plotYieldVsF: Plot the yield of a species against the fishing mortality on...
In mizer: Dynamic Multi-Species Size Spectrum Modelling

plotYieldVsF

R Documentation

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(),
  ...
)

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()`.

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").

Examples


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")

mizer documentation built on Aug. 31, 2026, 5:08 p.m.