After running a projection, the total yield of each species by fishing gear can be plotted against time.
Usage
plotYieldGear(
sim,
species = NULL,
gears = 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.
- gears
A vector of gear names to be included in the plot. Default is all gears.
- 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)
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.
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.
See also
plotting_functions, getYieldGear()
Other plotting functions:
animateSpectra(),
plot,MizerSim,missing-method,
plotBiomass(),
plotDiet(),
plotFMort(),
plotFeedingLevel(),
plotGrowthCurves(),
plotPredMort(),
plotSpectra(),
plotYield(),
plotting_functions
Examples
# \donttest{
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)
#> 'data.frame': 1212 obs. of 4 variables:
#> $ Year : num 0 0.2 0.4 0.6 0.8 1 1.2 1.4 1.6 1.8 ...
#> $ Yield : num 2.21e+11 1.86e+11 1.60e+11 1.42e+11 1.30e+11 ...
#> $ Species: Factor w/ 12 levels "Sprat","Sandeel",..: 1 1 1 1 1 1 1 1 1 1 ...
#> $ Gear : Factor w/ 4 levels "Industrial","Pelagic",..: 1 1 1 1 1 1 1 1 1 1 ...
# }