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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

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
singleSpeciesSteady()
Set initial abundances to single-species steady state abundances
alignResource()
Rescale resource to be in line with fish community

New plotting functions

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.
getMaxF()
Maximum viable fisheries effort for species
maxFthreshold()
Determines maximum the threshold where fisheries effort should stop
yieldCalculator()
Calculates yield from steady sim

Others

validSim()
Returns a valid simulation by removing non-finite results
distanceSSLogYield()
Measure distance between current and previous state in terms of yield.
getMaxF()
Maximum viable fisheries effort for species
maxFthreshold()
Determines maximum the threshold where fisheries effort should stop
yieldCalculator()
Calculates yield from steady sim