| 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 |