plotYieldGear.Rd

% Generated by roxygen2: do not edit by hand
% Please edit documentation in R/plots.R
\name{plotYieldGear}
\alias{plotYieldGear}
\alias{plotYieldGear.MizerSim}
\alias{plotlyYieldGear}
\title{Plot the total yield of each species by gear through time}
\usage{
plotYieldGear(object, ...)

\method{plotYieldGear}{MizerSim}(
  object,
  species = NULL,
  gears = NULL,
  total = FALSE,
  highlight = NULL,
  return_data = FALSE,
  ...
)

plotlyYieldGear(object, species = NULL, total = FALSE, highlight = NULL, ...)
}
\arguments{
\item{object}{An object of class \linkS4class{MizerSim}}

\item{...}{Other arguments (currently unused)}

\item{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.}

\item{gears}{A vector of gear names to be included in the plot. Default is
all gears.}

\item{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.}

\item{highlight}{Name or vector of names of the species to be highlighted.}

\item{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}
}
\value{
A ggplot2 object, unless \code{return_data = TRUE}, in which case a data
frame with the four variables 'Year', 'Yield', 'Species' and 'Gear' is
returned.
}
\description{
After running a projection, the total yield of each species by fishing gear
can be plotted against time.
}
\details{
This plot is pretty easy to do by hand. It just
gets the biomass using the \code{\link[=getYieldGear]{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.
}
\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)
}
}
\seealso{
\link{plotting_functions},  \code{\link[=getYieldGear]{getYieldGear()}}

Other plotting functions:
\code{\link[=addPlot]{addPlot()}},
\code{\link[=animate.ArrayTimeBySpeciesBySize]{animate.ArrayTimeBySpeciesBySize()}},
\code{\link{plot}},
\code{\link[=plot2]{plot2()}},
\code{\link[=plotBiomass]{plotBiomass()}},
\code{\link[=plotCDF]{plotCDF()}},
\code{\link[=plotCDF2]{plotCDF2()}},
\code{\link[=plotDiet]{plotDiet()}},
\code{\link[=plotFMort]{plotFMort()}},
\code{\link[=plotFeedingLevel]{plotFeedingLevel()}},
\code{\link[=plotGrowthCurves]{plotGrowthCurves()}},
\code{\link{plotMizerParams}},
\code{\link{plotMizerSim}},
\code{\link[=plotPredMort]{plotPredMort()}},
\code{\link[=plotRelative]{plotRelative()}},
\code{\link[=plotSpectra]{plotSpectra()}},
\code{\link[=plotSpectra2]{plotSpectra2()}},
\code{\link[=plotSpectraRelative]{plotSpectraRelative()}},
\code{\link[=plotYield]{plotYield()}},
\code{\link{plotting_functions}}
}
\concept{plotting functions}