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 |