Multi-Species sIZE Spectrum Modelling in R


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Documentation for package ‘mizer’ version 1.0.1

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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