plotM2: Alias for 'plotPredMort()'

In mizer: Dynamic Multi-Species Size Spectrum Modelling

Alias for plotPredMort()

Description

An alias provided for backward compatibility with mizer version <= 1.0

Usage

plotM2(
  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(), plot, plot2(), plotBiomass(), plotCDF(), plotCDF2(), plotDiet(), plotFMort(), plotFeedingLevel(), plotGrowthCurves(), plotMizerParams, plotMizerSim, plotRelative(), plotSpectra(), plotSpectra2(), plotSpectraRelative(), plotYield(), plotYieldGear(), plotYieldVsF(), plotting_functions

Examples

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)

mizer documentation built on Aug. 31, 2026, 5:08 p.m.