# Dynamic Multi-Species Size Spectrum Modelling

## Documentation for package ‘mizer’ version 3.1.0

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

A B C D E F G I K L M N O P R S T U V W

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

## -- A --

addPlot | Add lines to an existing plot
addPlot.ArraySpeciesBySize | Add lines to an existing plot
addPlot.ArrayTimeBySpecies | 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
age_mat_vB.data.frame | Calculate age at maturity from von Bertalanffy growth parameters
age_mat_vB.default | Calculate age at maturity from von Bertalanffy growth parameters
age_mat_vB.MizerParams | Calculate age at maturity from von Bertalanffy growth parameters
animate | Animate size-dependent quantities through time
animate.ArrayTimeBySpeciesBySize | Animate size-dependent quantities through time
animate.MizerSim | Animate size-dependent quantities through time
animateSpectra | Animate size-dependent quantities through time
ArrayResourceBySize | S3 class for resource size spectra
ArraySpeciesBySize | S3 class for species x size rate arrays
ArrayTimeByResourceBySize | S3 class for time x resource-size arrays
ArrayTimeBySpecies | S3 class for time x species arrays
ArrayTimeBySpeciesBySize | S3 class for time x species x size arrays
as.data.frame | Convert mizer arrays to data frames
as.data.frame.ArraySpeciesBySize | Convert mizer arrays to data frames
as.data.frame.ArrayTimeBySpecies | Convert mizer arrays to data frames
as.data.frame.ArrayTimeBySpeciesBySize | Convert mizer arrays to data frames

## -- B --

balance_resource_logistic | Project resource using logistic model
balance_resource_semichemostat | Project resource using semichemostat model
BevertonHoltRDD | Beverton Holt function to calculate density-dependent reproduction rate
box_pred_kernel | Box predation kernel

## -- C --

calculated_species_params | Species parameters
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
catchability | Set fishing parameters
catchability<- | Set fishing parameters
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

## -- D --

defaults_edition | Default editions
default_pred_kernel_params | Set defaults for predation kernel parameters
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
dw | Size bins
dw_full | Size bins

## -- E --

emptyParams | Create empty MizerParams object of the right size
expandSizeGrid | Expand the size grid
expandSizeGrid.MizerParams | Expand the size grid
ext_diffusion | Set external diffusion rate
ext_diffusion<- | Set external diffusion rate
ext_encounter | Set external encounter rate
ext_encounter<- | Set external encounter rate
ext_mort | Set external mortality rate
ext_mort<- | Set external mortality rate

## -- F --

finalN | Size spectra at end of simulation
finalNOther | Time series of other components
finalNResource | Size spectra at end of simulation
finalParams | Extract the final state from a simulation

## -- G --

gear_params | Gear parameters
gear_params<- | Gear parameters
getBiomass | Calculate the total biomass of each species within a size range at each time step.
getCatchability | Set fishing parameters
getColours | Set line colours and line types to be used in mizer plots
getCommunitySlope | Calculate the slope of the community abundance
getComponent | Add a dynamical ecosystem component
getCriticalFeedingLevel | Get critical feeding level
getDiet | Get diet of predator at size, resolved by prey species
getDiffusion | Get diffusion rate from predation
getEffort | Fishing effort used in simulation
getEGrowth | Get energy rate available for growth
getEncounter | Get encounter rate
getERepro | Get energy rate available for reproduction
getEReproAndGrowth | Get energy rate available for reproduction and growth
getESpawning | Alias for 'getERepro()'
getExtEncounter | Set external encounter rate
getExtMort | Set external mortality rate
getFeedingLevel | Get feeding level
getFlux | Get flux into size bins
getFlux.MizerParams | Get flux into size bins
getFlux.MizerSim | Get flux into size bins
getFluxGradient | Get flux gradient
getFluxGradient.MizerParams | Get flux gradient
getFluxGradient.MizerSim | Get flux gradient
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
getGrowthCurves | Get growth curves giving weight as a function of age
getInitialEffort | Set fishing parameters
getLinetypes | Set line colours and line types to be used in mizer plots
getM2 | Alias for 'getPredMort()'
getM2Background | Alias for 'getResourceMort()'
getMaturityProportion | Set reproduction parameters
getMaxIntakeRate | Set maximum intake rate
getMeanMaxWeight | Calculate the mean maximum weight of the community
getMeanWeight | Calculate the mean weight of the community
getMetabolicRate | Set metabolic rate
getMetadata | Set metadata for a model
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
getPredKernel | Set predation kernel
getPredMort | Get total predation mortality rate
getPredRate | Get predation rate
getProportionOfLargeFish | Calculate the proportion of large fish
getRateFunction | Set own rate function to replace mizer rate function
getRates | Get all rates
getRDD | Get density dependent reproduction rate
getRDI | Get density independent rate of egg production
getRegisteredExtensions | Get the registered mizer extension chain
getReproductionLevel | Get reproduction level
getReproductionProportion | Set reproduction parameters
getRequiredRDD | Determine reproduction rate needed for initial egg abundance
getResourceMort | Get predation mortality rate for resource
getSearchVolume | Set search volume
getSelectivity | Set fishing parameters
getSimParams | Extract the projection parameters used to produce a simulation
getSSB | Calculate the SSB of species
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
given_species_params | Species parameters
given_species_params<- | Species parameters

## -- I --

idxFinalT | Size spectra at end of simulation
indicator_functions | Description of indicator functions
initialN | Initial values for fish spectra
initialN.MizerParams | Initial values for fish spectra
initialN.MizerSim | Initial values for fish spectra
initialN<- | Initial values for fish spectra
initialNOther | Initial values for other ecosystem components
initialNOther<- | Initial values for other ecosystem components
initialNResource | Initial value for resource spectrum
initialNResource.MizerParams | Initial value for resource spectrum
initialNResource.MizerSim | Initial value for resource spectrum
initialNResource<- | Initial value for resource spectrum
initialParams | Extract the initial state from a simulation
initial_effort | Initial fishing effort
initial_effort<- | Initial fishing effort
intake_max | Set maximum intake rate
intake_max<- | Set maximum intake rate
inter | Alias for 'NS_interaction'
interaction_matrix | Set species interaction matrix
interaction_matrix<- | Set species interaction matrix
is.ArrayResourceBySize | Test if an object is an ArrayResourceBySize
is.ArraySpeciesBySize | Test if an object is a ArraySpeciesBySize
is.ArrayTimeByResourceBySize | Test if an object is an ArrayTimeByResourceBySize
is.ArrayTimeBySpecies | Test if an object is a ArrayTimeBySpecies
is.ArrayTimeBySpeciesBySize | Test if an object is an ArrayTimeBySpeciesBySize

## -- K --

knife_edge | Weight based knife-edge selectivity function

## -- L --

l2w | Length-weight conversion
lognormal_pred_kernel | Lognormal predation kernel

## -- M --

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
maturity | Set reproduction parameters
maturity<- | Set reproduction parameters
metab | Set metabolic rate
metab<- | Set metabolic rate
mizer | 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
mizerEncounter | Get encounter rate during projection
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
mizerFeedingLevel | Get feeding level 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
mizerMort | Get total mortality rate needed to project standard mizer model
MizerParams | Alias for 'set_multispecies_model()'
MizerParams-class | A class to hold the parameters for a size based model.
mizerPredMort | Get total predation mortality rate needed to project standard mizer model
mizerPredRate | Get predation rate needed to project standard mizer model
mizerRates | Get all rates 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
MizerSim | Constructor for the 'MizerSim' class
MizerSim-class | A class to hold the results of a simulation

## -- N --

N | Time series of size spectra
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
NOther | Time series of other components
NResource | Time series of size spectra
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

## -- O --

other_params | Set own rate function to replace mizer rate function
other_params<- | Set own rate function to replace mizer rate function

## -- P --

plot | Plot mizer arrays
plot.ArrayResourceBySize | Plot mizer arrays
plot.ArraySpeciesBySize | Plot mizer arrays
plot.ArrayTimeByResourceBySize | Plot mizer arrays
plot.ArrayTimeBySpecies | Plot mizer arrays
plot.ArrayTimeBySpeciesBySize | Plot mizer arrays
plot.MizerParams | Summary plot for 'MizerParams' objects
plot.MizerSim | Summary plot for 'MizerSim' objects
plot2 | Compare two mizer arrays in a single plot
plot2.ArraySpeciesBySize | Compare two mizer arrays in a single plot
plot2.ArrayTimeBySpecies | Compare two mizer arrays in a single plot
plot2.ArrayTimeBySpeciesBySize | Compare two mizer arrays in a single plot
plotBiomass | Plot the biomass of species through time
plotBiomass.MizerSim | Plot the biomass of species through time
plotBiomassObservedVsModel | Plotting observed vs. model biomass data
plotCDF | Plot cumulative abundance or biomass distributions
plotCDF.MizerParams | Plot cumulative abundance or biomass distributions
plotCDF.MizerSim | 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.
plotDiet.MizerParams | Plot diet, resolved by prey species, as function of predator at size.
plotDiet.MizerSim | Plot diet, resolved by prey species, as function of predator at size.
plotFeedingLevel | Plot the feeding level of species by size
plotFeedingLevel.MizerParams | Plot the feeding level of species by size
plotFeedingLevel.MizerSim | Plot the feeding level of species by size
plotFMort | Plot total fishing mortality of each species by size
plotFMort.MizerParams | Plot total fishing mortality of each species by size
plotFMort.MizerSim | Plot total fishing mortality of each species by size
plotGrowthCurves | Plot growth curves
plotGrowthCurves.MizerParams | Plot growth curves
plotGrowthCurves.MizerSim | Plot growth curves
plotHover | Create a hover-enabled plotly plot from a mizer object
plotHover.ArrayResourceBySize | Create a hover-enabled plotly plot from a mizer object
plotHover.ArraySpeciesBySize | Create a hover-enabled plotly plot from a mizer object
plotHover.ArrayTimeByResourceBySize | Create a hover-enabled plotly plot from a mizer object
plotHover.ArrayTimeBySpecies | Create a hover-enabled plotly plot from a mizer object
plotHover.ArrayTimeBySpeciesBySize | Create a hover-enabled plotly plot from a mizer object
plotHover.mizer_plot | Create a hover-enabled plotly plot from a mizer object
plotlyBiomass | Plot the biomass of species through time
plotlyBiomassObservedVsModel | Plotting observed vs. model biomass data
plotlyCDF | Plot cumulative abundance or biomass distributions
plotlyCDF2 | Compare cumulative abundance or biomass distributions from two objects
plotlyDiet | Plot diet, resolved by prey species, as function of predator at size.
plotlyFeedingLevel | Plot the feeding level of species by size
plotlyFMort | Plot total fishing mortality of each species by size
plotlyGrowthCurves | Plot growth curves
plotlyPredMort | Plot predation mortality rate of each species against size
plotlySpectra | Plot abundance and biomass spectra
plotlySpectra2 | Compare abundance and biomass spectra from two objects
plotlySpectraRelative | Plot relative difference between abundance spectra
plotlyYield | Plot the total yield of species through time
plotlyYieldGear | Plot the total yield of each species by gear through time
plotlyYieldObservedVsModel | Plotting observed vs. model yields
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
plotPredMort.MizerParams | Plot predation mortality rate of each species against size
plotPredMort.MizerSim | Plot predation mortality rate of each species against size
plotRelative | Plot relative difference between two mizer arrays
plotRelative.ArraySpeciesBySize | Plot relative difference between two mizer arrays
plotRelative.ArrayTimeBySpecies | Plot relative difference between two mizer arrays
plotRelative.ArrayTimeBySpeciesBySize | Plot relative difference between two mizer arrays
plotSpectra | Plot abundance and biomass spectra
plotSpectra.MizerParams | Plot abundance and biomass spectra
plotSpectra.MizerSim | Plot abundance and biomass spectra
plotSpectra2 | Compare abundance and biomass spectra from two objects
plotSpectraRelative | Plot relative difference between abundance spectra
plotting_functions | Description of the plotting functions
plotYield | Plot the total yield of species through time
plotYield.MizerSim | Plot the total yield of species through time
plotYieldGear | Plot the total yield of each species by gear through time
plotYieldGear.MizerSim | Plot the total yield of each species by gear through time
plotYieldObservedVsModel | Plotting observed vs. model yields
power_law_pred_kernel | Power-law predation kernel
pred_kernel | Set predation kernel
pred_kernel<- | Set predation kernel
print | Print mizer objects
print.ArraySpeciesBySize | Print mizer objects
print.ArrayTimeBySpecies | Print mizer objects
print.ArrayTimeBySpeciesBySize | Print mizer objects
print.summary.ArraySpeciesBySize | Print mizer objects
print.summary.ArrayTimeBySpecies | Print mizer objects
print.summary.ArrayTimeBySpeciesBySize | Print mizer objects
project | Project size spectrum forward in time
project.MizerParams | Project size spectrum forward in time
project.MizerSim | Project size spectrum forward in time
projectDiffusion | Calculate diffusion rate
projectDiffusion.MizerParams | Calculate diffusion rate
projectEGrowth | Get energy rate available for growth needed to project standard mizer model
projectEGrowth.MizerParams | Get energy rate available for growth needed to project standard mizer model
projectEncounter | Get encounter rate during projection
projectEncounter.MizerParams | Get encounter rate during projection
projectERepro | Get energy rate available for reproduction needed to project standard mizer model
projectERepro.MizerParams | Get energy rate available for reproduction needed to project standard mizer model
projectEReproAndGrowth | Get energy rate available for reproduction and growth needed to project standard mizer model
projectEReproAndGrowth.MizerParams | Get energy rate available for reproduction and growth needed to project standard mizer model
projectFeedingLevel | Get feeding level needed to project standard mizer model
projectFeedingLevel.MizerParams | Get feeding level needed to project standard mizer model
projectFMort | Get the total fishing mortality rate from all fishing gears
projectFMort.MizerParams | Get the total fishing mortality rate from all fishing gears
projectMort | Get total mortality rate needed to project standard mizer model
projectMort.MizerParams | Get total mortality rate needed to project standard mizer model
projectPredMort | Get total predation mortality rate needed to project standard mizer model
projectPredMort.MizerParams | Get total predation mortality rate needed to project standard mizer model
projectPredRate | Get predation rate needed to project standard mizer model
projectPredRate.MizerParams | Get predation rate needed to project standard mizer model
projectRates | Get all rates needed to project standard mizer model
projectRDD | Get density-dependent reproduction rate during projection
projectRDD.MizerParams | Get density-dependent reproduction rate during projection
projectRDI | Get density-independent rate of reproduction needed to project standard mizer model
projectRDI.MizerParams | Get density-independent rate of reproduction needed to project standard mizer model
projectResourceMort | Get predation mortality rate for resource needed to project standard mizer model
projectResourceMort.MizerParams | Get predation mortality rate for resource needed to project standard mizer model
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_n_no_diffusion | Project values for first time step of Euler method
project_n_tr_bdf2 | Project values with the TR-BDF2 method
project_simple | Project abundances by a given number of time steps into the future
psi | Set reproduction parameters

## -- R --

readParams | Save and restore mizer objects
readSim | Save and restore mizer objects
recordExtension | Record an extension and its version stamp on a mizer object
registerExtension | Register a single mizer extension for this R session
registerExtensions | Register mizer extensions for this R session
removeBackgroundSpecies | Remove all background species
removeComponent | Add a dynamical ecosystem component
removeSpecies | Remove species
renameGear | Rename gears
renameSpecies | Rename species
repro_prop | Set reproduction parameters
repro_prop<- | Set reproduction parameters
resource_capacity | Set resource dynamics
resource_capacity<- | Set resource dynamics
resource_constant | Keep resource abundance constant
resource_dynamics | Set resource dynamics
resource_dynamics<- | Set resource dynamics
resource_level | Set resource dynamics
resource_level<- | Set resource dynamics
resource_logistic | Project resource using logistic model
resource_params | Resource parameters
resource_params<- | Resource parameters
resource_rate | Set resource dynamics
resource_rate<- | Set resource dynamics
resource_semichemostat | Project resource using semichemostat model
RickerRDD | Ricker function to calculate density-dependent reproduction rate

## -- S --

saveParams | Save and restore mizer objects
saveSim | Save and restore mizer objects
scaleModel | Change scale of the model
scaleRates | Rescale all rates in a mizer model
search_vol | Set search volume
search_vol<- | Set search volume
second_order_w | Get or set the second_order_w flags
second_order_w<- | Get or set the second_order_w flags
selectivity | Set fishing parameters
selectivity<- | Set fishing parameters
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
setExtDiffusion.MizerParams | 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
setLinetypes | Set line colours and line types to be used in mizer plots
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
SheperdRDD | Sheperd function to calculate density-dependent reproduction rate
sigmoid_length | Length based sigmoid selectivity function
sigmoid_weight | Weight based sigmoidal selectivity function
species_params | Species parameters
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.ArraySpeciesBySize | Display the structure of mizer objects
str.ArrayTimeBySpecies | Display the structure of mizer objects
str.ArrayTimeBySpeciesBySize | Display the structure of mizer objects
str.MizerParams | Display the structure of mizer objects
str.MizerSim | Display the structure of mizer objects
summary | Summarise mizer objects
summary.ArraySpeciesBySize | Summarise mizer objects
summary.ArrayTimeBySpecies | Summarise mizer objects
summary.ArrayTimeBySpeciesBySize | Summarise mizer objects
summary.MizerParams | Summarise mizer objects
summary.MizerSim | Summarise mizer objects
summary_functions | Description of summary functions

## -- T --

truncated_lognormal_pred_kernel | Truncated lognormal predation kernel

## -- U --

use_predation_diffusion | Get or set the use_predation_diffusion flag
use_predation_diffusion<- | Get or set the use_predation_diffusion flag

## -- V --

validEffortVector | Make a valid effort vector
validGearParams | Check validity of gear parameters and set defaults
validGivenSpeciesParams | Validate species parameter data frame
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 --

w | Size bins
w2l | Length-weight conversion
w_full | Size bins