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"use_predation_diffusion<-", "valid_gears_arg", "valid_species_arg", "validEffortVector", "validGearParams", "validGivenSpeciesParams", "validParams", "validSim", "validSpeciesParams", "w", "w_full", "w2l", "with_info_level" ], "_datasets": [ { "name": "inter", "title": "Alias for 'NS_interaction'", "object": "inter", "class": [ "matrix", "array" ], "fields": [ "Sprat", "Sandeel", "N.pout", "Herring", "Dab", "Whiting", "Sole", "Gurnard", "Plaice", "Haddock", "Cod", "Saithe" ], "rows": 12, "table": true, "tojson": true }, { "name": "NS_interaction", "title": "Example interaction matrix for the North Sea example", "object": "NS_interaction", "class": [ "matrix", "array" ], "fields": [ "Sprat", "Sandeel", "N.pout", "Herring", "Dab", "Whiting", "Sole", "Gurnard", "Plaice", "Haddock", "Cod", "Saithe" ], "rows": 12, "table": true, "tojson": true }, { "name": "NS_params", "title": "Example MizerParams object for the North Sea example", "object": "NS_params", "class": [ "MizerParams" ], "fields": [], "table": false, "tojson": false }, { "name": "NS_sim", "title": "Example MizerSim object for the North Sea example", "object": "NS_sim", "class": [ "MizerSim" ], "fields": [], "table": false, "tojson": false }, { "name": "NS_species_params", "title": "Example species parameter set based on the North Sea", "object": "NS_species_params", "class": [ "given_species_params", "species_params", "data.frame" ], "fields": [ "species", "w_max", "w_mat", "beta", "sigma", "k_vb", "R_max", "w_inf" ], "rows": 12, "table": true, "tojson": true }, { "name": "NS_species_params_gears", "title": "Example species parameter set based on the North Sea with different gears", "object": "NS_species_params_gears", "class": [ "given_species_params", "species_params", "data.frame" ], "fields": [ "species", "w_max", "w_mat", "beta", "sigma", "k_vb", "gear", "R_max", "w_inf" ], "rows": 12, "table": true, "tojson": true } ], "_help": [ { "page": "mizer-package", "title": "mizer: Multi-species size-based modelling in R", "topics": [ "mizer-package", "mizer" ] }, { "page": "addPlot", "title": "Add lines to an existing plot", "concept": [ "plotting functions" ], "topics": [ "addPlot", "addPlot.ArrayResourceBySize", "addPlot.ArraySpeciesBySize", "addPlot.ArrayTimeByResourceBySize", "addPlot.ArrayTimeBySpecies", "addPlot.ArrayTimeBySpeciesBySize" ] }, { "page": "addSpecies", "title": "Add new species", "topics": [ "addSpecies" ] }, { "page": "adjustSizeGrid", "title": "Adjust the size grid", "topics": [ "adjustSizeGrid", "adjustSizeGrid.MizerParams" ] }, { "page": "age_mat", "title": "Calculate age at maturity", "concept": [ "helper" ], "topics": [ "age_mat" ] }, { "page": "age_mat_vB", "title": "Calculate age at maturity from von Bertalanffy growth parameters", "concept": [ "helper" ], "topics": [ "age_mat_vB", "age_mat_vB.data.frame", "age_mat_vB.default", "age_mat_vB.MizerParams" ] }, { "page": "animate", "title": "Animate size-dependent quantities through time", "concept": [ "plotting functions" ], "topics": [ "animate", "animate.ArrayTimeByResourceBySize", "animate.ArrayTimeBySpeciesBySize", "animate.MizerSim", "animateSpectra" ] }, { "page": "ArrayResourceBySize", "title": "S3 class for resource size spectra", "topics": [ "ArrayResourceBySize", "is.ArrayResourceBySize" ] }, { "page": "ArraySpeciesBySize", "title": "S3 class for species x size rate arrays", "topics": [ "ArraySpeciesBySize", "is.ArraySpeciesBySize" ] }, { "page": "ArrayTimeByResourceBySize", "title": "S3 class for time x resource-size arrays", "topics": [ "ArrayTimeByResourceBySize", "is.ArrayTimeByResourceBySize" ] }, { "page": "ArrayTimeBySpecies", "title": "S3 class for time x species arrays", "topics": [ "ArrayTimeBySpecies", "is.ArrayTimeBySpecies" ] }, { "page": "ArrayTimeBySpeciesBySize", "title": "S3 class for time x species x size arrays", "topics": [ "ArrayTimeBySpeciesBySize", "is.ArrayTimeBySpeciesBySize" ] }, { "page": "as.data.frame", "title": "Convert mizer arrays to data frames", "topics": [ "as.data.frame", "as.data.frame.ArraySpeciesBySize", "as.data.frame.ArrayTimeBySpecies", "as.data.frame.ArrayTimeBySpeciesBySize" ] }, { "page": "BevertonHoltRDD", "title": "Beverton Holt function to calculate density-dependent reproduction rate", "concept": [ "functions calculating density-dependent reproduction rate" ], "topics": [ "BevertonHoltRDD" ] }, { "page": "bin_average_weight", "title": "Bin-average the weight of a size-spectrum integral", "topics": [ "bin_average_weight" ] }, { "page": "box_pred_kernel", "title": "Box predation kernel", "concept": [ "predation kernel" ], "topics": [ "box_pred_kernel" ] }, { "page": "calc_selectivity", "title": "Calculate selectivity from gear parameters", "concept": [ "helper" ], "topics": [ "calc_selectivity" ] }, { "page": "calibrateBiomass", "title": "Calibrate the model scale to match total observed biomass", "topics": [ "calibrateBiomass" ] }, { "page": "calibrateNumber", "title": "Calibrate the model scale to match total observed number", "topics": [ "calibrateNumber" ] }, { "page": "coerceToExtensionClass", "title": "Coerce a mizer object to its extension class", "concept": [ "extension tools" ], "topics": [ "coerceToExtensionClass" ] }, { "page": "compareParams", "title": "Compare two MizerParams objects and print out differences", "topics": [ "compareParams" ] }, { "page": "completeSpeciesParams", "title": "Alias for 'validSpeciesParams()'", "concept": [ "deprecated" ], "topics": [ "completeSpeciesParams" ] }, { "page": "constant_other", "title": "Helper function to keep other components constant", "concept": [ "helper" ], "topics": [ "constant_other" ] }, { "page": "constantEggRDI", "title": "Choose egg production to keep egg density constant", "concept": [ "functions calculating density-dependent reproduction rate" ], "topics": [ "constantEggRDI" ] }, { "page": "constantRDD", "title": "Give constant reproduction rate", "concept": [ "functions calculating density-dependent reproduction rate" ], "topics": [ "constantRDD" ] }, { "page": "customFunction", "title": "Replace a mizer function with a custom version", "topics": [ "customFunction" ] }, { "page": "default_info_level", "title": "The default level of information that mizer gives", "concept": [ "info signalling functions" ], "topics": [ "default_info_level" ] }, { "page": "default_pred_kernel_params", "title": "Set defaults for predation kernel parameters", "concept": [ "helper" ], "topics": [ "default_pred_kernel_params" ] }, { "page": "defaults_edition", "title": "Default editions", "topics": [ "defaults_edition" ] }, { "page": "different", "title": "Check whether two objects are different", "concept": [ "helper" ], "topics": [ "different" ] }, { "page": "distanceMaxRelRDI", "title": "Measure distance between current and previous state in terms of RDI", "concept": [ "distance functions", "helper" ], "topics": [ "distanceMaxRelRDI" ] }, { "page": "distanceSSLogN", "title": "Measure distance between current and previous state in terms of fish abundances", "concept": [ "distance functions", "helper" ], "topics": [ "distanceSSLogN" ] }, { "page": "double_sigmoid_length", "title": "Length based double-sigmoid selectivity function", "concept": [ "selectivity functions" ], "topics": [ "double_sigmoid_length" ] }, { "page": "emptyParams", "title": "Create empty MizerParams object of the right size", "concept": [ "helper" ], "topics": [ "emptyParams" ] }, { "page": "encounter_kernel", "title": "The predation kernel as used by the encounter quadrature", "topics": [ "encounter_kernel" ] }, { "page": "expandSizeGrid", "title": "Expand the size grid", "concept": [ "deprecated" ], "topics": [ "expandSizeGrid", "expandSizeGrid.MizerParams" ] }, { "page": "finalN", "title": "Size spectra at end of simulation", "topics": [ "finalN", "finalNResource", "idxFinalT" ] }, { "page": "findSteadyState", "title": "Find the steady state of a model", "topics": [ "findSteadyState" ] }, { "page": "frozen_rate_params", "title": "Which parameters feed which frozen array", "concept": [ "info signalling functions" ], "topics": [ "frozen_rate_params" ] }, { "page": "gaussian_mixture_pred_kernel", "title": "Gaussian-mixture predation kernel", "concept": [ "predation kernel" ], "topics": [ "gaussian_mixture_pred_kernel" ] }, { "page": "gear_params", "title": "Gear parameters", "concept": [ "functions for setting parameters" ], "topics": [ "gear_params", "gear_params.data.frame", "gear_params.gear_params", "gear_params.MizerParams", "gear_params.MizerSim", "gear_params<-", "gear_params<-.MizerParams", "is.gear_params" ] }, { "page": "get_f0_default", "title": "Get default value for f0", "concept": [ "functions calculating defaults", "helper" ], "topics": [ "get_f0_default" ] }, { "page": "get_gamma_default", "title": "Get default value for gamma", "concept": [ "functions calculating defaults", "helper" ], "topics": [ "get_gamma_default" ] }, { "page": "get_h_default", "title": "Get default value for h", "concept": [ "functions calculating defaults", "helper" ], "topics": [ "get_h_default" ] }, { "page": "get_initial_n", "title": "Calculate initial population abundances", "concept": [ "helper" ], "topics": [ "get_initial_n" ] }, { "page": "get_ks_default", "title": "Get default value for 'ks'", "concept": [ "functions calculating defaults", "helper" ], "topics": [ "get_ks_default" ] }, { "page": "get_phi", "title": "Get values from feeding kernel function", "concept": [ "helper" ], "topics": [ "get_phi" ] }, { "page": "get_size_range_array", "title": "Get size range array", "concept": [ "helper" ], "topics": [ "get_size_range_array" ] }, { "page": "get_steady_state_n", "title": "Calculate steady state abundance", "concept": [ "helper" ], "topics": [ "get_steady_state_n" ] }, { "page": "get_time_elements", "title": "Get array indices for a time range in a MizerSim object", "concept": [ "helper" ], "topics": [ "get_time_elements" ] }, { "page": "get_yield_observed", "title": "Observed yield of each species", "concept": [ "helper" ], "topics": [ "get_yield_observed" ] }, { "page": "getBiomass", "title": "Calculate the total biomass of each species within a size range at each time step.", "concept": [ "summary functions", "summary_function" ], "topics": [ "getBiomass" ] }, { "page": "getCommunitySlope", "title": "Calculate the slope of the community abundance", "concept": [ "functions for calculating indicators", "summary_function" ], "topics": [ "getCommunitySlope" ] }, { "page": "getCriticalFeedingLevel", "title": "Get critical feeding level", "topics": [ "getCriticalFeedingLevel" ] }, { "page": "getDiet", "title": "Get diet of predator at size, resolved by prey species", "concept": [ "summary functions", "summary_function" ], "topics": [ "getDiet" ] }, { "page": "getDiffusion", "title": "Get diffusion rate from predation", "concept": [ "rate functions" ], "topics": [ "getDiffusion" ] }, { "page": "getDiscreteStability", "title": "Analyse the stability of mizer's numerical time step", "topics": [ "getDiscreteStability" ] }, { "page": "getEffort", "title": "Fishing effort used in simulation", "topics": [ "getEffort" ] }, { "page": "getEGrowth", "title": "Get energy rate available for growth", "concept": [ "rate functions" ], "topics": [ "getEGrowth" ] }, { "page": "getEncounter", "title": "Get encounter rate", "concept": [ "rate functions" ], "topics": [ "getEncounter" ] }, { "page": "getERepro", "title": "Get energy rate available for reproduction", "concept": [ "rate functions" ], "topics": [ "getERepro" ] }, { "page": "getEReproAndGrowth", "title": "Get energy rate available for reproduction and growth", "concept": [ "rate functions" ], "topics": [ "getEReproAndGrowth" ] }, { "page": "getESpawning", "title": "Alias for 'getERepro()'", "concept": [ "deprecated" ], "topics": [ "getESpawning" ] }, { "page": "getFeedingLevel", "title": "Get feeding level", "concept": [ "rate functions" ], "topics": [ "getFeedingLevel" ] }, { "page": "getFlux", "title": "Get flux into size bins", "concept": [ "rate functions" ], "topics": [ "getFlux", "getFlux.MizerParams", "getFlux.MizerSim" ] }, { "page": "getFluxGradient", "title": "Get flux gradient", "concept": [ "rate functions" ], "topics": [ "getFluxGradient", "getFluxGradient.MizerParams", "getFluxGradient.MizerSim" ] }, { "page": "getFMort", "title": "Get the total fishing mortality rate from all fishing gears by time, species and size.", "concept": [ "rate functions" ], "topics": [ "getFMort" ] }, { "page": "getFMortGear", "title": "Get the fishing mortality by time, gear, species and size", "concept": [ "rate functions" ], "topics": [ "getFMortGear" ] }, { "page": "getGrowthCurves", "title": "Get growth curves giving weight as a function of age", "concept": [ "summary functions" ], "topics": [ "getGrowthCurves" ] }, { "page": "getM2", "title": "Alias for 'getPredMort()'", "concept": [ "deprecated" ], "topics": [ "getM2" ] }, { "page": "getM2Background", "title": "Alias for 'getResourceMort()'", "concept": [ "deprecated" ], "topics": [ "getM2Background" ] }, { "page": "getMeanMaxWeight", "title": "Calculate the mean maximum weight of the community", "concept": [ "functions for calculating indicators", "summary_function" ], "topics": [ "getMeanMaxWeight" ] }, { "page": "getMeanWeight", "title": "Calculate the mean size of the community", "concept": [ "functions for calculating indicators", "summary_function" ], "topics": [ "getMeanLength", "getMeanWeight" ] }, { "page": "getMort", "title": "Get total mortality rate", "concept": [ "rate functions" ], "topics": [ "getMort" ] }, { "page": "getN", "title": "Calculate the number of individuals within a size range", "concept": [ "summary functions", "summary_function" ], "topics": [ "getN" ] }, { "page": "getOscillationModeSim", "title": "Construct a MizerSim of the leading oscillatory mode", "topics": [ "getOscillationModeSim" ] }, { "page": "getParams", "title": "Extract the model state from a simulation", "topics": [ "finalParams", "getParams", "initialParams" ] }, { "page": "getPhiPrey", "title": "Get available energy", "concept": [ "deprecated" ], "topics": [ "getPhiPrey" ] }, { "page": "getPredMort", "title": "Get total predation mortality rate", "concept": [ "rate functions" ], "topics": [ "getPredMort" ] }, { "page": "getPredRate", "title": "Get predation rate", "concept": [ "rate functions" ], "topics": [ "getPredRate" ] }, { "page": "getProportionOfLargeFish", "title": "Calculate the proportion of large fish", "concept": [ "functions for calculating indicators", "summary_function" ], "topics": [ "getProportionOfLargeFish" ] }, { "page": "getRates", "title": "Get all rates", "concept": [ "rate functions" ], "topics": [ "getRates" ] }, { "page": "getRDD", "title": "Get density dependent reproduction rate", "concept": [ "rate functions" ], "topics": [ "getRDD" ] }, { "page": "getRDI", "title": "Get density independent rate of egg production", "concept": [ "rate functions" ], "topics": [ "getRDI" ] }, { "page": "getRequiredRDD", "title": "Determine reproduction rate needed for initial egg abundance", "topics": [ "getRequiredRDD" ] }, { "page": "getResourceMort", "title": "Get predation mortality rate for resource", "concept": [ "rate functions" ], "topics": [ "getResourceMort" ] }, { "page": "getSimParams", "title": "Extract the projection parameters used to produce a simulation", "topics": [ "getSimParams" ] }, { "page": "getSSB", "title": "Calculate the SSB of species", "concept": [ "summary functions", "summary_function" ], "topics": [ "getSSB" ] }, { "page": "getStability", "title": "Analyse the dynamic stability of a mizer steady state", "topics": [ "getStability" ] }, { "page": "getSteadyResidual", "title": "How far a model is from its steady state", "concept": [ "summary functions", "summary_function" ], "topics": [ "getSteadyResidual" ] }, { "page": "getTimes", "title": "Times for which simulation results are available", "topics": [ "getTimes" ] }, { "page": "getTrophicLevel", "title": "Get trophic level of individuals at size", "concept": [ "summary functions", "summary_function" ], "topics": [ "getTrophicLevel" ] }, { "page": "getTrophicLevelBySpecies", "title": "Get mean trophic level of each species", "concept": [ "summary functions", "summary_function" ], "topics": [ "getTrophicLevelBySpecies" ] }, { "page": "getYield", "title": "Calculate the rate at which biomass of each species is fished", "concept": [ "summary functions", "summary_function" ], "topics": [ "getYield" ] }, { "page": "getYieldGear", "title": "Calculate the rate at which biomass of each species is fished by each gear", "concept": [ "summary functions", "summary_function" ], "topics": [ "getYieldGear" ] }, { "page": "getZ", "title": "Alias for 'getMort()'", "concept": [ "deprecated" ], "topics": [ "getZ" ] }, { "page": "indicator_functions", "title": "Description of indicator functions", "topics": [ "indicator_functions" ] }, { "page": "initial_effort", "title": "Initial fishing effort", "topics": [ "initial_effort", "initial_effort<-" ] }, { "page": "initialN-set", "title": "Initial values for fish spectra", "topics": [ "initialN", "initialN.MizerParams", "initialN.MizerSim", "initialN<-" ] }, { "page": "initialNOther-set", "title": "Initial values for other ecosystem components", "concept": [ "extension tools" ], "topics": [ "initialNOther", "initialNOther<-" ] }, { "page": "initialNResource-set", "title": "Initial value for resource spectrum", "topics": [ "initialNResource", "initialNResource.MizerParams", "initialNResource.MizerSim", "initialNResource<-" ] }, { "page": "inter", "title": "Alias for 'NS_interaction'", "concept": [ "deprecated" ], "topics": [ "inter" ] }, { "page": "isSteady", "title": "Check whether a model is at steady state", "topics": [ "isSteady", "isSteady.MizerParams" ] }, { "page": "knife_edge", "title": "Weight based knife-edge selectivity function", "concept": [ "selectivity functions" ], "topics": [ "knife_edge" ] }, { "page": "knife_edge_length", "title": "Length based knife-edge selectivity function", "concept": [ "selectivity functions" ], "topics": [ "knife_edge_length" ] }, { "page": "l2w", "title": "Length-weight conversion", "concept": [ "helper" ], "topics": [ "l2w", "w2l" ] }, { "page": "lognormal_pred_kernel", "title": "Lognormal predation kernel", "concept": [ "predation kernel" ], "topics": [ "lognormal_pred_kernel" ] }, { "page": "markBackground", "title": "Designate species as background species", "topics": [ "markBackground" ] }, { "page": "matchBiomasses", "title": "Match biomasses to observations", "topics": [ "matchBiomasses" ] }, { "page": "matchGrowth", "title": "Adjust model to produce observed growth", "topics": [ "matchGrowth" ] }, { "page": "matchNumbers", "title": "Match numbers to observations", "topics": [ "matchNumbers" ] }, { "page": "mizerDiffusion", "title": "Calculate diffusion rate", "topics": [ "mizerDiffusion", "projectDiffusion", "projectDiffusion.MizerParams" ] }, { "page": "mizerEGrowth", "title": "Get energy rate available for growth needed to project standard mizer model", "concept": [ "mizer rate functions" ], "topics": [ "mizerEGrowth", "projectEGrowth", "projectEGrowth.MizerParams" ] }, { "page": "mizerEncounter", "title": "Get encounter rate during projection", "concept": [ "mizer rate functions" ], "topics": [ "mizerEncounter", "projectEncounter", "projectEncounter.MizerParams" ] }, { "page": "mizerERepro", "title": "Get energy rate available for reproduction needed to project standard mizer model", "concept": [ "mizer rate functions" ], "topics": [ "mizerERepro", "projectERepro", "projectERepro.MizerParams" ] }, { "page": "mizerEReproAndGrowth", "title": "Get energy rate available for reproduction and growth needed to project standard mizer model", "concept": [ "mizer rate functions" ], "topics": [ "mizerEReproAndGrowth", "projectEReproAndGrowth", "projectEReproAndGrowth.MizerParams" ] }, { "page": "mizerFeedingLevel", "title": "Get feeding level needed to project standard mizer model", "concept": [ "mizer rate functions" ], "topics": [ "mizerFeedingLevel", "projectFeedingLevel", "projectFeedingLevel.MizerParams" ] }, { "page": "mizerFMort", "title": "Get the total fishing mortality rate from all fishing gears", "concept": [ "mizer rate functions" ], "topics": [ "mizerFMort", "projectFMort", "projectFMort.MizerParams" ] }, { "page": "mizerFMortGear", "title": "Get the fishing mortality needed to project standard mizer model", "concept": [ "mizer rate functions" ], "topics": [ "mizerFMortGear" ] }, { "page": "mizerMort", "title": "Get total mortality rate needed to project standard mizer model", "concept": [ "mizer rate functions" ], "topics": [ "mizerMort", "projectMort", "projectMort.MizerParams" ] }, { "page": "MizerParams", "title": "Alias for 'set_multispecies_model()'", "concept": [ "deprecated" ], "topics": [ "MizerParams" ] }, { "page": "MizerParams-class", "title": "A class to hold the parameters for a size based model.", "topics": [ "MizerParams-class" ] }, { "page": "mizerPredMort", "title": "Get total predation mortality rate needed to project standard mizer model", "concept": [ "mizer rate functions" ], "topics": [ "mizerPredMort", "projectPredMort", "projectPredMort.MizerParams" ] }, { "page": "mizerPredRate", "title": "Get predation rate needed to project standard mizer model", "concept": [ "mizer rate functions" ], "topics": [ "mizerPredRate", "projectPredRate", "projectPredRate.MizerParams" ] }, { "page": "mizerRates", "title": "Get all rates needed to project standard mizer model", "concept": [ "mizer rate functions" ], "topics": [ "mizerRates", "projectRates" ] }, { "page": "mizerRDI", "title": "Get density-independent rate of reproduction needed to project standard mizer model", "concept": [ "mizer rate functions" ], "topics": [ "mizerRDI", "projectRDI", "projectRDI.MizerParams" ] }, { "page": "mizerResourceMort", "title": "Get predation mortality rate for resource needed to project standard mizer model", "concept": [ "mizer rate functions" ], "topics": [ "mizerResourceMort", "projectResourceMort", "projectResourceMort.MizerParams" ] }, { "page": "MizerScan", "title": "S3 class for the result of a parameter scan", "concept": [ "scan", "scan functions" ], "topics": [ "is.MizerScan", "MizerScan" ] }, { "page": "MizerSim", "title": "Constructor for the 'MizerSim' class", "topics": [ "MizerSim" ] }, { "page": "MizerSim-class", "title": "A class to hold the results of a simulation", "topics": [ "MizerSim-class" ] }, { "page": "N", "title": "Time series of size spectra", "topics": [ "N", "NResource" ] }, { "page": "needs_upgrading", "title": "Determine whether a MizerParams or MizerSim object needs to be upgraded", "concept": [ "helper" ], "topics": [ "needs_upgrading" ] }, { "page": "newCommunityParams", "title": "Set up parameters for a community-type model", "concept": [ "functions for setting up models" ], "topics": [ "newCommunityParams" ] }, { "page": "newMultispeciesParams", "title": "Set up parameters for a general multispecies model", "concept": [ "functions for setting up models" ], "topics": [ "newMultispeciesParams" ] }, { "page": "newSingleSpeciesParams", "title": "Set up parameters for a single species in a power-law background", "concept": [ "functions for setting up models" ], "topics": [ "newSingleSpeciesParams" ] }, { "page": "newTraitParams", "title": "Set up parameters for a trait-based multispecies model", "concept": [ "functions for setting up models" ], "topics": [ "newTraitParams" ] }, { "page": "noRDD", "title": "Give density-independent reproduction rate", "concept": [ "functions calculating density-dependent reproduction rate" ], "topics": [ "noRDD" ] }, { "page": "NOther", "title": "Time series of other components", "concept": [ "extension tools" ], "topics": [ "finalNOther", "NOther" ] }, { "page": "NS_interaction", "title": "Example interaction matrix for the North Sea example", "topics": [ "NS_interaction" ] }, { "page": "NS_params", "title": "Example MizerParams object for the North Sea example", "concept": [ "example parameter objects" ], "topics": [ "NS_params" ] }, { "page": "NS_sim", "title": "Example MizerSim object for the North Sea example", "concept": [ "example parameter objects" ], "topics": [ "NS_sim" ] }, { "page": "NS_species_params", "title": "Example species parameter set based on the North Sea", "topics": [ "NS_species_params" ] }, { "page": "NS_species_params_gears", "title": "Example species parameter set based on the North Sea with different gears", "topics": [ "NS_species_params_gears" ] }, { "page": "other_mort", "title": "Extra contributions to the mortality and encounter rates", "concept": [ "extension tools" ], "topics": [ "other_encounter", "other_encounter<-", "other_mort", "other_mort<-" ] }, { "page": "plot", "title": "Plot mizer arrays", "concept": [ "plotting functions" ], "topics": [ "plot" ] }, { "page": "plot.MizerScan", "title": "Plot method for 'MizerScan' objects", "concept": [ "scan", "scan functions" ], "topics": [ "plot.MizerScan" ] }, { "page": "plot2", "title": "Compare two mizer arrays in a single plot", "concept": [ "plotting functions" ], "topics": [ "plot2", "plot2.ArrayResourceBySize", "plot2.ArraySpeciesBySize", "plot2.ArrayTimeByResourceBySize", "plot2.ArrayTimeBySpecies", "plot2.ArrayTimeBySpeciesBySize" ] }, { "page": "plotBiomass", "title": "Plot the biomass of species through time", "concept": [ "plotting functions" ], "topics": [ "plotBiomass", "plotBiomass.MizerSim", "plotlyBiomass" ] }, { "page": "plotBiomassObservedVsModel", "title": "Plotting observed vs. model biomass data", "topics": [ "plotBiomassObservedVsModel", "plotlyBiomassObservedVsModel" ] }, { "page": "plotCDF", "title": "Plot cumulative abundance or biomass distributions", "concept": [ "plotting functions" ], "topics": [ "plotCDF", "plotCDF.MizerParams", "plotCDF.MizerSim", "plotlyCDF" ] }, { "page": "plotCDF2", "title": "Compare cumulative abundance or biomass distributions from two objects", "concept": [ "plotting functions" ], "topics": [ "plotCDF2", "plotlyCDF2" ] }, { "page": "plotDiet", "title": "Plot diet, resolved by prey species, as function of predator at size.", "concept": [ "plotting functions" ], "topics": [ "plotDiet", "plotDiet.MizerParams", "plotDiet.MizerSim", "plotlyDiet" ] }, { "page": "plotFeedingLevel", "title": "Plot the feeding level of species by size", "concept": [ "plotting functions" ], "topics": [ "plotFeedingLevel", "plotFeedingLevel.MizerParams", "plotFeedingLevel.MizerSim", "plotlyFeedingLevel" ] }, { "page": "plotFMort", "title": "Plot total fishing mortality of each species by size", "concept": [ "plotting functions" ], "topics": [ "plotFMort", "plotFMort.MizerParams", "plotFMort.MizerSim", "plotlyFMort" ] }, { "page": "plotGrowthCurves", "title": "Plot growth curves", "concept": [ "plotting functions" ], "topics": [ "plotGrowthCurves", "plotGrowthCurves.MizerParams", "plotGrowthCurves.MizerSim", "plotlyGrowthCurves" ] }, { "page": "plotHover", "title": "Create a hover-enabled plotly plot from a mizer object", "concept": [ "plotting functions" ], "topics": [ "plotHover", "plotHover.ArrayResourceBySize", "plotHover.ArraySpeciesBySize", "plotHover.ArrayTimeByResourceBySize", "plotHover.ArrayTimeBySpecies", "plotHover.ArrayTimeBySpeciesBySize", "plotHover.MizerScan", "plotHover.mizer_plot" ] }, { "page": "plotM2", "title": "Alias for 'plotPredMort()'", "concept": [ "deprecated" ], "topics": [ "plotM2" ] }, { "page": "plotMizerParams", "title": "Summary plot for 'MizerParams' objects", "concept": [ "plotting functions" ], "topics": [ "plot.MizerParams", "plotMizerParams" ] }, { "page": "plotMizerSim", "title": "Summary plot for 'MizerSim' objects", "concept": [ "plotting functions" ], "topics": [ "plot.MizerSim", "plotMizerSim" ] }, { "page": "plotPredMort", "title": "Plot predation mortality rate of each species against size", "concept": [ "plotting functions" ], "topics": [ "plotlyPredMort", "plotPredMort", "plotPredMort.MizerParams", "plotPredMort.MizerSim" ] }, { "page": "plotRelative", "title": "Plot relative difference between two mizer arrays", "concept": [ "plotting functions" ], "topics": [ "plotRelative", "plotRelative.ArrayResourceBySize", "plotRelative.ArraySpeciesBySize", "plotRelative.ArrayTimeByResourceBySize", "plotRelative.ArrayTimeBySpecies", "plotRelative.ArrayTimeBySpeciesBySize" ] }, { "page": "plotSpectra", "title": "Plot abundance and biomass spectra", "concept": [ "plotting functions" ], "topics": [ "plotlySpectra", "plotSpectra", "plotSpectra.MizerParams", "plotSpectra.MizerSim" ] }, { "page": "plotSpectra2", "title": "Compare abundance and biomass spectra from two objects", "concept": [ "plotting functions" ], "topics": [ "plotlySpectra2", "plotSpectra2" ] }, { "page": "plotSpectraRelative", "title": "Plot relative difference between abundance spectra", "concept": [ "plotting functions" ], "topics": [ "plotlySpectraRelative", "plotSpectraRelative" ] }, { "page": "plotting_functions", "title": "Description of the plotting functions", "concept": [ "plotting functions" ], "topics": [ "plotting_functions" ] }, { "page": "plotYield", "title": "Plot the total yield of species through time", "concept": [ "plotting functions" ], "topics": [ "plotlyYield", "plotYield", "plotYield.MizerSim" ] }, { "page": "plotYieldGear", "title": "Plot the total yield of each species by gear through time", "concept": [ "plotting functions" ], "topics": [ "plotlyYieldGear", "plotYieldGear", "plotYieldGear.MizerSim" ] }, { "page": "plotYieldObservedVsModel", "title": "Plotting observed vs. model yields", "topics": [ "plotlyYieldObservedVsModel", "plotYieldObservedVsModel" ] }, { "page": "plotYieldVsF", "title": "Plot the yield of a species against the fishing mortality on it", "concept": [ "plotting functions", "scan", "scan functions" ], "topics": [ "plotYieldVsF" ] }, { "page": "power_law_pred_kernel", "title": "Power-law predation kernel", "concept": [ "predation kernel" ], "topics": [ "power_law_pred_kernel" ] }, { "page": "print", "title": "Print mizer objects", "topics": [ "print", "print.ArraySpeciesBySize", "print.ArrayTimeBySpecies", "print.ArrayTimeBySpeciesBySize", "print.summary.ArraySpeciesBySize", "print.summary.ArrayTimeBySpecies", "print.summary.ArrayTimeBySpeciesBySize" ] }, { "page": "print.mizer_plot", "title": "Print a mizer plot", "topics": [ "print.mizer_plot" ] }, { "page": "project", "title": "Project size spectrum forward in time", "topics": [ "project", "project.MizerParams", "project.MizerSim" ] }, { "page": "project_n", "title": "Project values for first time step of Euler method", "concept": [ "helper" ], "topics": [ "project_n", "project_n_no_diffusion" ] }, { "page": "project_n_2", "title": "Project values with a predictor-corrector method", "concept": [ "helper" ], "topics": [ "project_n_2" ] }, { "page": "project_n_tr_bdf2", "title": "Project values with the TR-BDF2 method", "concept": [ "helper" ], "topics": [ "project_n_tr_bdf2" ] }, { "page": "project_simple", "title": "Project abundances by a given number of time steps into the future", "concept": [ "helper" ], "topics": [ "project_simple" ] }, { "page": "projectRDD", "title": "Get density-dependent reproduction rate during projection", "topics": [ "projectRDD", "projectRDD.MizerParams" ] }, { "page": "projectUntilSettled", "title": "Project the dynamics until they settle", "topics": [ "projectUntilSettled" ] }, { "page": "reconcileSpeciesParams", "title": "Reconcile the species parameters with the given species parameters", "concept": [ "helper" ], "topics": [ "reconcileSpeciesParams" ] }, { "page": "record_given_species_params", "title": "Record the species parameters that have changed", "concept": [ "helper" ], "topics": [ "record_given_species_params" ] }, { "page": "recordExtension", "title": "Record an extension and its version stamp on a mizer object", "concept": [ "extension tools" ], "topics": [ "recordExtension" ] }, { "page": "removeBackgroundSpecies", "title": "Remove all background species", "topics": [ "removeBackgroundSpecies" ] }, { "page": "removeSpecies", "title": "Remove species", "topics": [ "removeSpecies" ] }, { "page": "renameGear", "title": "Rename gears", "topics": [ "renameGear" ] }, { "page": "renameSpecies", "title": "Rename species", "topics": [ "renameSpecies" ] }, { "page": "resource_constant", "title": "Keep resource abundance constant", "concept": [ "resource dynamics functions" ], "topics": [ "resource_constant" ] }, { "page": "resource_logistic", "title": "Project resource using logistic model", "concept": [ "resource dynamics functions" ], "topics": [ "balance_resource_logistic", "resource_logistic" ] }, { "page": "resource_params", "title": "Resource parameters", "topics": [ "resource_params", "resource_params<-" ] }, { "page": "resource_semichemostat", "title": "Project resource using semichemostat model", "concept": [ "resource dynamics functions" ], "topics": [ "balance_resource_semichemostat", "resource_semichemostat" ] }, { "page": "RickerRDD", "title": "Ricker function to calculate density-dependent reproduction rate", "concept": [ "functions calculating density-dependent reproduction rate" ], "topics": [ "RickerRDD" ] }, { "page": "saveParams", "title": "Save and restore mizer objects", "topics": [ "readParams", "readSim", "saveParams", "saveSim" ] }, { "page": "scaleModel", "title": "Change scale of the model", "topics": [ "scaleModel" ] }, { "page": "scaleRates", "title": "Rescale all rates in a mizer model", "topics": [ "scaleRates" ] }, { "page": "scanEffort", "title": "Setters for scanning a model", "concept": [ "scan", "scan functions" ], "topics": [ "scanEffort", "scanFishingMortality", "scanSpeciesParam" ] }, { "page": "scanModel", "title": "Scan a model over a range of values", "concept": [ "scan", "scan functions" ], "topics": [ "scanModel" ] }, { "page": "second_order_w", "title": "Get or set the second_order_w flags", "topics": [ "second_order_w", "second_order_w<-" ] }, { "page": "set_community_model", "title": "Deprecated function for setting up parameters for a community-type model", "concept": [ "deprecated" ], "topics": [ "set_community_model" ] }, { "page": "set_multispecies_model", "title": "Deprecated obsolete function for setting up multispecies parameters", "concept": [ "deprecated" ], "topics": [ "set_multispecies_model" ] }, { "page": "set_species_param_default", "title": "Set a species parameter to a default value", "concept": [ "helper" ], "topics": [ "set_species_param_default" ] }, { "page": "set_trait_model", "title": "Deprecated function for setting up parameters for a trait-based model", "concept": [ "deprecated" ], "topics": [ "set_trait_model" ] }, { "page": "setBevertonHolt", "title": "Set Beverton-Holt reproduction without changing the steady state", "topics": [ "reproduction_level", "reproduction_level<-", "setBevertonHolt" ] }, { "page": "setColours", "title": "Set line colours and line types to be used in mizer plots", "topics": [ "getColours", "getLinetypes", "setColours", "setLinetypes" ] }, { "page": "setComponent", "title": "Add a dynamical ecosystem component", "concept": [ "extension tools" ], "topics": [ "getComponent", "removeComponent", "setComponent" ] }, { "page": "setExtDiffusion", "title": "Set external diffusion rate", "concept": [ "functions for setting parameters" ], "topics": [ "ext_diffusion", "ext_diffusion<-", "setExtDiffusion", "setExtDiffusion.MizerParams" ] }, { "page": "setExtEncounter", "title": "Set external encounter rate", "concept": [ "functions for setting parameters" ], "topics": [ "ext_encounter", "ext_encounter<-", "setExtEncounter" ] }, { "page": "setExtMort", "title": "Set external mortality rate", "concept": [ "functions for setting parameters" ], "topics": [ "ext_mort", "ext_mort<-", "setExtMort" ] }, { "page": "setFishing", "title": "Set fishing parameters", "concept": [ "functions for setting parameters" ], "topics": [ "catchability", "catchability<-", "selectivity", "selectivity<-", "setFishing" ] }, { "page": "setInitialValues", "title": "Set initial values to values from a simulation", "concept": [ "deprecated" ], "topics": [ "setInitialValues" ] }, { "page": "setInteraction", "title": "Set species interaction matrix", "concept": [ "functions for setting parameters" ], "topics": [ "interaction_matrix", "interaction_matrix<-", "setInteraction" ] }, { "page": "setMaxIntakeRate", "title": "Set maximum intake rate", "concept": [ "functions for setting parameters" ], "topics": [ "intake_max", "intake_max<-", "setMaxIntakeRate" ] }, { "page": "setMetabolicRate", "title": "Set metabolic rate", "concept": [ "functions for setting parameters" ], "topics": [ "metab", "metab<-", "setMetabolicRate" ] }, { "page": "setMetadata", "title": "Set metadata for a model", "topics": [ "getMetadata", "setMetadata" ] }, { "page": "setParams", "title": "Set or change any model parameters", "concept": [ "functions for setting parameters" ], "topics": [ "setParams" ] }, { "page": "setPredKernel", "title": "Set predation kernel", "concept": [ "functions for setting parameters" ], "topics": [ "pred_kernel", "pred_kernel<-", "setPredKernel" ] }, { "page": "setRateFunction", "title": "Set own rate function to replace mizer rate function", "concept": [ "extension tools" ], "topics": [ "getRateFunction", "other_params", "other_params<-", "setRateFunction" ] }, { "page": "setReproduction", "title": "Set reproduction parameters", "concept": [ "functions for setting parameters" ], "topics": [ "maturity", "maturity<-", "psi", "repro_prop", "repro_prop<-", "setReproduction" ] }, { "page": "setResource", "title": "Set resource dynamics", "topics": [ "resource_capacity", "resource_capacity<-", "resource_dynamics", "resource_dynamics<-", "resource_level", "resource_level<-", "resource_rate", "resource_rate<-", "setResource" ] }, { "page": "setRmax", "title": "Alias for 'setBevertonHolt()'", "concept": [ "deprecated" ], "topics": [ "setRmax" ] }, { "page": "setSearchVolume", "title": "Set search volume", "concept": [ "functions for setting parameters" ], "topics": [ "search_vol", "search_vol<-", "setSearchVolume" ] }, { "page": "SheperdRDD", "title": "Sheperd function to calculate density-dependent reproduction rate", "concept": [ "functions calculating density-dependent reproduction rate" ], "topics": [ "SheperdRDD" ] }, { "page": "sigmoid_length", "title": "Length based sigmoid selectivity function", "concept": [ "selectivity functions" ], "topics": [ "sigmoid_length" ] }, { "page": "sigmoid_weight", "title": "Weight based sigmoidal selectivity function", "concept": [ "selectivity functions" ], "topics": [ "sigmoid_weight" ] }, { "page": "signal_frozen", "title": "Signal that a change the user made cannot take effect", "concept": [ "info signalling functions" ], "topics": [ "signal_frozen" ] }, { "page": "signal_frozen_changes", "title": "Signal the changes to species parameters that cannot take effect", "concept": [ "info signalling functions" ], "topics": [ "signal_frozen_changes" ] }, { "page": "signal_gear_params_changes", "title": "Signal a gear parameter changed through the given species parameters", "concept": [ "info signalling functions" ], "topics": [ "signal_gear_params_changes" ] }, { "page": "signal_ignored_changes", "title": "Signal the changes that are ignored because another parameter was given", "concept": [ "info signalling functions" ], "topics": [ "signal_ignored_changes" ] }, { "page": "signal_info", "title": "Signal information about a choice mizer made", "concept": [ "info signalling functions" ], "topics": [ "signal_info" ] }, { "page": "signal_not_recalculated", "title": "Signal that a rate array was not recalculated because it is frozen", "concept": [ "info signalling functions" ], "topics": [ "signal_not_recalculated" ] }, { "page": "signal_removed_species_params", "title": "Signal that species parameter columns have been removed", "concept": [ "info signalling functions" ], "topics": [ "signal_removed_species_params" ] }, { "page": "sizeIntegral", "title": "Integrate a quantity over the size spectrum", "topics": [ "sizeIntegral" ] }, { "page": "species_params", "title": "Species parameters", "concept": [ "functions for setting parameters" ], "topics": [ "calculated_species_params", "given_species_params", "given_species_params.data.frame", "given_species_params.given_species_params", "given_species_params.MizerParams", "given_species_params.MizerSim", "given_species_params<-", "given_species_params<-.MizerParams", "is.given_species_params", "is.species_params", "species_params", "species_params.data.frame", "species_params.MizerParams", "species_params.MizerSim", "species_params.species_params", "species_params<-", "species_params<-.MizerParams" ] }, { "page": "steadySingleSpecies", "title": "Set initial abundances to solution of steady-state equation with current rates", "topics": [ "steadySingleSpecies" ] }, { "page": "str", "title": "Display the structure of mizer objects", "topics": [ "str", "str.ArraySpeciesBySize", "str.ArrayTimeBySpecies", "str.ArrayTimeBySpeciesBySize", "str.MizerParams", "str.MizerSim" ] }, { "page": "summary", "title": "Summarise mizer objects", "topics": [ "summary", "summary.ArraySpeciesBySize", "summary.ArrayTimeBySpecies", "summary.ArrayTimeBySpeciesBySize", "summary.MizerParams", "summary.MizerSim" ] }, { "page": "summary_functions", "title": "Description of summary functions", "topics": [ "summary_functions" ] }, { "page": "superseded_accessors", "title": "Superseded 'get'-prefixed aliases for values stored in a model", "concept": [ "deprecated" ], "topics": [ "getCatchability", "getExtEncounter", "getExtMort", "getInitialEffort", "getInteraction", "getMaturityProportion", "getMaxIntakeRate", "getMetabolicRate", "getPredKernel", "getReproductionLevel", 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