# Generated by roxygen2: do not edit by hand

S3method("[",ArrayResourceBySize)
S3method("[",ArraySpeciesBySize)
S3method("[",ArrayTimeByResourceBySize)
S3method("[",ArrayTimeBySpecies)
S3method("[",ArrayTimeBySpeciesBySize)
S3method("catchability<-",MizerParams)
S3method("initialN<-",MizerParams)
S3method("initialNResource<-",MizerParams)
S3method("maturity<-",MizerParams)
S3method("selectivity<-",MizerParams)
S3method(N,MizerSim)
S3method(NResource,MizerSim)
S3method(Ops,ArrayResourceBySize)
S3method(Ops,ArraySpeciesBySize)
S3method(Ops,ArrayTimeByResourceBySize)
S3method(Ops,ArrayTimeBySpecies)
S3method(Ops,ArrayTimeBySpeciesBySize)
S3method(addPlot,ArraySpeciesBySize)
S3method(addPlot,ArrayTimeBySpecies)
S3method(addSpecies,MizerParams)
S3method(age_mat,MizerParams)
S3method(age_mat_vB,MizerParams)
S3method(age_mat_vB,data.frame)
S3method(age_mat_vB,default)
S3method(animate,ArrayTimeBySpeciesBySize)
S3method(animate,MizerSim)
S3method(as.data.frame,ArrayResourceBySize)
S3method(as.data.frame,ArraySpeciesBySize)
S3method(as.data.frame,ArrayTimeByResourceBySize)
S3method(as.data.frame,ArrayTimeBySpecies)
S3method(as.data.frame,ArrayTimeBySpeciesBySize)
S3method(calibrateBiomass,MizerParams)
S3method(calibrateNumber,MizerParams)
S3method(calibrateYield,MizerParams)
S3method(catchability,MizerParams)
S3method(compareParams,MizerParams)
S3method(distanceMaxRelRDI,MizerParams)
S3method(distanceSSLogN,MizerParams)
S3method(expandSizeGrid,MizerParams)
S3method(finalN,MizerSim)
S3method(finalNResource,MizerSim)
S3method(finalParams,MizerSim)
S3method(getBiomass,MizerParams)
S3method(getBiomass,MizerSim)
S3method(getCatchability,MizerParams)
S3method(getColours,MizerParams)
S3method(getCommunitySlope,MizerParams)
S3method(getCommunitySlope,MizerSim)
S3method(getCriticalFeedingLevel,MizerParams)
S3method(getDiet,MizerParams)
S3method(getDiet,MizerSim)
S3method(getDiffusion,MizerParams)
S3method(getDiffusion,MizerSim)
S3method(getEGrowth,MizerParams)
S3method(getEGrowth,MizerSim)
S3method(getERepro,MizerParams)
S3method(getERepro,MizerSim)
S3method(getEReproAndGrowth,MizerParams)
S3method(getEReproAndGrowth,MizerSim)
S3method(getEffort,MizerSim)
S3method(getEncounter,MizerParams)
S3method(getEncounter,MizerSim)
S3method(getExtEncounter,MizerParams)
S3method(getExtMort,MizerParams)
S3method(getFMort,MizerParams)
S3method(getFMort,MizerSim)
S3method(getFMortGear,MizerParams)
S3method(getFMortGear,MizerSim)
S3method(getFeedingLevel,MizerParams)
S3method(getFeedingLevel,MizerSim)
S3method(getFlux,MizerParams)
S3method(getFlux,MizerSim)
S3method(getFluxGradient,MizerParams)
S3method(getFluxGradient,MizerSim)
S3method(getGrowthCurves,MizerParams)
S3method(getGrowthCurves,MizerSim)
S3method(getInitialEffort,MizerParams)
S3method(getInteraction,MizerParams)
S3method(getLinetypes,MizerParams)
S3method(getMaturityProportion,MizerParams)
S3method(getMaxIntakeRate,MizerParams)
S3method(getMeanMaxWeight,MizerParams)
S3method(getMeanMaxWeight,MizerSim)
S3method(getMeanWeight,MizerParams)
S3method(getMeanWeight,MizerSim)
S3method(getMetabolicRate,MizerParams)
S3method(getMetadata,MizerParams)
S3method(getMort,MizerParams)
S3method(getMort,MizerSim)
S3method(getN,MizerParams)
S3method(getN,MizerSim)
S3method(getParams,MizerSim)
S3method(getPredKernel,MizerParams)
S3method(getPredMort,MizerParams)
S3method(getPredMort,MizerSim)
S3method(getPredRate,MizerParams)
S3method(getPredRate,MizerSim)
S3method(getProportionOfLargeFish,MizerParams)
S3method(getProportionOfLargeFish,MizerSim)
S3method(getRDD,MizerParams)
S3method(getRDD,MizerSim)
S3method(getRDI,MizerParams)
S3method(getRDI,MizerSim)
S3method(getRates,MizerParams)
S3method(getReproductionLevel,MizerParams)
S3method(getReproductionProportion,MizerParams)
S3method(getRequiredRDD,MizerParams)
S3method(getResourceMort,MizerParams)
S3method(getSSB,MizerParams)
S3method(getSSB,MizerSim)
S3method(getSearchVolume,MizerParams)
S3method(getSelectivity,MizerParams)
S3method(getSimParams,MizerSim)
S3method(getTimes,MizerSim)
S3method(getTrophicLevel,MizerParams)
S3method(getTrophicLevelBySpecies,MizerParams)
S3method(getYield,MizerParams)
S3method(getYield,MizerSim)
S3method(getYieldGear,MizerParams)
S3method(getYieldGear,MizerSim)
S3method(idxFinalT,MizerSim)
S3method(initialN,MizerParams)
S3method(initialN,MizerSim)
S3method(initialNResource,MizerParams)
S3method(initialNResource,MizerSim)
S3method(matchBiomasses,MizerParams)
S3method(matchGrowth,MizerParams)
S3method(matchNumbers,MizerParams)
S3method(matchYields,MizerParams)
S3method(maturity,MizerParams)
S3method(plot,ArrayResourceBySize)
S3method(plot,ArraySpeciesBySize)
S3method(plot,ArrayTimeByResourceBySize)
S3method(plot,ArrayTimeBySpecies)
S3method(plot,ArrayTimeBySpeciesBySize)
S3method(plot,MizerParams)
S3method(plot,MizerSim)
S3method(plot2,ArraySpeciesBySize)
S3method(plot2,ArrayTimeBySpecies)
S3method(plot2,ArrayTimeBySpeciesBySize)
S3method(plotBiomass,MizerSim)
S3method(plotBiomassObservedVsModel,MizerParams)
S3method(plotBiomassObservedVsModel,MizerSim)
S3method(plotCDF,MizerParams)
S3method(plotCDF,MizerSim)
S3method(plotDiet,MizerParams)
S3method(plotDiet,MizerSim)
S3method(plotFMort,MizerParams)
S3method(plotFMort,MizerSim)
S3method(plotFeedingLevel,MizerParams)
S3method(plotFeedingLevel,MizerSim)
S3method(plotGrowthCurves,MizerParams)
S3method(plotGrowthCurves,MizerSim)
S3method(plotHover,ArrayResourceBySize)
S3method(plotHover,ArraySpeciesBySize)
S3method(plotHover,ArrayTimeByResourceBySize)
S3method(plotHover,ArrayTimeBySpecies)
S3method(plotHover,ArrayTimeBySpeciesBySize)
S3method(plotHover,mizer_plot)
S3method(plotPredMort,MizerParams)
S3method(plotPredMort,MizerSim)
S3method(plotRelative,ArraySpeciesBySize)
S3method(plotRelative,ArrayTimeBySpecies)
S3method(plotRelative,ArrayTimeBySpeciesBySize)
S3method(plotSpectra,MizerParams)
S3method(plotSpectra,MizerSim)
S3method(plotYield,MizerSim)
S3method(plotYieldGear,MizerSim)
S3method(plotYieldObservedVsModel,MizerParams)
S3method(plotYieldObservedVsModel,MizerSim)
S3method(print,ArrayResourceBySize)
S3method(print,ArraySpeciesBySize)
S3method(print,ArrayTimeByResourceBySize)
S3method(print,ArrayTimeBySpecies)
S3method(print,ArrayTimeBySpeciesBySize)
S3method(print,summary.ArrayResourceBySize)
S3method(print,summary.ArraySpeciesBySize)
S3method(print,summary.ArrayTimeByResourceBySize)
S3method(print,summary.ArrayTimeBySpecies)
S3method(print,summary.ArrayTimeBySpeciesBySize)
S3method(project,MizerParams)
S3method(project,MizerSim)
S3method(projectDiffusion,MizerParams)
S3method(projectEGrowth,MizerParams)
S3method(projectERepro,MizerParams)
S3method(projectEReproAndGrowth,MizerParams)
S3method(projectEncounter,MizerParams)
S3method(projectFMort,MizerParams)
S3method(projectFeedingLevel,MizerParams)
S3method(projectMort,MizerParams)
S3method(projectPredMort,MizerParams)
S3method(projectPredRate,MizerParams)
S3method(projectRDD,MizerParams)
S3method(projectRDI,MizerParams)
S3method(projectRates,MizerParams)
S3method(projectResourceMort,MizerParams)
S3method(projectToSteady,MizerParams)
S3method(project_simple,MizerParams)
S3method(removeSpecies,MizerParams)
S3method(renameGear,MizerParams)
S3method(renameSpecies,MizerParams)
S3method(saveParams,MizerParams)
S3method(saveSim,MizerSim)
S3method(scaleModel,MizerParams)
S3method(scaleRates,MizerParams)
S3method(selectivity,MizerParams)
S3method(setBevertonHolt,MizerParams)
S3method(setColours,MizerParams)
S3method(setExtDiffusion,MizerParams)
S3method(setExtEncounter,MizerParams)
S3method(setExtMort,MizerParams)
S3method(setFishing,MizerParams)
S3method(setInitialValues,MizerParams)
S3method(setInteraction,MizerParams)
S3method(setLinetypes,MizerParams)
S3method(setMaxIntakeRate,MizerParams)
S3method(setMetabolicRate,MizerParams)
S3method(setMetadata,MizerParams)
S3method(setParams,MizerParams)
S3method(setPredKernel,MizerParams)
S3method(setReproduction,MizerParams)
S3method(setResource,MizerParams)
S3method(setSearchVolume,MizerParams)
S3method(steady,MizerParams)
S3method(steadySingleSpecies,MizerParams)
S3method(str,ArrayResourceBySize)
S3method(str,ArraySpeciesBySize)
S3method(str,ArrayTimeByResourceBySize)
S3method(str,ArrayTimeBySpecies)
S3method(str,ArrayTimeBySpeciesBySize)
S3method(str,MizerParams)
S3method(str,MizerSim)
S3method(summary,ArrayResourceBySize)
S3method(summary,ArraySpeciesBySize)
S3method(summary,ArrayTimeByResourceBySize)
S3method(summary,ArrayTimeBySpecies)
S3method(summary,ArrayTimeBySpeciesBySize)
S3method(summary,MizerParams)
S3method(summary,MizerSim)
S3method(utils::upgrade,MizerParams)
S3method(utils::upgrade,MizerSim)
S3method(validParams,MizerParams)
S3method(validSim,MizerSim)
export("catchability<-")
export("ext_diffusion<-")
export("ext_encounter<-")
export("ext_mort<-")
export("gear_params<-")
export("given_species_params<-")
export("initialN<-")
export("initialNOther<-")
export("initialNResource<-")
export("initial_effort<-")
export("intake_max<-")
export("interaction_matrix<-")
export("maturity<-")
export("metab<-")
export("other_params<-")
export("pred_kernel<-")
export("repro_prop<-")
export("resource_capacity<-")
export("resource_dynamics<-")
export("resource_level<-")
export("resource_params<-")
export("resource_rate<-")
export("search_vol<-")
export("second_order_w<-")
export("selectivity<-")
export("species_params<-")
export("use_predation_diffusion<-")
export(ArrayResourceBySize)
export(ArraySpeciesBySize)
export(ArrayTimeByResourceBySize)
export(ArrayTimeBySpecies)
export(ArrayTimeBySpeciesBySize)
export(BevertonHoltRDD)
export(MizerParams)
export(MizerSim)
export(N)
export(NOther)
export(NResource)
export(RickerRDD)
export(SheperdRDD)
export(addPlot)
export(addSpecies)
export(age_mat)
export(age_mat_vB)
export(animate)
export(animateSpectra)
export(apply_wlim)
export(balance_resource_logistic)
export(balance_resource_semichemostat)
export(box_pred_kernel)
export(calc_selectivity)
export(calculated_species_params)
export(calibrateBiomass)
export(calibrateNumber)
export(calibrateYield)
export(catchability)
export(clearExtensionChain)
export(coerceToExtensionClass)
export(compareParams)
export(completeSpeciesParams)
export(constantEggRDI)
export(constantRDD)
export(constant_other)
export(customFunction)
export(default_pred_kernel_params)
export(defaults_edition)
export(distanceMaxRelRDI)
export(distanceSSLogN)
export(double_sigmoid_length)
export(dw)
export(dw_full)
export(emptyParams)
export(expandSizeGrid)
export(ext_diffusion)
export(ext_encounter)
export(ext_mort)
export(finalN)
export(finalNOther)
export(finalNResource)
export(finalParams)
export(gear_params)
export(getBiomass)
export(getCatchability)
export(getColours)
export(getCommunitySlope)
export(getComponent)
export(getCriticalFeedingLevel)
export(getDiet)
export(getDiffusion)
export(getEGrowth)
export(getERepro)
export(getEReproAndGrowth)
export(getESpawning)
export(getEffort)
export(getEncounter)
export(getExtEncounter)
export(getExtMort)
export(getFMort)
export(getFMortGear)
export(getFeedingLevel)
export(getFlux)
export(getFluxGradient)
export(getGrowthCurves)
export(getInitialEffort)
export(getInteraction)
export(getLinetypes)
export(getM2)
export(getM2Background)
export(getMaturityProportion)
export(getMaxIntakeRate)
export(getMeanMaxWeight)
export(getMeanWeight)
export(getMetabolicRate)
export(getMetadata)
export(getMort)
export(getN)
export(getParams)
export(getPhiPrey)
export(getPredKernel)
export(getPredMort)
export(getPredRate)
export(getProportionOfLargeFish)
export(getRDD)
export(getRDI)
export(getRateFunction)
export(getRates)
export(getRegisteredExtensions)
export(getReproductionLevel)
export(getReproductionProportion)
export(getRequiredRDD)
export(getResourceCapacity)
export(getResourceDynamics)
export(getResourceLevel)
export(getResourceMort)
export(getResourceRate)
export(getSSB)
export(getSearchVolume)
export(getSelectivity)
export(getSimParams)
export(getTimes)
export(getTrophicLevel)
export(getTrophicLevelBySpecies)
export(getYield)
export(getYieldGear)
export(getZ)
export(get_f0_default)
export(get_gamma_default)
export(get_h_default)
export(get_initial_n)
export(get_ks_default)
export(get_phi)
export(get_size_range_array)
export(get_time_elements)
export(given_species_params)
export(idxFinalT)
export(initialN)
export(initialNOther)
export(initialNResource)
export(initialParams)
export(initial_effort)
export(intake_max)
export(interaction_matrix)
export(is.ArrayResourceBySize)
export(is.ArraySpeciesBySize)
export(is.ArrayTimeByResourceBySize)
export(is.ArrayTimeBySpecies)
export(is.ArrayTimeBySpeciesBySize)
export(knife_edge)
export(l2w)
export(log_breaks)
export(lognormal_pred_kernel)
export(markBackground)
export(matchBiomasses)
export(matchGrowth)
export(matchNumbers)
export(matchYields)
export(maturity)
export(melt)
export(metab)
export(mizerDiffusion)
export(mizerEGrowth)
export(mizerERepro)
export(mizerEReproAndGrowth)
export(mizerEncounter)
export(mizerFMort)
export(mizerFMortGear)
export(mizerFeedingLevel)
export(mizerMort)
export(mizerPredMort)
export(mizerPredRate)
export(mizerRDI)
export(mizerRates)
export(mizerResourceMort)
export(newCommunityParams)
export(newMultispeciesParams)
export(newSingleSpeciesParams)
export(newTraitParams)
export(noRDD)
export(other_params)
export(parsePlotLog)
export(plot2)
export(plotBiomass)
export(plotBiomassObservedVsModel)
export(plotCDF)
export(plotCDF2)
export(plotDataFrame)
export(plotDiet)
export(plotFMort)
export(plotFeedingLevel)
export(plotGrowthCurves)
export(plotHover)
export(plotM2)
export(plotPredMort)
export(plotRelative)
export(plotSpectra)
export(plotSpectra2)
export(plotSpectraRelative)
export(plotYield)
export(plotYieldGear)
export(plotYieldObservedVsModel)
export(plotlyBiomass)
export(plotlyBiomassObservedVsModel)
export(plotlyCDF)
export(plotlyCDF2)
export(plotlyDiet)
export(plotlyFMort)
export(plotlyFeedingLevel)
export(plotlyGrowthCurves)
export(plotlyPredMort)
export(plotlySpectra)
export(plotlySpectra2)
export(plotlySpectraRelative)
export(plotlyYield)
export(plotlyYieldGear)
export(plotlyYieldObservedVsModel)
export(power_law_pred_kernel)
export(pred_kernel)
export(project)
export(projectDiffusion)
export(projectEGrowth)
export(projectERepro)
export(projectEReproAndGrowth)
export(projectEncounter)
export(projectFMort)
export(projectFeedingLevel)
export(projectMort)
export(projectPredMort)
export(projectPredRate)
export(projectRDD)
export(projectRDI)
export(projectRates)
export(projectResourceMort)
export(projectToSteady)
export(project_n)
export(project_n_2)
export(project_n_tr_bdf2)
export(project_simple)
export(psi)
export(readParams)
export(readSim)
export(recordExtension)
export(registerExtension)
export(registerExtensions)
export(removeBackgroundSpecies)
export(removeComponent)
export(removeSpecies)
export(renameGear)
export(renameSpecies)
export(repro_prop)
export(resource_capacity)
export(resource_constant)
export(resource_dynamics)
export(resource_level)
export(resource_logistic)
export(resource_params)
export(resource_rate)
export(resource_semichemostat)
export(saveParams)
export(saveSim)
export(scaleModel)
export(scaleRates)
export(search_vol)
export(second_order_w)
export(selectivity)
export(setBevertonHolt)
export(setColours)
export(setComponent)
export(setExtDiffusion)
export(setExtEncounter)
export(setExtMort)
export(setFishing)
export(setInitialValues)
export(setInteraction)
export(setLinetypes)
export(setMaxIntakeRate)
export(setMetabolicRate)
export(setMetadata)
export(setParams)
export(setPredKernel)
export(setRateFunction)
export(setReproduction)
export(setResource)
export(setRmax)
export(setSearchVolume)
export(set_community_model)
export(set_multispecies_model)
export(set_species_param_default)
export(set_trait_model)
export(sigmoid_length)
export(sigmoid_weight)
export(species_params)
export(steady)
export(steadySingleSpecies)
export(truncated_lognormal_pred_kernel)
export(use_predation_diffusion)
export(validEffortVector)
export(validGearParams)
export(validGivenSpeciesParams)
export(validParams)
export(validSim)
export(validSpeciesParams)
export(valid_gears_arg)
export(valid_species_arg)
export(w)
export(w2l)
export(w_full)
exportClasses(MizerParams)
exportClasses(MizerSim)
import(assertthat)
import(dplyr)
import(ggplot2)
import(methods)
importFrom(Rcpp,sourceCpp)
importFrom(grDevices,col2rgb)
importFrom(lifecycle,deprecated)
importFrom(plotly,ggplotly)
importFrom(plotly,plotlyOutput)
importFrom(plotly,renderPlotly)
importFrom(reshape2,melt)
importFrom(rlang,cnd_muffle)
importFrom(rlang,signal)
importFrom(stats,complete.cases)
importFrom(stats,cor.test)
importFrom(stats,fft)
importFrom(stats,lm)
importFrom(stats,mvfft)
importFrom(stats,pnorm)
importFrom(stats,runif)
importFrom(stats,setNames)
importFrom(utils,data)
importFrom(utils,getS3method)
importFrom(utils,globalVariables)
importFrom(utils,modifyList)
importFrom(utils,packageVersion)
useDynLib(mizer)
