mizer (version 2.3.0)

plotYield: Plot the total yield of species through time

Description

After running a projection, the total yield of each species across all fishing gears can be plotted against time. The yield is obtained with getYield().

Usage

plotYield(
  sim,
  sim2,
  species = NULL,
  total = FALSE,
  log = TRUE,
  highlight = NULL,
  return_data = FALSE,
  ...
)
plotlyYield(
  sim,
  sim2,
  species = NULL,
  total = FALSE,
  log = TRUE,
  highlight = NULL,
  ...
)

Arguments

sim

An object of class '>MizerSim

sim2

An optional second object of class '>MizerSim. If this is provided its yields will be shown on the same plot in bolder lines.

species

The species to be selected. Optional. By default all target species are selected. A vector of species names, or a numeric vector with the species indices, or a logical vector indicating for each species whether it is to be selected (TRUE) or not.

total

A boolean value that determines whether the total over all species in the system is plotted as well. Note that even if the plot only shows a selection of species, the total is including all species. Default is FALSE.

log

Boolean whether yield should be plotted on a logarithmic axis. Defaults to true.

highlight

Name or vector of names of the species to be highlighted.

return_data

A boolean value that determines whether the formatted data used for the plot is returned instead of the plot itself. Default value is FALSE

...

Other arguments (currently unused)

Value

A ggplot2 object, unless return_data = TRUE, in which case a data frame with the three variables 'Year', 'Yield', 'Species' is returned.

See Also

plotting_functions, getYield()

Other plotting functions: animateSpectra(), plot,MizerSim,missing-method, plotBiomass(), plotDiet(), plotFMort(), plotFeedingLevel(), plotGrowthCurves(), plotPredMort(), plotSpectra(), plotYieldGear(), plotting_functions

Examples

# NOT RUN {
params <- NS_params
sim <- project(params, effort = 1, t_max = 20, t_save = 0.2, progress_bar = FALSE)
plotYield(sim)
plotYield(sim, species = c("Cod", "Herring"), total = TRUE)

# Comparing with yield from twice the effort
sim2 <- project(params, effort=2, t_max=20, t_save = 0.2, progress_bar = FALSE)
plotYield(sim, sim2, species = c("Cod", "Herring"), log = FALSE)

# Returning the data frame
fr <- plotYield(sim, return_data = TRUE)
str(fr)
# }