Man pages for mizer
Multi-Species sIZE Spectrum Modelling in R

addSpeciesAdd more species into an ecosystem with background species.
display_framesDisplay frames
getBiomassCalculate the total biomass of each species within a size...
getBiomassFrameGet data frame of biomass of species through time, ready for...
getCommunitySlopeCalculate the slope of the community abundance
getEGrowthGet energy rate available for growth
getEReproAndGrowthGet energy after metabolism and movement
getESpawningGet energy rate available for reproduction
getFeedingLevelGet feeding level
getFMortGet the total fishing mortality rate from all fishing gears...
getFMortGearGet the fishing mortality by time, gear, species and size
get_initial_nCalculate initial population abundances for the community...
getM2getM2 method for the size based model
getM2BackgroundGet predation mortality rate for plankton
getMeanMaxWeightCalculate the mean maximum weight of the community
getMeanWeightCalculate the mean weight of the community
getNCalculate the total abundance in terms of numbers of species...
getPhiPreyGet available energy
getPredRateGet predation rate
getProportionOfLargeFishCalculate the proportion of large fish
getRDDGet density dependent recruitment
getRDIGet density independent recruitment
getSSBCalculate the SSB of species
getSSBFrameGet data frame of spawning stock biomass of species through...
getYieldCalculate the total yield of each species
getYieldGearCalculate the total yield per gear and species
getZGet total mortality rate
interExample interaction matrix for the North Sea example
knife_edgeSize based knife-edge selectivity function
log_breaksHelper function to produce nice breaks on logarithmic axes
mizermizer: Multi-species size-based modelling in R
MizerParamsConstructors for objects of 'MizerParams' class
MizerParams-classA class to hold the parameters for a size based model.
MizerSimConstructor for the 'MizerSim' class
MizerSim-classMizerSim
NS_species_paramsExample parameter set based on the North Sea
NS_species_params_gearsExample parameter set based on the North Sea with different...
plotBiomassPlot the biomass of species through time
plotFeedingLevelPlot the feeding level of species by size
plotFMortPlot total fishing mortality of each species by size
plotGrowthCurvesPlot growth curves giving weight as a function of age
plotM2Plot predation mortality rate of each species against size
plotMizerSimSummary plot for 'MizerSim' objects
plotSpectraPlot the abundance spectra
plotYieldPlot the total yield of species through time
plotYieldGearPlot the total yield of each species by gear through time
projectproject method for the size based modelling
project_methodsMethods used for projecting
retune_abundanceRetunes abundance of background species.
setBackgroundDesignate species as background species
set_community_modelSets up parameters for a community-type model
set_scaling_modelSets up parameters for a scale free trait-based model
set_trait_modelSets up parameters for a trait-based model
sigmoid_lengthLength based sigmoid selectivity function
steadyTune params object to be at steady state
summary-MizerParams-methodSummarize MizerParams object
summary-MizerSim-methodSummarize MizerSim object
wrapper_functionsFunctions used for setting up models
mizer documentation built on May 1, 2018, 9:04 a.m.