Package index • mizerExperimental

Interactively tuning a multispecies model

tuneParams(): Launch shiny gadget for tuning parameters

tuneGrowth(): Tune Growth

Tabs for tuning gadget

abundanceTab() abundanceTabUI(): Abundance tab for tuning gadget

biomassTab() biomassTabUI(): Biomass tab for tuning gadget

catchTab() catchTabUI(): Serve tab with catch data

deathTab() deathTabUI(): Serve tab with death plots

dietTab() dietTabUI(): Serve tab with diet plot

growthTab() growthTabUI(): Growth tab for tuning gadget inheritParams biomassTab

numberTab() numberTabUI(): Number tab for tuning gadget

ratesTab() ratesTabUI(): Serve tab with rates plots

reproTab() reproTabUI(): Serve tab with plot of reproductive success rates

resourceTab() resourceTabUI(): Serve tab with resource plots

spectraTab() spectraTabUI(): tuneParams tab showing size spectra

stomachTab(): Serve tab with stomach data

Controls for tuning gadget

abundanceControl() abundanceControlUI(): Controlling egg abundance in the tuning gadget

fishingControl() fishingControlUI(): Controlling the fishing parameters in the tuning gadget

growthControl() growthControlUI(): A single slider that adjusts both h and gamma

interactionControl() interactionControlUI(): Controlling the interaction matrix in the tuning gadget

otherControl() otherControlUI(): Controlling the species parameters not included in other controls

predationControl() predationControlUI(): Controlling the predation parameters in the tuning gadget

reproductionControl() reproductionControlUI(): Controlling the reproduction parameters in the tuning gadget

resourceControl() resourceControlUI(): Controlling the resource parameters in the tuning gadget

Helper functions for model tuning

matchYield(): Match observed yields

markBackground(): Designate species as background species

adjustBackgroundSpecies(): Retunes abundance of background species.

removeBackgroundSpecies(): Remove all background species

scaleAbundance(): Rescale Abundance

scaleDownBackground(): Scale background down by a factor

updateInitialValues(): Update the initial values

pruneSpecies(): Removes species with abundance below a threshold

getYieldVsF(): Calculate a yield-vs-F curve

alignResource(): Rescale resource to be in line with fish community

Plotting functions

plotBiomassFlux(): Plot biomass flux

plotBiomassRelative() plotlyBiomassRelative(): Plot change in biomass over time

plotBiomassVsSpecies(): Plot the biomass against species

plotDeath() plotlyDeath(): Plot the sources of external, predation and fishing mortality per species and size

plotEnergyBudget() plotlyEnergyBudget(): Plot the energy budget of each species through size.

plotNumberVsSpecies(): Plot the number against species

plotResourceLevel(): Plot the proportion of the resource spectrum(s) compared to their carrying capacity

plotResourcePred() plotlyResourcePred(): Plot the mortality applied on the resource spectrum(s)

plotSpectra2(): Show two size spectra in the same plot

plotSpectraRelative() plotlySpectraRelative(): Plot the relative difference between two spectra

plotYieldRelative() plotlyYieldRelative(): Plot change in yield over time

plotYieldVsF(): Plot a yield-vs-F curve

plotYieldVsSize() plotlyYieldVsSize(): Plot the size distribution of the catch

plotYieldVsSpecies(): Plot the yield against species

Helper functions for `plotYieldVsF()`

distanceSSLogYield(): Measure distance between current and previous state in terms of yield.

yieldCalculator(): Calculates yield from steady sim