ArraySpeciesBySize      S3 class for species x size rate arrays
ArrayTimeBySpecies      S3 class for time x species arrays
ArrayTimeBySpeciesBySize
                        S3 class for time x species x size arrays
BevertonHoltRDD         Beverton Holt function to calculate
                        density-dependent reproduction rate
MizerParams             Alias for 'set_multispecies_model()'
MizerParams-class       A class to hold the parameters for a size based
                        model.
MizerSim                Constructor for the 'MizerSim' class
MizerSim-class          A class to hold the results of a simulation
N                       Time series of size spectra
NOther                  Time series of other components
NS_interaction          Example interaction matrix for the North Sea
                        example
NS_params               Example MizerParams object for the North Sea
                        example
NS_sim                  Example MizerSim object for the North Sea
                        example
NS_species_params       Example species parameter set based on the
                        North Sea
NS_species_params_gears
                        Example species parameter set based on the
                        North Sea with different gears
RickerRDD               Ricker function to calculate density-dependent
                        reproduction rate
SheperdRDD              Sheperd function to calculate density-dependent
                        reproduction rate
addPlot                 Add lines to an existing plot
addSpecies              Add new species
age_mat                 Calculate age at maturity
age_mat_vB              Calculate age at maturity from von Bertalanffy
                        growth parameters
animate.ArrayTimeBySpeciesBySize
                        Animate size-dependent quantities through time
as.data.frame           Convert mizer arrays to data frames
box_pred_kernel         Box predation kernel
calc_selectivity        Calculate selectivity from gear parameters
calibrateBiomass        Calibrate the model scale to match total
                        observed biomass
calibrateNumber         Calibrate the model scale to match total
                        observed number
calibrateYield          Calibrate the model scale to match total
                        observed yield
clearExtensionChain     Clear the registered extension chain
coerceToExtensionClass
                        Coerce a mizer object to its registered
                        extension class
compareParams           Compare two MizerParams objects and print out
                        differences
completeSpeciesParams   Alias for 'validSpeciesParams()'
constantEggRDI          Choose egg production to keep egg density
                        constant
constantRDD             Give constant reproduction rate
constant_other          Helper function to keep other components
                        constant
customFunction          Replace a mizer function with a custom version
default_pred_kernel_params
                        Set defaults for predation kernel parameters
defaults_edition        Default editions
different               Check whether two objects are different
distanceMaxRelRDI       Measure distance between current and previous
                        state in terms of RDI
distanceSSLogN          Measure distance between current and previous
                        state in terms of fish abundances
double_sigmoid_length   Length based double-sigmoid selectivity
                        function
emptyParams             Create empty MizerParams object of the right
                        size
expandSizeGrid          Expand the size grid
finalN                  Size spectra at end of simulation
finalParams             Extract the final state from a simulation
gear_params             Gear parameters
getBiomass              Calculate the total biomass of each species
                        within a size range at each time step.
getCommunitySlope       Calculate the slope of the community abundance
getCriticalFeedingLevel
                        Get critical feeding level
getDiet                 Get diet of predator at size, resolved by prey
                        species
getDiffusion            Get diffusion rate from predation
getEGrowth              Get energy rate available for growth
getERepro               Get energy rate available for reproduction
getEReproAndGrowth      Get energy rate available for reproduction and
                        growth
getESpawning            Alias for 'getERepro()'
getEffort               Fishing effort used in simulation
getEncounter            Get encounter rate
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
getFlux                 Get flux into size bins
getGrowthCurves         Get growth curves giving weight as a function
                        of age
getM2                   Alias for 'getPredMort()'
getM2Background         Alias for 'getResourceMort()'
getMeanMaxWeight        Calculate the mean maximum weight of the
                        community
getMeanWeight           Calculate the mean weight of the community
getMort                 Get total mortality rate
getN                    Calculate the number of individuals within a
                        size range
getParams               Extract the model state from a simulation
getPhiPrey              Get available energy
getPredMort             Get total predation mortality rate
getPredRate             Get predation rate
getProportionOfLargeFish
                        Calculate the proportion of large fish
getRDD                  Get density dependent reproduction rate
getRDI                  Get density independent rate of egg production
getRates                Get all rates
getRegisteredExtensions
                        Get the registered mizer extension chain
getReproductionLevel    Get reproduction level
getRequiredRDD          Determine reproduction rate needed for initial
                        egg abundance
getResourceMort         Get predation mortality rate for resource
getSSB                  Calculate the SSB of species
getSimParams            Extract the projection parameters used to
                        produce a simulation
getTimes                Times for which simulation results are
                        available
getTrophicLevel         Get trophic level of individuals at size
getTrophicLevelBySpecies
                        Get mean trophic level of each species
getYield                Calculate the rate at which biomass of each
                        species is fished
getYieldGear            Calculate the rate at which biomass of each
                        species is fished by each gear
getZ                    Alias for 'getMort()'
get_f0_default          Get default value for f0
get_gamma_default       Get default value for gamma
get_initial_n           Calculate initial population abundances
get_ks_default          Get default value for 'ks'
get_phi                 Get values from feeding kernel function
get_size_range_array    Get size range array
get_steady_state_n      Calculate steady state abundance
get_time_elements       Get array indices for a time range in a
                        MizerSim object
indicator_functions     Description of indicator functions
initialN<-              Initial values for fish spectra
initialNOther<-         Initial values for other ecosystem components
initialNResource<-      Initial value for resource spectrum
initialParams           Extract the initial state from a simulation
initial_effort          Initial fishing effort
inter                   Alias for 'NS_interaction'
is.ArraySpeciesBySize   Test if an object is a ArraySpeciesBySize
is.ArrayTimeBySpecies   Test if an object is a ArrayTimeBySpecies
is.ArrayTimeBySpeciesBySize
                        Test if an object is an
                        ArrayTimeBySpeciesBySize
knife_edge              Weight based knife-edge selectivity function
l2w                     Length-weight conversion
lognormal_pred_kernel   Lognormal predation kernel
markBackground          Designate species as background species
matchBiomasses          Match biomasses to observations
matchGrowth             Adjust model to produce observed growth
matchNumbers            Match numbers to observations
matchYields             Match yields to observations
mizer-package           mizer: Multi-species size-based modelling in R
mizerDiffusion          Calculate diffusion rate
mizerEGrowth            Get energy rate available for growth needed to
                        project standard mizer model
mizerERepro             Get energy rate available for reproduction
                        needed to project standard mizer model
mizerEReproAndGrowth    Get energy rate available for reproduction and
                        growth needed to project standard mizer model
mizerEncounter          Get encounter rate during projection
mizerFMort              Get the total fishing mortality rate from all
                        fishing gears
mizerFMortGear          Get the fishing mortality needed to project
                        standard mizer model
mizerFeedingLevel       Get feeding level needed to project standard
                        mizer model
mizerMort               Get total mortality rate needed to project
                        standard mizer model
mizerPredMort           Get total predation mortality rate needed to
                        project standard mizer model
mizerPredRate           Get predation rate needed to project standard
                        mizer model
mizerRDI                Get density-independent rate of reproduction
                        needed to project standard mizer model
mizerRates              Get all rates needed to project standard mizer
                        model
mizerResourceMort       Get predation mortality rate for resource
                        needed to project standard mizer model
needs_upgrading         Determine whether a MizerParams or MizerSim
                        object needs to be upgraded
newCommunityParams      Set up parameters for a community-type model
newMultispeciesParams   Set up parameters for a general multispecies
                        model
newSingleSpeciesParams
                        Set up parameters for a single species in a
                        power-law background
newTraitParams          Set up parameters for a trait-based
                        multispecies model
noRDD                   Give density-independent reproduction rate
plot                    Plot mizer arrays
plot2                   Compare two mizer arrays in a single plot
plotBiomass             Plot the biomass of species through time
plotBiomassObservedVsModel
                        Plotting observed vs. model biomass data
plotCDF                 Plot cumulative abundance or biomass
                        distributions
plotCDF2                Compare cumulative abundance or biomass
                        distributions from two objects
plotDiet                Plot diet, resolved by prey species, as
                        function of predator at size.
plotFMort               Plot total fishing mortality of each species by
                        size
plotFeedingLevel        Plot the feeding level of species by size
plotGrowthCurves        Plot growth curves
plotHover.ArraySpeciesBySize
                        Create a hover-enabled plotly plot from a mizer
                        object
plotM2                  Alias for 'plotPredMort()'
plotMizerParams         Summary plot for 'MizerParams' objects
plotMizerSim            Summary plot for 'MizerSim' objects
plotPredMort            Plot predation mortality rate of each species
                        against size
plotRelative            Plot relative difference between two mizer
                        arrays
plotSpectra             Plot abundance and biomass spectra
plotSpectra2            Compare abundance and biomass spectra from two
                        objects
plotSpectraRelative     Plot relative difference between abundance
                        spectra
plotYield               Plot the total yield of species through time
plotYieldGear           Plot the total yield of each species by gear
                        through time
plotYieldObservedVsModel
                        Plotting observed vs. model yields
plotting_functions      Description of the plotting functions
power_law_pred_kernel   Power-law predation kernel
print                   Print mizer objects
project                 Project size spectrum forward in time
projectRDD              Get density-dependent reproduction rate during
                        projection
projectToSteady         Project to steady state
project_n               Project values for first time step of Euler
                        method
project_n_2             Project values with a predictor-corrector
                        method
project_simple          Project abundances by a given number of time
                        steps into the future
registerExtension       Register a single mizer extension for this R
                        session
registerExtensions      Register mizer extensions for this R session
removeBackgroundSpecies
                        Remove all background species
removeSpecies           Remove species
renameGear              Rename gears
renameSpecies           Rename species
resource_constant       Keep resource abundance constant
resource_logistic       Project resource using logistic model
resource_params         Resource parameters
resource_semichemostat
                        Project resource using semichemostat model
saveParams              Save and restore mizer objects
scaleModel              Change scale of the model
scaleRates              Rescale all rates in a mizer model
setBevertonHolt         Set Beverton-Holt reproduction without changing
                        the steady state
setColours              Set line colours and line types to be used in
                        mizer plots
setComponent            Add a dynamical ecosystem component
setExtDiffusion         Set external diffusion rate
setExtEncounter         Set external encounter rate
setExtMort              Set external mortality rate
setFishing              Set fishing parameters
setInitialValues        Set initial values to values from a simulation
setInteraction          Set species interaction matrix
setMaxIntakeRate        Set maximum intake rate
setMetabolicRate        Set metabolic rate
setMetadata             Set metadata for a model
setParams               Set or change any model parameters
setPredKernel           Set predation kernel
setRateFunction         Set own rate function to replace mizer rate
                        function
setReproduction         Set reproduction parameters
setResource             Set resource dynamics
setRmax                 Alias for 'setBevertonHolt()'
setSearchVolume         Set search volume
set_community_model     Deprecated function for setting up parameters
                        for a community-type model
set_multispecies_model
                        Deprecated obsolete function for setting up
                        multispecies parameters
set_species_param_default
                        Set a species parameter to a default value
set_trait_model         Deprecated function for setting up parameters
                        for a trait-based model
sigmoid_length          Length based sigmoid selectivity function
sigmoid_weight          Weight based sigmoidal selectivity function
species_params          Species parameters
steady                  Set initial values to a steady state for the
                        model
steadySingleSpecies     Set initial abundances to solution of
                        steady-state equation with current rates
str                     Display the structure of mizer objects
str.MizerParams         Display structure of MizerParams object
str.MizerSim            Display structure of MizerSim object
summary                 Summarise mizer objects
summary.MizerParams     Summarize MizerParams object
summary.MizerSim        Summarize MizerSim object
summary_functions       Description of summary functions
truncated_lognormal_pred_kernel
                        Truncated lognormal predation kernel
use_predation_diffusion
                        Get or set the use_predation_diffusion flag
validEffortVector       Make a valid effort vector
validGearParams         Check validity of gear parameters and set
                        defaults
validParams             Validate MizerParams object and upgrade if
                        necessary
validSim                Validate MizerSim object and upgrade if
                        necessary
validSpeciesParams      Validate species parameter data frame
valid_gears_arg         Helper function to assure validity of gears
                        argument
valid_species_arg       Helper function to assure validity of species
                        argument
w                       Size bins
