Plot method for MizerScan objects

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 class '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,
  ...
)

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.

Value

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

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.

See also

scanModel(), MizerScan(), plotting_functions

Other scan functions: MizerScan(), plotYieldVsF(), scanEffort(), scanModel()

Examples

# \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)

# }