mizer (version 3.4.0)

plotYieldVsF: Plot the yield of a species against the fishing mortality on it

Description

Varies the fishing mortality on one species over a range of values, leaving the fishing on every other species unchanged, and plots the long-term yield of that species against it. The fishing mortality at which the yield is largest is \(F_{MSY}\), and is marked on the plot by default.

This is scanModel() with scanFishingMortality() as its setter and getYield() as the quantity it measures. Use scanModel() directly to vary something other than the fishing mortality on a single species, to measure something other than the yield, or to follow more than one species at once.

At each fishing mortality the model is projected until it settles, and what is plotted depends on what it settled on. At a fixed point the yield is read straight off the settled state. On a limit cycle it is averaged over exactly one period, and the band around the line shows the range the yield covers over that cycle, so an oscillation is displayed rather than silently averaged away. Fishing mortalities at which the model settled on neither are marked with a cross and should not be relied on; raise t_max for those.

The scan starts from the fishing mortality the model currently sits at and works outwards in both directions, each arm warm-starting from the attractor reached at the previous value.

Usage

plotYieldVsF(
  params,
  species,
  F_range,
  F_min = 0,
  F_max = 1.5,
  no_steps = 16,
  gear = NULL,
  style = "ribbon",
  mark_max = TRUE,
  reference_lines = TRUE,
  log_y = FALSE,
  log = NULL,
  return_data = FALSE,
  progress_bar = interactive(),
  ...
)

Value

A ggplot2 object, or, if return_data = TRUE, the MizerScan object holding the data. The fishing mortality giving the largest yield is available from that object as attr(scan, "at_max").

Arguments

params

A MizerParams object.

species

The name of the species whose fishing mortality is varied. Only one species at a time.

F_range

A numeric vector of fishing mortalities for the x-axis. If missing it is built as seq(F_min, F_max, length.out = no_steps).

F_min, F_max, no_steps

Used to build F_range when that is missing.

gear

The name of the gear whose fishing mortality on the species is varied. Only needed when several gears catch the species; if NULL (default), the fishing mortality from all of them is replaced. See scanFishingMortality().

style

How the range covered on a limit cycle is drawn, see plot.MizerScan(). The default "ribbon" draws the average as a line inside the band.

mark_max

Whether to mark the fishing mortality at which the yield is largest, which is \(F_{MSY}\). Default TRUE.

reference_lines

Whether to draw reference lines (the current fishing mortality as "Current F", and the F_MSY species parameter if the species has one) as vertical lines. See plot.MizerScan().

log_y, log

Whether to use a logarithmic y-axis, see parsePlotLog(). Unlike most mizer plots this defaults to FALSE, because the yield is exactly zero at zero fishing mortality and a logarithmic axis would drop the point that anchors the curve.

return_data

If TRUE the MizerScan object underlying the plot is returned instead of the plot. Default FALSE.

progress_bar

If TRUE a text progress bar is shown while the fishing mortalities are swept. Defaults to interactive().

...

Further arguments are passed on to scanModel().

See Also

scanModel(), scanFishingMortality(), plot.MizerScan(), getYield()

Other plotting functions: addPlot(), animate(), plot, plot2(), plotBiomass(), plotCDF(), plotCDF2(), plotDiet(), plotFMort(), plotFeedingLevel(), plotGrowthCurves(), plotMizerParams, plotMizerSim, plotPredMort(), plotRelative(), plotSpectra(), plotSpectra2(), plotSpectraRelative(), plotYield(), plotYieldGear(), plotting_functions

Other scan functions: MizerScan(), plot.MizerScan(), scanEffort(), scanModel()

Examples

# \donttest{
plotYieldVsF(NS_params, "Cod", F_max = 1.5, no_steps = 8)

# The fishing mortality that maximises the yield
scan <- plotYieldVsF(NS_params, "Cod", F_max = 1.5, no_steps = 8,
                     return_data = TRUE)
attr(scan, "at_max")
# }