MizerParams             Constructors for objects of 'MizerParams' class
MizerParams-class       A class to hold the parameters for a size based
                        model.
MizerSim                Constructor for the 'MizerSim' class
MizerSim-class          MizerSim
NS_species_params       Example parameter set based on the North Sea
NS_species_params_gears
                        Example parameter set based on the North Sea
                        with different gears
addSpecies              Add more species into an ecosystem with
                        background species.
display_frames          Display frames
getBiomass              Calculate the total biomass of each species
                        within a size range at each time step.
getBiomassFrame         Get data frame of biomass of species through
                        time, ready for ggplot2
getCommunitySlope       Calculate the slope of the community abundance
getEGrowth              Get energy rate available for growth
getEReproAndGrowth      Get energy after metabolism and movement
getESpawning            Get energy rate available for reproduction
getFMort                Get the total fishing mortality rate from all
                        fishing gears by time, species and size.
getFMortGear            Get the fishing mortality by time, gear,
                        species and size
getFeedingLevel         Get feeding level
getM2                   getM2 method for the size based model
getM2Background         Get predation mortality rate for plankton
getMeanMaxWeight        Calculate the mean maximum weight of the
                        community
getMeanWeight           Calculate the mean weight of the community
getN                    Calculate the total abundance in terms of
                        numbers of species within a size range
getPhiPrey              Get available energy
getPredRate             Get predation rate
getProportionOfLargeFish
                        Calculate the proportion of large fish
getRDD                  Get density dependent recruitment
getRDI                  Get density independent recruitment
getSSB                  Calculate the SSB of species
getSSBFrame             Get data frame of spawning stock biomass of
                        species through time, ready for ggplot2
getYield                Calculate the total yield of each species
getYieldGear            Calculate the total yield per gear and species
getZ                    Get total mortality rate
get_initial_n           Calculate initial population abundances for the
                        community populations
inter                   Example interaction matrix for the North Sea
                        example
knife_edge              Size based knife-edge selectivity function
log_breaks              Helper function to produce nice breaks on
                        logarithmic axes
mizer                   mizer: Multi-species size-based modelling in R
plot,MizerSim,missing-method
                        Summary plot for 'MizerSim' objects
plotBiomass             Plot the biomass of species through time
plotFMort               Plot total fishing mortality of each species by
                        size
plotFeedingLevel        Plot the feeding level of species by size
plotGrowthCurves        Plot growth curves giving weight as a function
                        of age
plotM2                  Plot predation mortality rate of each species
                        against size
plotSpectra             Plot the abundance spectra
plotYield               Plot the total yield of species through time
plotYieldGear           Plot the total yield of each species by gear
                        through time
project                 project method for the size based modelling
project_methods         Methods used for projecting
retune_abundance        Retunes abundance of background species.
setBackground           Designate species as background species
set_community_model     Sets up parameters for a community-type model
set_scaling_model       Sets up parameters for a scale free trait-based
                        model
set_trait_model         Sets up parameters for a trait-based model
sigmoid_length          Length based sigmoid selectivity function
steady                  Tune params object to be at steady state
summary,MizerParams-method
                        Summarize MizerParams object
summary,MizerSim-method
                        Summarize MizerSim object
wrapper_functions       Functions used for setting up models
