# Multi-Species sIZE Spectrum Modelling in R

## Documentation for package ‘mizer’ version 1.0.1

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

## Help Pages

mizer-package | mizer: Multi-species size-based modelling in R
addSpecies | Add more species into an ecosystem with background species.
addSpecies-method | Add more species into an ecosystem with background species.
display_frames | Display frames
getBiomass | Calculate the total biomass of each species within a size range at each time step.
getBiomass-method | 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
getBiomassFrame-method | Get data frame of biomass of species through time, ready for ggplot2
getCommunitySlope | Calculate the slope of the community abundance
getCommunitySlope-method | Calculate the slope of the community abundance
getEGrowth | Get energy rate available for growth
getEGrowth-method | Get energy rate available for growth
getEReproAndGrowth | Get energy after metabolism and movement
getEReproAndGrowth-method | Get energy after metabolism and movement
getESpawning | Get energy rate available for reproduction
getESpawning-method | Get energy rate available for reproduction
getFeedingLevel | Get feeding level
getFeedingLevel-method | Get feeding level
getFMort | Get the total fishing mortality rate from all fishing gears by time, species and size.
getFMort-method | 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
getFMortGear-method | Get the fishing mortality by time, gear, species and size
getM2 | getM2 method for the size based model
getM2-method | getM2 method for the size based model
getM2Background | Get predation mortality rate for plankton
getM2Background-method | Get predation mortality rate for plankton
getMeanMaxWeight | Calculate the mean maximum weight of the community
getMeanMaxWeight-method | Calculate the mean maximum weight of the community
getMeanWeight | Calculate the mean weight of the community
getMeanWeight-method | Calculate the mean weight of the community
getN | Calculate the total abundance in terms of numbers of species within a size range
getN-method | Calculate the total abundance in terms of numbers of species within a size range
getPhiPrey | Get available energy
getPhiPrey-method | Get available energy
getPredRate | Get predation rate
getPredRate-method | Get predation rate
getProportionOfLargeFish | Calculate the proportion of large fish
getProportionOfLargeFish-method | Calculate the proportion of large fish
getRDD | Get density dependent recruitment
getRDD-method | Get density dependent recruitment
getRDI | Get density independent recruitment
getRDI-method | Get density independent recruitment
getSSB | Calculate the SSB of species
getSSB-method | Calculate the SSB of species
getSSBFrame | Get data frame of spawning stock biomass of species through time, ready for ggplot2
getSSBFrame-method | Get data frame of spawning stock biomass of species through time, ready for ggplot2
getYield | Calculate the total yield of each species
getYield-method | Calculate the total yield of each species
getYieldGear | Calculate the total yield per gear and species
getYieldGear-method | Calculate the total yield per gear and species
getZ | Get total mortality rate
getZ-method | Get total mortality rate
get_initial_n | Calculate initial population abundances for the community populations
inter | Example interaction matrix for the North Sea example
knife_edge | Size based knife-edge selectivity function
log_breaks | Helper function to produce nice breaks on logarithmic axes
mizer | mizer: Multi-species size-based modelling in R
mizer, | mizer: Multi-species size-based modelling in R
MizerParams | Constructors for objects of 'MizerParams' class
MizerParams-class | A class to hold the parameters for a size based model.
MizerParams-method | Constructors for objects of 'MizerParams' class
MizerSim | Constructor for the 'MizerSim' class
MizerSim-class | MizerSim
MizerSim-method | Constructor for the 'MizerSim' class
NS_species_params | Example parameter set based on the North Sea
NS_species_params_gears | Example parameter set based on the North Sea with different gears
plot-method | Summary plot for 'MizerSim' objects
plotBiomass | Plot the biomass of species through time
plotBiomass-method | Plot the biomass of species through time
plotFeedingLevel | Plot the feeding level of species by size
plotFeedingLevel-method | Plot the feeding level of species by size
plotFMort | Plot total fishing mortality of each species by size
plotFMort-method | Plot total fishing mortality of each species by size
plotGrowthCurves | Plot growth curves giving weight as a function of age
plotGrowthCurves-method | Plot growth curves giving weight as a function of age
plotM2 | Plot predation mortality rate of each species against size
plotM2-method | Plot predation mortality rate of each species against size
plotSpectra | Plot the abundance spectra
plotSpectra-method | Plot the abundance spectra
plotYield | Plot the total yield of species through time
plotYield-method | Plot the total yield of species through time
plotYieldGear | Plot the total yield of each species by gear through time
plotYieldGear-method | Plot the total yield of each species by gear through time
project | project method for the size based modelling
project-method | project method for the size based modelling
project_methods | Methods used for projecting
retune_abundance | Retunes abundance of background species.
setBackground | Designate species as background species
setBackground-method | Designate species as background species
set_community_model | Sets up parameters for a community-type model
set_scaling_model | Sets up parameters for a scale free trait-based model
set_trait_model | Sets up parameters for a trait-based model
sigmoid_length | Length based sigmoid selectivity function
steady | Tune params object to be at steady state
summary-method | Summarize MizerParams object
summary-method | Summarize MizerSim object
wrapper_functions | Functions used for setting up models