R: Plot total fishing mortality of each species by size

plotFMort {mizer}

R Documentation

Plot total fishing mortality of each species by size

Description

After running a projection, plot the total fishing mortality of each species by size. The total fishing mortality is averaged over the specified time range (a single value for the time range can be used to plot a single time step).

Usage

plotFMort(
  object,
  species = NULL,
  time_range,
  all.sizes = FALSE,
  highlight = NULL,
  return_data = FALSE,
  ...
)

plotlyFMort(object, species = NULL, time_range, highlight = NULL, ...)

Arguments

`object`	An object of class MizerSim or MizerParams.
`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.
`time_range`	The time range (either a vector of values, a vector of min and max time, or a single value) to average the abundances over. Default is the final time step. Ignored when called with a MizerParams object.
`all.sizes`	If TRUE, then fishing mortality is plotted also for sizes outside a species' size range. Default 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 three variables 'w', 'value', 'Species' is returned.

Examples


params <-  NS_params
sim <- project(params, effort=1, t_max=20, t_save = 2, progress_bar = FALSE)
plotFMort(sim)
plotFMort(sim, highlight = c("Cod", "Haddock"))
 
# Returning the data frame
fr <- plotFMort(sim, return_data = TRUE)
str(fr)