plotYieldGear: Plot the total yield of each species by gear through time

In sizespectrum/mizer: Dynamic Multi-Species Size Spectrum Modelling

Plot the total yield of each species by gear through time

Description

After running a projection, the total yield of each species by fishing gear can be plotted against time.

Usage

plotYieldGear(
  sim,
  species = NULL,
  total = FALSE,
  highlight = NULL,
  return_data = FALSE,
  ...
)

plotlyYieldGear(sim, species = NULL, total = FALSE, highlight = NULL, ...)

Arguments

sim	An object of class MizerSim
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.
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)

Details

This plot is pretty easy to do by hand. It just gets the biomass using the getYieldGear() method and plots using the ggplot2 package. You can then fiddle about with colours and linetypes etc. Just look at the source code for details.

Value

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

See Also

plotting_functions, getYieldGear()

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

Examples

params <-  NS_params
sim <- project(params, effort=1, t_max=20, t_save = 0.2, progress_bar = FALSE)
plotYieldGear(sim)
plotYieldGear(sim, species = c("Cod", "Herring"), total = TRUE)

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

sizespectrum/mizer documentation built on April 14, 2024, 3:08 a.m.