Package index

Creating a new model

Mizer allows the easy set-up of four different types of models, of increasing level of complexity. See https://sizespectrum.org/mizer/articles/mizer.html#size-spectrum-models for a description of these model types.

newSingleSpeciesParams() experimental: Set up parameters for a single species in a power-law background

newCommunityParams(): Set up parameters for a community-type model

newTraitParams(): Set up parameters for a trait-based multispecies model

newMultispeciesParams(): Set up parameters for a general multispecies model

mizer mizer-package: mizer: Multi-species size-based modelling in R

defaults_edition(): Default editions

Changing model parameters

After you have created a model, you will want to make changes to it while tuning the model and for investigating the impact of changes in parameters.

species_params() `species_params<-`() given_species_params() `given_species_params<-`() calculated_species_params(): Species parameters

gear_params() `gear_params<-`(): Gear parameters

`initialN<-`() initialN(): Initial values for fish spectra

`initialNResource<-`() initialNResource(): Initial value for resource spectrum

initial_effort() `initial_effort<-`() validEffortVector(): Initial fishing effort

Steady state tuning

The first task after creating a multi-species model is to tune the model parameters so that in its steady state the model reproduces average observed growth rates, abundances and fisheries yields.

steady(): Set initial values to a steady state for the model

steadySingleSpecies() experimental: Set initial abundances to single-species steady state abundances

matchGrowth(): Adjust model to produce observed growth

plotBiomassObservedVsModel() plotlyBiomassObservedVsModel() experimental: Plotting observed vs. model biomass data

calibrateBiomass() experimental: Calibrate the model scale to match total observed biomass

calibrateNumber() experimental: Calibrate the model scale to match total observed number

matchBiomasses() experimental: Match biomasses to observations

matchNumbers() experimental: Match numbers to observations

plotYieldObservedVsModel() plotlyYieldObservedVsModel() experimental: Plotting observed vs. model yields

calibrateYield() experimental: Calibrate the model scale to match total observed yield

matchYields() experimental: Match yields to observations

scaleModel() experimental: Change scale of the model

Dynamics tuning

After tuning the steady state, you need to tune the sensitivity of the dynamics to perturbations away from the steady state. The following functions allow you to change the model without destroying the steady state.

setBevertonHolt() experimental: Set Beverton-Holt reproduction without changing the steady state

setResource() resource_rate() `resource_rate<-`() resource_capacity() `resource_capacity<-`() resource_level() `resource_level<-`() resource_dynamics() `resource_dynamics<-`(): Set resource dynamics

setMetadata() getMetadata() experimental: Set metadata for a model

saveParams() readParams() experimental: Save a MizerParams object to file, and restore it

Running simulations

project(): Project size spectrum forward in time

projectToSteady() experimental: Project to steady state

setInitialValues(): Set initial values to values from a simulation

Accessing results

N() NResource(): Time series of size spectra

finalN() finalNResource(): Size spectra at end of simulation

idxFinalT(): Time index at end of simulation

getEffort(): Fishing effort used in simulation

getTimes(): Times for which simulation results are available

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 rate at which biomass of each species is fished

getYieldGear(): Calculate the rate at which biomass of each species is fished by each gear

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

animateSpectra() experimental: Animation of the abundance spectra

plotBiomass() plotlyBiomass(): Plot the biomass of species through time

plotBiomassObservedVsModel() plotlyBiomassObservedVsModel() experimental: Plotting observed vs. model biomass data

plotDiet() experimental: Plot diet, resolved by prey species, as function of predator at size.

plotFMort() plotlyFMort(): Plot total fishing mortality of each species by size

plotFeedingLevel() plotlyFeedingLevel(): Plot the feeding level of species by size

plotGrowthCurves() plotlyGrowthCurves(): Plot growth curves

plot(<MizerSim>,<missing>) plot(<MizerParams>,<missing>): Summary plot for MizerSim objects

plotPredMort() plotlyPredMort(): Plot predation mortality rate of each species against size

plotSpectra() plotlySpectra(): Plot the abundance spectra

plotYield() plotlyYield(): Plot the total yield of species through time

plotYieldGear() plotlyYieldGear(): Plot the total yield of each species by gear through time

plotYieldObservedVsModel() plotlyYieldObservedVsModel() experimental: Plotting observed vs. model yields

setColours() getColours() setLinetypes() getLinetypes() experimental: Set line colours and line types to be used in mizer plots

Manipulating species list

addSpecies() experimental: Add new species

removeSpecies() experimental: Remove species

renameSpecies() experimental: Rename species

Setting custom rates

You can override the rates mizer calculates from the species parameters and gear parameters with your own rate arrays.

setParams(): Set or change any model parameters

setPredKernel() getPredKernel() pred_kernel() `pred_kernel<-`(): Set predation kernel

setSearchVolume() getSearchVolume() search_vol() `search_vol<-`(): Set search volume

setInteraction() interaction_matrix() `interaction_matrix<-`(): Set species interaction matrix

setMaxIntakeRate() getMaxIntakeRate() intake_max() `intake_max<-`(): Set maximum intake rate

setMetabolicRate() getMetabolicRate() metab() `metab<-`(): Set metabolic rate

setExtMort() getExtMort() ext_mort() `ext_mort<-`(): Set external mortality rate

setExtEncounter() getExtEncounter() ext_encounter() `ext_encounter<-`(): Set external encounter rate

setReproduction() getMaturityProportion() maturity() `maturity<-`() getReproductionProportion() repro_prop() `repro_prop<-`(): Set reproduction parameters

setFishing() getCatchability() catchability() `catchability<-`() getSelectivity() selectivity() `selectivity<-`() getInitialEffort(): Set fishing parameters

Calculating rates

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

getCriticalFeedingLevel(): Get critical feeding level

getMort(): Get total mortality rate

getResourceMort(): Get predation mortality rate for resource

getPredMort(): Get total predation mortality rate

getPredRate(): Get predation rate

getRDD(): Get density dependent reproduction rate

getRDI(): Get density independent rate of egg production

Extending Mizer

setRateFunction() getRateFunction() other_params() `other_params<-`(): Set own rate function to replace mizer rate function

setComponent() removeComponent(): Add a dynamical ecosystem component

getComponent(): Get information about other ecosystem components

`initialNOther<-`() initialNOther(): Initial values for other ecosystem components

NOther(): Time series of other components

finalNOther(): Values of other ecosystem components at end of simulation

customFunction() experimental: Replace a mizer function with a custom version

Predation kernels

box_pred_kernel(): Box predation kernel

lognormal_pred_kernel(): Lognormal predation kernel

power_law_pred_kernel(): Power-law predation kernel

truncated_lognormal_pred_kernel(): Truncated lognormal predation kernel

Fishing selectivity functions

double_sigmoid_length(): Length based double-sigmoid selectivity function

knife_edge(): Weight based knife-edge selectivity function

sigmoid_length(): Length based sigmoid selectivity function

sigmoid_weight(): Weight based sigmoidal selectivity function

Resource dynamics

resource_constant(): Keep resource abundance constant

resource_logistic() balance_resource_logistic(): Project resource using logistic model

resource_semichemostat() balance_resource_semichemostat(): Project resource using semichemostat model

setResource() resource_rate() `resource_rate<-`() resource_capacity() `resource_capacity<-`() resource_level() `resource_level<-`() resource_dynamics() `resource_dynamics<-`(): Set resource dynamics

resource_params() `resource_params<-`(): Resource parameters

Reproduction functions

BevertonHoltRDD(): Beverton Holt function to calculate density-dependent reproduction rate

RickerRDD() experimental: Ricker function to calculate density-dependent reproduction rate

SheperdRDD() experimental: Sheperd function to calculate density-dependent reproduction rate

constantEggRDI() experimental: Choose egg production to keep egg density constant

constantRDD() experimental: Give constant reproduction rate

noRDD(): Give density-independent reproduction rate

getReproductionLevel() experimental: Get reproduction level

Internal rate functions

These functions are used by project() to calculate instantaneous rates at each time step. You should use the get…() functions instead of the mizer…() functions.

mizerRates(): Get all rates needed to project standard mizer model

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 needed to project standard mizer model

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

mizerResourceMort(): Get predation mortality rate for resource needed to project standard mizer model

Internal helper functions

age_mat(): Calculate age at maturity

age_mat_vB(): Calculate age at maturity from von Bertalanffy growth parameters

calc_selectivity(): Calculate selectivity from gear parameters

completeSpeciesParams(): Complete species parameter data frame with default values

constant_other(): Helper function to keep other components constant

default_pred_kernel_params(): Set defaults for predation kernel parameters

different(): Check whether two objects are different

distanceMaxRelRDI() experimental: Measure distance between current and previous state in terms of RDI

distanceSSLogN() experimental: Measure distance between current and previous state in terms of fish abundances

emptyParams(): Create empty MizerParams object of the right size

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_required_reproduction(): Determine reproduction rate needed for initial egg abundance

get_size_range_array(): Get size range array

get_time_elements(): Get_time_elements

initial_effort() `initial_effort<-`() validEffortVector(): Initial fishing effort

l2w() w2l(): Length-weight conversion

needs_upgrading(): Determine whether a MizerParams or MizerSim object needs to be upgraded

project_simple(): Project abundances by a given number of time steps into the future

set_species_param_default(): Set a species parameter to a default value

validGearParams(): Check validity of gear parameters and set defaults

validSpeciesParams(): Validate species parameter data frame

valid_species_arg(): Helper function to assure validity of species argument

Classes

MizerParams-class: A class to hold the parameters for a size based model.

summary(<MizerParams>): Summarize MizerParams object

compareParams() experimental: Compare two MizerParams objects and print out differences

w() w_full() dw() dw_full(): Size bins

validParams(): Validate MizerParams object and upgrade if necessary using upgradeParams().

upgradeParams(): Upgrade MizerParams object from earlier mizer versions

MizerSim-class: A class to hold the results of a simulation

summary(<MizerSim>): Summarize MizerSim object

upgradeSim(): Upgrade MizerSim object from earlier mizer versions

MizerSim(): Constructor for the MizerSim class

getParams(): Extract the parameter object underlying a simulation

Example parameter sets

More example parameter sets are available via https://sizespectrum.org/mizerExamples

NS_params: Example MizerParams 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

NS_interaction: Example interaction matrix for the North Sea example

NS_sim: Example MizerSim object for the North Sea example

Deprecated

These functions are available for backwards compatibility with earlier versions of mizer

MizerParams() deprecated: Alias for set_multispecies_model()

getESpawning() deprecated: Alias for getERepro()

getM2() deprecated: Alias for getPredMort()

getM2Background() deprecated: Alias for getResourceMort()

getPhiPrey() deprecated: Get available energy

getZ() deprecated: Alias for getMort()

inter deprecated: Alias for NS_interaction

plotM2() deprecated: Alias for plotPredMort()

setRmax() deprecated: Alias for setBevertonHolt()

set_community_model() deprecated: Deprecated function for setting up parameters for a community-type model

set_multispecies_model() deprecated: Deprecated obsolete function for setting up multispecies parameters

set_trait_model() deprecated: Deprecated function for setting up parameters for a trait-based model