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

addSpeciesAdd more species into an ecosystem with background species.
box_pred_kernelBox predation kernel
carrion_dynamicsCarrion dynamics
detritus_dynamicsDetritus dynamics
displayFramesDisplay frames
emptyParamsCreate empty MizerParams object of the right size
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
getDietGet diet of predator at size, resolved by prey species
getEGrowthGet energy rate available for growth
getEncounterGet encounter rate
getEReproGet energy rate available for reproduction
getEReproAndGrowthGet energy rate available for reproduction and growth
getESpawningAlias for getERepro
getFeedingLevelGet feeding level
getFMortGet the total fishing mortality rate from all fishing gears...
getFMortGearGet the fishing mortality by time, gear, species and size
get_gamma_defaultGet default value for gamma
getGrowthCurvesGet growth curves giving weight as a function of age
get_h_defaultGet default value for h
get_initial_nCalculate initial population abundances for the community...
get_ks_defaultGet default value for ks
getM2Alias for getPredMort
getM2BackgroundAlias for getPlanktonMort
getMeanMaxWeightCalculate the mean maximum weight of the community
getMeanWeightCalculate the mean weight of the community
getMortGet total mortality rate
getNCalculate the number of individuals within a size range
get_phiGet values from feeding kernel function
getPlanktonMortGet predation mortality rate for plankton
getPredKernelGet predation kernel
getPredMortGet total predation mortality rate
getPredRateGet predation rate
getProportionOfLargeFishCalculate the proportion of large fish
getRatesGet all rates
getRDDGet density dependent recruitment
getRDIGet density independent rate of egg production
get_size_range_arrayGet size range array
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
getZAlias for getMort
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
lognormal_pred_kernelLognormal predation kernel
markBackgroundDesignate species as background species
mizermizer: Multi-species size-based modelling in R
MizerParamsAlias for set_multispecies_model
MizerParams-classA class to hold the parameters for a size based model.
MizerSimConstructor for the 'MizerSim' class
MizerSim-classA class to hold the results of a simulation
NS_species_paramsExample parameter set based on the North Sea
NS_species_params_gearsExample parameter set based on the North Sea with different...
plankton_semichemostatProject plankton using semichemostat model
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
plotlyBiomassPlot the biomass of species against time with plotly
plotlyFMortPlot total fishing mortality of each species by size with...
plotlyGrowthCurvesPlot growth curves giving weight as a function of age with...
plotlyPredMortPlot predation mortality rate of each species against size...
plotlySpectraPlotly plot of the abundance spectra
plotlyYieldPlot the total yield of species through time with plotly
plotlyYieldGearPlot the total yield of each species by gear through time...
plotM2Alias for plotPredMort
plotMizerSimSummary plot for 'MizerSim' objects
plotPredMortPlot predation mortality rate of each species against size
plotSpectraPlot the abundance spectra
plotting_functionsDescription of the plotting functions
plotYieldPlot the total yield of species through time
plotYieldGearPlot the total yield of each species by gear through time
projectProject size spectrum forward in time
project_methodsFunctions for calculating rates used for projecting
removeSpeciesRemove species from an ecosystem
retuneAbundanceRetunes abundance of background species.
setBMortSet background mortality rate
set_community_modelSets up parameters for a community-type model
setFishingSet fishing parameters
setInitialSet initial abundances
setIntakeMaxSet maximum intake rate
setInteractionSet species interation matrix
setMetabSet metabolic rate
set_multispecies_modelConstruct MizerParams object for general multispecies model
setParamsSet or change any model parameters
setPlanktonSet up plankton
setPredKernelSet predation kernel
setReproductionSet proportion of energy that is invested into reproduction
setResourceDynamicsSet resource dynamics
setResourceEncounterSet resource encounter rate
set_scaling_modelSets up parameters for a scale free trait-based model
setSearchVolumeSet search volume
set_species_param_defaultSet a species parameter to a default value
set_trait_modelSets up parameters for a trait-based model
sigmoid_lengthLength based sigmoid selectivity function
srrBevertonHoltBeverton Holt stock-recruitment function
steadyTune params object to be at steady state
summary_functionsDescription of summary functions
summary-MizerParams-methodSummarize MizerParams object
summary-MizerSim-methodSummarize MizerSim object
wrapper_functionsFunctions used for setting up models
drfinlayscott/mizer documentation built on May 15, 2019, 2:09 p.m.