# Multi-Species sIZE Spectrum Modelling in R

## Documentation for package ‘mizer’ version 2.0.0

- DESCRIPTION file.

## Help Pages

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

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

## -- B --

BevertonHoltRDD | Beverton Holt function to calculate density-dependent reproduction rate
box_pred_kernel | Box predation kernel

## -- C --

constantRDD | Give constant reproduction rate

## -- D --

double_sigmoid_length | Length based double-sigmoid selectivity function
dw | Size bins
dw_full | Size bins

## -- E --

effort | Fishing effort used in simulation
emptyParams | Create empty MizerParams object of the right size

## -- F --

finalN | Size spectra at end of simulation
finalNOther | Values of other ecosystem components at end of simulation
finalNResource | Size spectra at end of simulation

## -- G --

gear_params | Set fishing parameters
gear_params<- | Set fishing parameters
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
getCatchability | Set fishing parameters
getColours | Set line colours to be used in mizer plots
getCommunitySlope | Calculate the slope of the community abundance
getComponent | Get information about other ecosystem components
getCriticalFeedingLevel | Get critical feeding level
getDiet | Get diet of predator at size, resolved by prey species
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
getExtMort | Set external mortality rate
getFeedingLevel | Get feeding level
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
getInteraction | Set species interaction matrix
getLinetypes | Set linetypes 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
getMort | Get total mortality rate
getN | Calculate the number of individuals within a size range
getPhiPrey | Get available energy
getPredKernel | Get 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
getRDD | Get density dependent reproduction rate
getRDI | Get density independent rate of egg production
getReproductionProportion | Set reproduction parameters
getResourceCapacity | Set up resource
getResourceDynamics | Set up resource
getResourceMort | Get predation mortality rate for resource
getResourceRate | Set up resource
getSearchVolume | Set search volume
getSelectivity | Set fishing parameters
getSSB | Calculate the SSB of species
getYield | Calculate the total yield of each species
getYieldGear | Calculate the total yield per gear and species
getZ | Alias for getMort
get_initial_n | Calculate initial population abundances for the community populations
get_required_reproduction | Determine reproduction rate needed for initial egg abundance

## -- I --

idxFinalT | Time index at end of simulation
indicator_functions | Description of indicator functions
initialN | 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<- | Initial value for resource spectrum
inter | Example interaction matrix for the North Sea example

## -- K --

knife_edge | Weight based knife-edge selectivity function

## -- L --

lognormal_pred_kernel | Lognormal predation kernel

## -- M --

mizer | mizer: Multi-species size-based modelling in R
mizerEGrowth | Get energy rate available for growth needed to project standard mizer model
mizerEncounter | Get encounter rate 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
mizerFeedingLevel | Get feeding level needed to project standard mizer model
mizerFMort | Get the total fishing mortality rate from all fishing gears by time, species and size needed to project standard mizer model
mizerFMortGear | Get the fishing mortality by time, gear, species and size 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
newCommunityParams | Set up parameters for a community-type model
newMultispeciesParams | Set up parameters for a general multispecies model
newTraitParams | Set up parameters for a trait-based model
noRDD | Give density-independent reproduction rate
NOther | Time series of other components
NResource | Time series of size spectra
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

## -- P --

params | Extract the parameter object underlying a simulation
plot-method | Summary plot for 'MizerSim' objects
plotBiomass | Plot the biomass of species through time
plotDiet | Plot diet
plotFeedingLevel | Plot the feeding level of species by size
plotFMort | Plot total fishing mortality of each species by size
plotGrowthCurves | Plot growth curves giving weight as a function of age
plotlyBiomass | Plot the biomass of species through time
plotlyFeedingLevel | Plot the feeding level of species by size
plotlyFMort | Plot total fishing mortality of each species by size
plotlyGrowthCurves | Plot growth curves giving weight as a function of age
plotlyPredMort | Plot predation mortality rate of each species against size
plotlySpectra | Plot the abundance spectra
plotlyYield | Plot the total yield of species through time
plotlyYieldGear | Plot the total yield of each species by gear through time
plotM2 | Alias for plotPredMort
plotPredMort | Plot predation mortality rate of each species against size
plotSpectra | Plot the abundance spectra
plotting_functions | Description of the plotting functions
plotYield | Plot the total yield of species through time
plotYieldGear | Plot the total yield of each species by gear through time
power_law_pred_kernel | Power-law predation kernel
project | Project size spectrum forward in time

## -- R --

removeComponent | Add a dynamical ecosystem component
resource_constant | Keep resource abundance constant
resource_params | Set up resource
resource_params<- | Set up resource
resource_semichemostat | Project resource using semichemostat model
retune_erepro | Retune reproduction efficiency to maintain initial egg abundances
RickerRDD | Ricker function to calculate density-dependent reproduction rate

## -- S --

setColours | Set line colours to be used in mizer plots
setComponent | Add a dynamical ecosystem component
setExtMort | Set external mortality rate
setFishing | Set fishing parameters
setInitialValues | Set initial values to final values of a simulation
setInteraction | Set species interaction matrix
setLinetypes | Set linetypes to be used in mizer plots
setMaxIntakeRate | Set maximum intake rate
setMetabolicRate | Set metabolic rate
setParams | Species parameters
setPredKernel | Set predation kernel
setRateFunction | Set own rate function to replace mizer rate function
setReproduction | Set reproduction parameters
setResource | Set up resource
setRmax | Set maximum reproduction rate
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_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
summary-method | Summarize MizerParams object
summary-method | Summarize MizerSim object
summary_functions | Description of summary functions

## -- T --

test_dyn | Dummy function used during testing only
times | Times for which simulation results are available
truncated_lognormal_pred_kernel | Truncated lognormal predation kernel

## -- U --

upgradeParams | Upgrade MizerParams object from earlier mizer versions
upgradeSim | Upgrade MizerSim object from earlier mizer versions

## -- V --

validGearParams | Check validity of gear parameters and set defaults for missing but required parameters or transfer them from species_params if available
validSpeciesParams | Check validity of species parameters and set defaults for missing but required parameters

## -- W --

w | Size bins
w_full | Size bins