Plot the total yield of species through time

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(
  object,
  sim2,
  species = NULL,
  total = FALSE,
  log_x = FALSE,
  log_y = TRUE,
  log = NULL,
  ylim = c(NA, NA),
  tlim = c(NA, NA),
  highlight = NULL,
  return_data = FALSE,
  ...
)

Arguments

object

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 yield from all species is plotted as well. Default is FALSE.

log_x

If TRUE, use a log10 x-axis. Default is FALSE.

log_y

If TRUE, use a log10 y-axis. Default is TRUE.

log

Character string specifying which axes should use log10 scales, in the same form as the base plot() argument. For example, "x", "y", "xy" or "". If supplied, this overrides log_x and log_y. For backward compatibility, TRUE and FALSE are interpreted as setting only log_y.

ylim

A numeric vector of length two providing lower and upper limits for the y axis. Use NA to refer to the existing minimum or maximum.

tlim

A numeric vector of length two providing lower and upper limits for the time axis, e.g. c(1980, 2000). Use NA to apply no limit at that end. Default is c(NA, NA).

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 is FALSE.

...

Arguments passed to getYield().

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

Examples

# \donttest{
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)
#> 'data.frame':	1212 obs. of  3 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 ...
# }