Multi-Species sIZE Spectrum Modelling in R


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Documentation for package ‘mizer’ version 0.4

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mizer-package mizer: Multi-species size-based modelling in R
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.
getCommunitySlope Calculate the slope of the community abundance
getCommunitySlope-method Calculate the slope of the community abundance
getEGrowth getEGrowth method for the size based model
getEGrowth-method getEGrowth method for the size based model
getEReproAndGrowth getEReproAndGrowth method for the size based model
getEReproAndGrowth-method getEReproAndGrowth method for the size based model
getESpawning getESpawning method for the size based model
getESpawning-method getESpawning method for the size based model
getFeedingLevel getFeedingLevel method for the size based model
getFeedingLevel-method getFeedingLevel method for the size based model
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 getM2Background method for the size based model
getM2Background-method getM2Background method for the size based model
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 getPhiPrey method for the size based model
getPhiPrey-method getPhiPrey method for the size based model
getPredRate 'getPredRate' method for the size based model
getPredRate-method 'getPredRate' method for the size based model
getProportionOfLargeFish Calculate the proportion of large fish
getProportionOfLargeFish-method Calculate the proportion of large fish
getRDD getRDD method for the size based model
getRDD-method getRDD method for the size based model
getRDI getRDI method for the size based model
getRDI-method getRDI method for the size based model
getSSB Calculate the SSB of species
getSSB-method Calculate the SSB of species
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 getZ method for the size based model
getZ-method getZ method for the size based model
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
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 each species through time
plotBiomass-method Plot the biomass of each species through time
plotFeedingLevel Plot the feeding level of each species by size
plotFeedingLevel-method Plot the feeding level of each species by size
plotFMort Plot total fishing mortality of each species by size
plotFMort-method Plot total fishing mortality of each species by size
plotM2 Plot M2 of each species by size
plotM2-method Plot M2 of each species by size
plotSpectra Plot the abundance spectra of each species and the background population
plotSpectra-method Plot the abundance spectra of each species and the background population
plotYield Plot the total yield of each species through time
plotYield-method Plot the total yield of each 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
set_community_model Sets up parameters for a community-type model
set_trait_model Sets up parameters for a trait-based model
sigmoid_length Length based sigmoid selectivity function
summary-method Summarize MizerParams object
summary-method Summarize MizerSim object