Function reference • mizer

Creating a new model Mizer allows the easy set-up of four different types of models, of increasing levels of complexity. See https://sizespectrum.org/mizer/dev/articles/mizer.html#size-spectrum-models for a description of these model types.
`newMultispeciesParams()`	Construct MizerParams object for general multispecies model
`newCommunityParams()`	Set up parameters for a community-type model
`newTraitParams()`	Set up parameters for a trait-based model
`newSheldonParams()`	Set up parameters for a single-species in a Sheldon power-law background
Interactively tuning a model
`tuneParams()`	Launch shiny gadget for tuning parameters
`markBackground()`	Designate species as background species
`addSpecies()`	Add new species
`steady()`	Tune params object to be at steady state
`retuneBackground()`	Retunes abundance of background species.
`rescaleAbundance()`	Rescale Abundance
`rescaleSystem()`	Rescale System
`retuneReproductionEfficiency()`	Retune reproduction efficiency to maintain initial egg abundances
`pruneSpecies()`	Removes species with abundance below a threshold
`setRmax()`	Set maximum recruitment
Setting or changing model parameters
`setParams()`	Set or change any model parameters
`setPredKernel()`	Set predation kernel
`setSearchVolume()`	Set search volume
`setInteraction()`	Set species interaction matrix
`setIntakeMax()`	Set maximum intake rate
`setMetab()`	Set metabolic rate
`setBMort()`	Set background mortality rate
`setReproduction()`	Set reproduction parameters
`setFishing()`	Set fishing parameters
`setPlankton()`	Set up plankton
`setInitial()`	Set initial abundances
`upgradeParams()`	Upgrade MizerParams object from earlier mizer versions
`removeSpecies()`	Remove species from an ecosystem
`renameSpecies()`	Rename species
Running simulations
`project()`	Project size spectrum forward in time
Analysing results
`summary_functions`	Description of summary functions
`getDiet()`	Get diet of predator at size, resolved by prey species
`getBiomass()`	Calculate the total biomass of each species within a size range at each time step.
`getN()`	Calculate the number of individuals within a size range
`getSSB()`	Calculate the SSB of species
`getYield()`	Calculate the total yield of each species
`getYieldGear()`	Calculate the total yield per gear and species
`getGrowthCurves()`	Get growth curves giving weight as a function of age
Calculating indicators
`indicator_functions`	Description of indicator functions
`getProportionOfLargeFish()`	Calculate the proportion of large fish
`getCommunitySlope()`	Calculate the slope of the community abundance
`getMeanWeight()`	Calculate the mean weight of the community
`getMeanMaxWeight()`	Calculate the mean maximum weight of the community
Plotting results
`plotting_functions`	Description of the plotting functions
`plotBiomass()`	Plot the biomass of species through time
`plotDiet()`	Plot diet
`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()`	Alias for plotPredMort
`plot(<MizerSim>,<missing>)` `plot(<MizerParams>,<missing>)`	Summary plot for `MizerSim` objects
`plotPredMort()`	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
`plotlyBiomass()`	Plot the biomass of species against time with plotly
`plotlyFMort()`	Plot total fishing mortality of each species by size with plotly
`plotlyFeedingLevel()`	Plot the feeding level of species by size with plotly
`plotlyGrowthCurves()`	Plot growth curves giving weight as a function of age with plotly
`plotlyPredMort()`	Plot predation mortality rate of each species against size with plotly
`plotlySpectra()`	Plotly plot of the abundance spectra
`plotlyYield()`	Plot the total yield of species through time with plotly
`plotlyYieldGear()`	Plot the total yield of each species by gear through time with plotly
`animateSpectra()`	Animation of the abundance spectra
`getBiomassFrame()`	Get data frame of biomass of species through time, ready for ggplot2
`getSSBFrame()`	Get data frame of spawning stock biomass of species through time, ready for ggplot2
`displayFrames()`	Display frames
Calculating rates used in the model
`getRates()`	Get all rates
`getEncounter()`	Get encounter rate
`getEGrowth()`	Get energy rate available for growth
`getERepro()`	Get energy rate available for reproduction
`getEReproAndGrowth()`	Get energy rate available for reproduction and growth
`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
`getMort()`	Get total mortality rate
`getPlanktonMort()`	Get predation mortality rate for plankton
`getPredMort()`	Get total predation mortality rate
`getPredRate()`	Get predation rate
`getRDD()`	Get density dependent rate of larvae production
`getRDI()`	Get density independent rate of egg production
`getPredKernel()`	Get predation kernel
Functions used in the model
`lognormal_pred_kernel()`	Lognormal predation kernel
`box_pred_kernel()`	Box predation kernel
`power_law_pred_kernel()`	Power-law predation kernel
`knife_edge()`	Weight based knife-edge selectivity function
`sigmoid_length()`	Length based sigmoid selectivity function
`sigmoid_weight()`	Weight based sigmoidal selectivity function
`double_sigmoid_length()`	Length based double-sigmoid selectivity function
`plankton_semichemostat()`	Project plankton using semichemostat model
`plankton_constant()`	Keep plankton abundance constant
`srrBevertonHolt()`	Beverton Holt stock-recruitment function
`srrConstant()`	Set the recruitment function for constant recruitment
`srrNone()`	Identity stock-recruitment function
`srrRicker()`	Ricker stock-recruitment function
`srrSheperd()`	Sheperd stock-recruitment function
Internal helper functions
`set_species_param_default()`	Set a species parameter to a default value
`get_h_default()`	Get default value for h
`get_gamma_default()`	Get default value for gamma
`get_ks_default()`	Get default value for ks
`get_phi()`	Get values from feeding kernel function
`log_breaks()`	Helper function to produce nice breaks on logarithmic axes
`get_initial_n()`	Calculate initial population abundances for the community populations
`get_required_recruitment()`	Determine recruitment rate needed for initial egg abundance
Classes
`MizerParams-class`	A class to hold the parameters for a size based model.
`MizerSim-class`	A class to hold the results of a simulation
`MizerSim()`	Constructor for the `MizerSim` class
`summary(<MizerParams>)`	Summarize MizerParams object
`summary(<MizerSim>)`	Summarize MizerSim object
Example parameter sets
`Baltic_params`	Example MizerParams object for the Central Baltic Sea
`Barents_params`	Example MizerParams object for the Barents Sea
`Benguela_params`	Example MizerParams object for the Benguela current
`NEUSCS_params`	Example MizerParams object for the North East US Continental Shelf (NEUSCS) with 24 species.
`NS_params`	Example MizerParams object for the North Sea example
`NS_species_params`	Example species parameter set based on the North Sea
`NorthSea_params`	Example MizerParams object for the North Sea with 10 species.
`NS_species_params_gears`	Example species parameter set based on the North Sea with different gears
`inter`	Example interaction matrix for the North Sea example
Deprecated These functions are available for backwards compatibility with earlier versions of mizer
`set_multispecies_model()`	Deprecated obsolete function for setting up multispecies parameters
`set_community_model()`	Deprecated function for setting up parameters for a community-type model
`set_trait_model()`	Deprecated function for setting up parameters for a trait-based model
`MizerParams()`	Alias for set_multispecies_model
`getESpawning()`	Alias for getERepro
`getM2()`	Alias for getPredMort
`getM2Background()`	Alias for getPlanktonMort
`getZ()`	Alias for getMort

Reference

Creating a new model

Interactively tuning a model

Setting or changing model parameters

Running simulations

Analysing results

Calculating indicators

Plotting results

Calculating rates used in the model

Functions used in the model

Internal helper functions

Classes

Example parameter sets

Deprecated

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