| mizer: Multi-species size-based modelling in R | mizer-package mizer |
| Add lines to an existing plot | addPlot addPlot.ArraySpeciesBySize addPlot.ArrayTimeBySpecies |
| Add new species | addSpecies |
| Adjust the size grid | adjustSizeGrid adjustSizeGrid.MizerParams |
| Calculate age at maturity | age_mat |
| Calculate age at maturity from von Bertalanffy growth parameters | age_mat_vB age_mat_vB.data.frame age_mat_vB.default age_mat_vB.MizerParams |
| Animate size-dependent quantities through time | animate animate.ArrayTimeBySpeciesBySize animate.MizerSim animateSpectra |
| S3 class for resource size spectra | ArrayResourceBySize |
| S3 class for species x size rate arrays | ArraySpeciesBySize |
| S3 class for time x resource-size arrays | ArrayTimeByResourceBySize |
| S3 class for time x species arrays | ArrayTimeBySpecies |
| S3 class for time x species x size arrays | ArrayTimeBySpeciesBySize |
| Convert mizer arrays to data frames | as.data.frame as.data.frame.ArraySpeciesBySize as.data.frame.ArrayTimeBySpecies as.data.frame.ArrayTimeBySpeciesBySize |
| Beverton Holt function to calculate density-dependent reproduction rate | BevertonHoltRDD |
| Box predation kernel | box_pred_kernel |
| Calculate selectivity from gear parameters | calc_selectivity |
| Calibrate the model scale to match total observed biomass | calibrateBiomass |
| Calibrate the model scale to match total observed number | calibrateNumber |
| Calibrate the model scale to match total observed yield | calibrateYield |
| Clear the registered extension chain | clearExtensionChain |
| Coerce a mizer object to its registered extension class | coerceToExtensionClass |
| Compare two MizerParams objects and print out differences | compareParams |
| Alias for 'validSpeciesParams()' | completeSpeciesParams |
| Helper function to keep other components constant | constant_other |
| Choose egg production to keep egg density constant | constantEggRDI |
| Give constant reproduction rate | constantRDD |
| Replace a mizer function with a custom version | customFunction |
| Set defaults for predation kernel parameters | default_pred_kernel_params |
| Default editions | defaults_edition |
| Check whether two objects are different | different |
| Measure distance between current and previous state in terms of RDI | distanceMaxRelRDI |
| Measure distance between current and previous state in terms of fish abundances | distanceSSLogN |
| Length based double-sigmoid selectivity function | double_sigmoid_length |
| Create empty MizerParams object of the right size | emptyParams |
| Expand the size grid | expandSizeGrid expandSizeGrid.MizerParams |
| Size spectra at end of simulation | finalN finalNResource idxFinalT |
| Extract the final state from a simulation | finalParams |
| Gear parameters | gear_params gear_params.data.frame gear_params.gear_params gear_params.MizerParams gear_params.MizerSim gear_params<- gear_params<-.MizerParams |
| Get default value for f0 | get_f0_default |
| Get default value for gamma | get_gamma_default |
| Calculate initial population abundances | get_initial_n |
| Get default value for 'ks' | get_ks_default |
| Get values from feeding kernel function | get_phi |
| Get size range array | get_size_range_array |
| Calculate steady state abundance | get_steady_state_n |
| Get array indices for a time range in a MizerSim object | get_time_elements |
| Calculate the total biomass of each species within a size range at each time step. | getBiomass |
| Calculate the slope of the community abundance | getCommunitySlope |
| Get critical feeding level | getCriticalFeedingLevel |
| Get diet of predator at size, resolved by prey species | getDiet |
| Get diffusion rate from predation | getDiffusion |
| Fishing effort used in simulation | getEffort |
| Get energy rate available for growth | getEGrowth |
| Get encounter rate | getEncounter |
| Get energy rate available for reproduction | getERepro |
| Get energy rate available for reproduction and growth | getEReproAndGrowth |
| Alias for 'getERepro()' | getESpawning |
| Get feeding level | getFeedingLevel |
| Get flux into size bins | getFlux getFlux.MizerParams getFlux.MizerSim |
| Get flux gradient | getFluxGradient getFluxGradient.MizerParams getFluxGradient.MizerSim |
| Get the total fishing mortality rate from all fishing gears by time, species and size. | getFMort |
| Get the fishing mortality by time, gear, species and size | getFMortGear |
| Get growth curves giving weight as a function of age | getGrowthCurves |
| Alias for 'getPredMort()' | getM2 |
| Alias for 'getResourceMort()' | getM2Background |
| Calculate the mean maximum weight of the community | getMeanMaxWeight |
| Calculate the mean weight of the community | getMeanWeight |
| Get total mortality rate | getMort |
| Calculate the number of individuals within a size range | getN |
| Extract the model state from a simulation | getParams |
| Get available energy | getPhiPrey |
| Get total predation mortality rate | getPredMort |
| Get predation rate | getPredRate |
| Calculate the proportion of large fish | getProportionOfLargeFish |
| Get all rates | getRates |
| Get density dependent reproduction rate | getRDD |
| Get density independent rate of egg production | getRDI |
| Get the registered mizer extension chain | getRegisteredExtensions |
| Get reproduction level | getReproductionLevel |
| Determine reproduction rate needed for initial egg abundance | getRequiredRDD |
| Get predation mortality rate for resource | getResourceMort |
| Extract the projection parameters used to produce a simulation | getSimParams |
| Calculate the SSB of species | getSSB |
| Times for which simulation results are available | getTimes |
| Get trophic level of individuals at size | getTrophicLevel |
| Get mean trophic level of each species | getTrophicLevelBySpecies |
| Calculate the rate at which biomass of each species is fished | getYield |
| Calculate the rate at which biomass of each species is fished by each gear | getYieldGear |
| Alias for 'getMort()' | getZ |
| Description of indicator functions | indicator_functions |
| Initial fishing effort | initial_effort initial_effort<- |
| Initial values for fish spectra | initialN initialN.MizerParams initialN.MizerSim initialN<- |
| Initial values for other ecosystem components | initialNOther initialNOther<- |
| Initial value for resource spectrum | initialNResource initialNResource.MizerParams initialNResource.MizerSim initialNResource<- |
| Extract the initial state from a simulation | initialParams |
| Alias for 'NS_interaction' | inter |
| Test if an object is an ArrayResourceBySize | is.ArrayResourceBySize |
| Test if an object is a ArraySpeciesBySize | is.ArraySpeciesBySize |
| Test if an object is an ArrayTimeByResourceBySize | is.ArrayTimeByResourceBySize |
| Test if an object is a ArrayTimeBySpecies | is.ArrayTimeBySpecies |
| Test if an object is an ArrayTimeBySpeciesBySize | is.ArrayTimeBySpeciesBySize |
| Test if an object is a gear_params object | is.gear_params |
| Test if an object is a given_species_params object | is.given_species_params |
| Test if an object is a species_params object | is.species_params |
| Weight based knife-edge selectivity function | knife_edge |
| Length-weight conversion | l2w w2l |
| Lognormal predation kernel | lognormal_pred_kernel |
| Designate species as background species | markBackground |
| Match biomasses to observations | matchBiomasses |
| Adjust model to produce observed growth | matchGrowth |
| Match numbers to observations | matchNumbers |
| Match yields to observations | matchYields |
| Calculate diffusion rate | mizerDiffusion projectDiffusion projectDiffusion.MizerParams |
| Get energy rate available for growth needed to project standard mizer model | mizerEGrowth projectEGrowth projectEGrowth.MizerParams |
| Get encounter rate during projection | mizerEncounter projectEncounter projectEncounter.MizerParams |
| Get energy rate available for reproduction needed to project standard mizer model | mizerERepro projectERepro projectERepro.MizerParams |
| Get energy rate available for reproduction and growth needed to project standard mizer model | mizerEReproAndGrowth projectEReproAndGrowth projectEReproAndGrowth.MizerParams |
| Get feeding level needed to project standard mizer model | mizerFeedingLevel projectFeedingLevel projectFeedingLevel.MizerParams |
| Get the total fishing mortality rate from all fishing gears | mizerFMort projectFMort projectFMort.MizerParams |
| Get the fishing mortality needed to project standard mizer model | mizerFMortGear |
| Get total mortality rate needed to project standard mizer model | mizerMort projectMort projectMort.MizerParams |
| Alias for 'set_multispecies_model()' | MizerParams |
| A class to hold the parameters for a size based model. | MizerParams-class |
| Get total predation mortality rate needed to project standard mizer model | mizerPredMort projectPredMort projectPredMort.MizerParams |
| Get predation rate needed to project standard mizer model | mizerPredRate projectPredRate projectPredRate.MizerParams |
| Get all rates needed to project standard mizer model | mizerRates projectRates |
| Get density-independent rate of reproduction needed to project standard mizer model | mizerRDI projectRDI projectRDI.MizerParams |
| Get predation mortality rate for resource needed to project standard mizer model | mizerResourceMort projectResourceMort projectResourceMort.MizerParams |
| Constructor for the 'MizerSim' class | MizerSim |
| A class to hold the results of a simulation | MizerSim-class |
| Time series of size spectra | N NResource |
| Determine whether a MizerParams or MizerSim object needs to be upgraded | needs_upgrading |
| Set up parameters for a community-type model | newCommunityParams |
| Set up parameters for a general multispecies model | newMultispeciesParams |
| Set up parameters for a single species in a power-law background | newSingleSpeciesParams |
| Set up parameters for a trait-based multispecies model | newTraitParams |
| Give density-independent reproduction rate | noRDD |
| Time series of other components | finalNOther NOther |
| Example interaction matrix for the North Sea example | NS_interaction |
| Example MizerParams object for the North Sea example | NS_params |
| Example MizerSim object for the North Sea example | NS_sim |
| Example species parameter set based on the North Sea | NS_species_params |
| Example species parameter set based on the North Sea with different gears | NS_species_params_gears |
| Plot mizer arrays | plot plot.ArrayResourceBySize plot.ArraySpeciesBySize plot.ArrayTimeByResourceBySize plot.ArrayTimeBySpecies plot.ArrayTimeBySpeciesBySize |
| Compare two mizer arrays in a single plot | plot2 plot2.ArraySpeciesBySize plot2.ArrayTimeBySpecies plot2.ArrayTimeBySpeciesBySize |
| Plot the biomass of species through time | plotBiomass plotBiomass.MizerSim plotlyBiomass |
| Plotting observed vs. model biomass data | plotBiomassObservedVsModel plotlyBiomassObservedVsModel |
| Plot cumulative abundance or biomass distributions | plotCDF plotCDF.MizerParams plotCDF.MizerSim plotlyCDF |
| Compare cumulative abundance or biomass distributions from two objects | plotCDF2 plotlyCDF2 |
| Plot diet, resolved by prey species, as function of predator at size. | plotDiet plotDiet.MizerParams plotDiet.MizerSim plotlyDiet |
| Plot the feeding level of species by size | plotFeedingLevel plotFeedingLevel.MizerParams plotFeedingLevel.MizerSim plotlyFeedingLevel |
| Plot total fishing mortality of each species by size | plotFMort plotFMort.MizerParams plotFMort.MizerSim plotlyFMort |
| Plot growth curves | plotGrowthCurves plotGrowthCurves.MizerParams plotGrowthCurves.MizerSim plotlyGrowthCurves |
| Create a hover-enabled plotly plot from a mizer object | plotHover plotHover.ArrayResourceBySize plotHover.ArraySpeciesBySize plotHover.ArrayTimeByResourceBySize plotHover.ArrayTimeBySpecies plotHover.ArrayTimeBySpeciesBySize plotHover.mizer_plot |
| Alias for 'plotPredMort()' | plotM2 |
| Summary plot for 'MizerParams' objects | plot.MizerParams plotMizerParams |
| Summary plot for 'MizerSim' objects | plot.MizerSim plotMizerSim |
| Plot predation mortality rate of each species against size | plotlyPredMort plotPredMort plotPredMort.MizerParams plotPredMort.MizerSim |
| Plot relative difference between two mizer arrays | plotRelative plotRelative.ArraySpeciesBySize plotRelative.ArrayTimeBySpecies plotRelative.ArrayTimeBySpeciesBySize |
| Plot abundance and biomass spectra | plotlySpectra plotSpectra plotSpectra.MizerParams plotSpectra.MizerSim |
| Compare abundance and biomass spectra from two objects | plotlySpectra2 plotSpectra2 |
| Plot relative difference between abundance spectra | plotlySpectraRelative plotSpectraRelative |
| Description of the plotting functions | plotting_functions |
| Plot the total yield of species through time | plotlyYield plotYield plotYield.MizerSim |
| Plot the total yield of each species by gear through time | plotlyYieldGear plotYieldGear plotYieldGear.MizerSim |
| Plotting observed vs. model yields | plotlyYieldObservedVsModel plotYieldObservedVsModel |
| Power-law predation kernel | power_law_pred_kernel |
| Print mizer objects | print print.ArraySpeciesBySize print.ArrayTimeBySpecies print.ArrayTimeBySpeciesBySize print.summary.ArraySpeciesBySize print.summary.ArrayTimeBySpecies print.summary.ArrayTimeBySpeciesBySize |
| Project size spectrum forward in time | project project.MizerParams project.MizerSim |
| Project values for first time step of Euler method | project_n project_n_no_diffusion |
| Project values with a predictor-corrector method | project_n_2 |
| Project values with the TR-BDF2 method | project_n_tr_bdf2 |
| Project abundances by a given number of time steps into the future | project_simple |
| Get density-dependent reproduction rate during projection | projectRDD projectRDD.MizerParams |
| Project to steady state | projectToSteady |
| Record an extension and its version stamp on a mizer object | recordExtension |
| Register a single mizer extension for this R session | registerExtension |
| Register mizer extensions for this R session | registerExtensions |
| Remove all background species | removeBackgroundSpecies |
| Remove species | removeSpecies |
| Rename gears | renameGear |
| Rename species | renameSpecies |
| Keep resource abundance constant | resource_constant |
| Project resource using logistic model | balance_resource_logistic resource_logistic |
| Resource parameters | resource_params resource_params<- |
| Project resource using semichemostat model | balance_resource_semichemostat resource_semichemostat |
| Ricker function to calculate density-dependent reproduction rate | RickerRDD |
| Save and restore mizer objects | readParams readSim saveParams saveSim |
| Change scale of the model | scaleModel |
| Rescale all rates in a mizer model | scaleRates |
| Get or set the second_order_w flags | second_order_w second_order_w<- |
| Deprecated function for setting up parameters for a community-type model | set_community_model |
| Deprecated obsolete function for setting up multispecies parameters | set_multispecies_model |
| Set a species parameter to a default value | set_species_param_default |
| Deprecated function for setting up parameters for a trait-based model | set_trait_model |
| Set Beverton-Holt reproduction without changing the steady state | setBevertonHolt |
| Set line colours and line types to be used in mizer plots | getColours getLinetypes setColours setLinetypes |
| Add a dynamical ecosystem component | getComponent removeComponent setComponent |
| Set external diffusion rate | ext_diffusion ext_diffusion<- setExtDiffusion setExtDiffusion.MizerParams |
| Set external encounter rate | ext_encounter ext_encounter<- getExtEncounter setExtEncounter |
| Set external mortality rate | ext_mort ext_mort<- getExtMort setExtMort |
| Set fishing parameters | catchability catchability<- getCatchability getInitialEffort getSelectivity selectivity selectivity<- setFishing |
| Set initial values to values from a simulation | setInitialValues |
| Set species interaction matrix | interaction_matrix interaction_matrix<- setInteraction |
| Set maximum intake rate | getMaxIntakeRate intake_max intake_max<- setMaxIntakeRate |
| Set metabolic rate | getMetabolicRate metab metab<- setMetabolicRate |
| Set metadata for a model | getMetadata setMetadata |
| Set or change any model parameters | setParams |
| Set predation kernel | getPredKernel pred_kernel pred_kernel<- setPredKernel |
| Set own rate function to replace mizer rate function | getRateFunction other_params other_params<- setRateFunction |
| Set reproduction parameters | getMaturityProportion getReproductionProportion maturity maturity<- psi repro_prop repro_prop<- setReproduction |
| Set resource dynamics | resource_capacity resource_capacity<- resource_dynamics resource_dynamics<- resource_level resource_level<- resource_rate resource_rate<- setResource |
| Alias for 'setBevertonHolt()' | setRmax |
| Set search volume | getSearchVolume search_vol search_vol<- setSearchVolume |
| Sheperd function to calculate density-dependent reproduction rate | SheperdRDD |
| Length based sigmoid selectivity function | sigmoid_length |
| Weight based sigmoidal selectivity function | sigmoid_weight |
| Species parameters | 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 species_params species_params.data.frame species_params.MizerParams species_params.MizerSim species_params.species_params species_params<- species_params<-.MizerParams |
| Set initial values to a steady state for the model | steady |
| Find a steady state by directly solving the steady-state equation | steadyNewton steadyNewton.MizerParams |
| Set initial abundances to solution of steady-state equation with current rates | steadySingleSpecies |
| Display the structure of mizer objects | str str.ArraySpeciesBySize str.ArrayTimeBySpecies str.ArrayTimeBySpeciesBySize str.MizerParams str.MizerSim |
| Summarise mizer objects | summary summary.ArraySpeciesBySize summary.ArrayTimeBySpecies summary.ArrayTimeBySpeciesBySize summary.MizerParams summary.MizerSim |
| Description of summary functions | summary_functions |
| Truncated lognormal predation kernel | truncated_lognormal_pred_kernel |
| Get or set the use_predation_diffusion flag | use_predation_diffusion use_predation_diffusion<- |
| Helper function to assure validity of gears argument | valid_gears_arg |
| Helper function to assure validity of species argument | valid_species_arg |
| Make a valid effort vector | validEffortVector |
| Check validity of gear parameters and set defaults | validGearParams |
| Validate MizerParams object and upgrade if necessary | validParams |
| Validate MizerSim object and upgrade if necessary | validSim |
| Validate species parameter data frame | validGivenSpeciesParams validSpeciesParams |
| Size bins | dw dw_full w w_full |
