Function reference • mizerShelf

Detritus

detritus_biomass(): Detritus biomass

detritus_consumption(): Detritus consumption rate

detritus_dynamics(): Detritus dynamics

detritus_lifetime() `detritus_lifetime<-`(): Expected detritus lifetime

getDetritusConsumption(): Get detritus consumption rates by consumer species

getDetritusProduction(): Detritus production rate

newDetritusCarrionParams(): Create new mizer model with detritus and carrion components

plotDetritusConsumption(): Plot carrion consumption rates

plotDetritusProduction(): Plot detritus production rates

rescale_detritus(): Rescale detritus biomass without changing detritus consumption

tune_carrion_detritus(): Tune carrion and detritus to steady state

Carrion

carrion_biomass(): Carrion biomass

carrion_consumption_ms(): Mass-specific carrion consumption rate

carrion_dynamics(): Carrion dynamics

carrion_human_origin(): Proportion of carrion production that is of human origin

carrion_lifetime() `carrion_lifetime<-`(): Expected carrion lifetime

getCarrionConsumption(): Get carrion consumption rates

getCarrionProduction(): Carrion production rate

newDetritusCarrionParams(): Create new mizer model with detritus and carrion components

plotCarrionConsumption(): Plot carrion consumption rates

plotCarrionProduction(): Plot carrion production rates

rescale_carrion(): Rescale carrion biomass without changing anything else

tune_carrion_detritus(): Tune carrion and detritus to steady state

Plots

plotBiomass() plotlyBiomass(): Plot the biomass of species and unstructured components through time

plotCarrionConsumption(): Plot carrion consumption rates

plotCarrionProduction(): Plot carrion production rates

plotDeath() plotlyDeath(): Plot death rates

plotDetritusConsumption(): Plot carrion consumption rates

plotDetritusProduction(): Plot detritus production rates

plotYieldMinusDiscards(): Plot yield minus discards

Mortality

gearMort(): Excess gear mortality rate

seMort(): Total mortality rate in the shelf ecosystem model

Others

encounter_contribution(): Contribution of unstructured components to the encounter rate

removeSpecies(): Remove some species from the model

addSpecies(): Add new species

scaleModel(): Scale Model Parameters

Example model

NWMed_catch: Catch size distribution for the NW Mediterranean shelf around Blanes

NWMed_params: MizerParams object for the NW Mediterranean shelf model