values = seq(0, 1, 0.25),
                  set_func = scanEffort(), species = c("Cod", "Herring"))
plot(scan)
plot(scan, style = "envelope", mark_max = TRUE)
# }