Package index • mizerEcopath

Building model

Functions to prepare model parameters and control interaction states.

newAllometricParams(): Set up parameters for a model with allometric encounter and mortality rates

isAllometric(): Test whether a model has allometric encounter and mortality rates

makeInteracting(): Enable predator–prey interactions using an interaction matrix

makeNoninteracting(): Make model non-interacting

setFeedingLevel(): Set constant feeding level for each species in a non-interacting model

Calibrating model

Tools to match model output to empirical observations.

matchCatch(): Match the observed catch and yield

matchConsumption(): Match the model’s total consumption to observed estimates

matchGonadicProportionOnce(): Match the gonadic proportion of a species to a given value.

matchDiet(): Match the diet matrix of the model to an observed diet matrix

alignResource(): Align resource abundance to fish abundance

setResourceInteraction(): Set resource interaction to absorb external encounter rate

Working with Ecopath

Functions for importing and validating data.

addEcopathParams(): Add Ecopath parameters to species parameters

addEcopathCatchTotal(): Sets up gear parameters from Ecopath catch data

reduceEcopathDiet(): Reduce Ecopath diet matrix to mizer species

validEcopathParams(): Validate Ecopath parameter data frame

validEcopathCatch(): Validate Ecopath Catch data frame

fillDefaultsFromFishBase(): Fill Species Traits Using FishBase

Shiny gadget

Interactive interface for tuning mizer model parameters.

tuneEcopath() experimental: Launch shiny gadget for matching mizer model to Ecopath data

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

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

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

exponentControl() exponentControlUI(): Controlling the allometric exponents

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

matchControl() matchControlUI(): Controlling the matching

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

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

Calculating rates

Extract rates and other parameters from the model.

getConsumption(): Get consumption rate for each species

getDiffusion(): Get diffusion rate

getUnassimilated(): Get unassimilated food

getProduction(): Get production rate as defined by Ecopath

getTotalProduction(): Get total production rate for each species

getSomaticProduction(): Get somatic production for each species

getGonadicProduction(): Get gonadic production for each species

getOffspringProduction(): Get rate at which offspring biomass is produced

getReproductiveLoss(): Get rate of biomass loss due to reproduction

getRespiration(): Get respiration rate as defined by Ecopath

getMetabolicRespiration(): Get metabolic respiration for each species

getEcotrophicEfficiency(): Get Ecotrophic Efficiency for each species

getM0B(): Get rate at which biomass is lost due to external mortality

getM2B(): Get rate at which biomass is lost due to predation mortality

getZB(): Get rate at which biomass is lost due to mortality

getDietMatrix(): Get diet matrix

getResourceEncounterRate(): Get resource encounter rate

Plotting

Basic visualisations

plotConsumptionVsSpecies(): Plot the Consumption against species

plotProductionVsSpecies(): Plot the production against species

Helper functions

Internal tools to support calibration and simulation.

prepare_data(): Prepare a TMB Objective Function for Optimising Model Parameters

update_params(): Function that updates params object with new parameter values

precompute_weights(): Precompute weights for integration of density over observed bins

valid_catch(): Validate and extract catch data for a single species

Obsolete?

Functions retained for compatibility or reference but not in active use.

matchEcopath() isEcopathMatched(): Match the model to the Ecopath data

matchExtMortOnce(): Match the external mortality to that required by the ecopath production rate.

matchProduction() matchProductionOnce() isProductionMatched(): Match the model's production rate to empirical observations/estimates

matchRespirationOnce(): Match the respiration rate to that required by the ecopath production rate.

Data sets

Example input and output objects for illustrating functions.

species_params_example: Example species parameters from a few Celtic Sea species.

ecopath_diet_example: Ecopath diet matrix from Lauria et al. (2016)

diet_matrix_example: Example reduced diet matrix for mizer