Plot predation mortality rate of each species against size

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

Usage

plotPredMort(
  object,
  species = NULL,
  all.sizes = FALSE,
  highlight = NULL,
  wlim = c(NA, NA),
  llim = c(NA, NA),
  size_axis = c("w", "l"),
  return_data = FALSE,
  log_x = TRUE,
  log_y = FALSE,
  log = 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.

all.sizes

If TRUE, then predation 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.

wlim

A numeric vector of length two providing lower and upper limits for the weight (x) axis. Use NA to auto-scale to the data range.

llim

A numeric vector of length two providing lower and upper limits for the length (x) axis when size_axis = "l". Use NA to auto-scale to the data range.

size_axis

Whether to plot size as weight ("w", default) or length ("l"), using the allometric weight-length relationship.

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.

log_x

If TRUE (default), use a log10 x-axis.

log_y

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

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.

...

Further arguments used by only some of the methods:

For MizerSim methods:

time_range

The time range (either a vector of values, a vector of min and max time, or a single value) to average the predation mortality over. Default is the final time step.

Value

A ggplot2 object, unless return_data = TRUE, in which case a data frame with the three variables 'w' (or 'l' if size_axis = "l"), 'value', 'Species' is returned.

See also

plotting_functions, getPredMort()

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

Examples

# \donttest{
params <-  NS_params
sim <- project(params, effort=1, t_max=20, t_save = 2, progress_bar = FALSE)
plotPredMort(sim)

plotPredMort(sim, time_range = 10:20)


# Returning the data frame
fr <- plotPredMort(sim, return_data = TRUE)
str(fr)
#> 'data.frame':	934 obs. of  4 variables:
#>  $ w                  : num  0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 0.001 ...
#>  $ Predation mortality: num  2.67 1.11 3.87 4.24 3.4 ...
#>  $ Species            : chr  "Sprat" "Sandeel" "N.pout" "Herring" ...
#>  $ Legend             : chr  "Sprat" "Sandeel" "N.pout" "Herring" ...
# }