mizer: Multi-species size-based modelling in R | mizer-package mizer |
Add new species | addSpecies |
Calculate age at maturity | age_mat |
Calculate age at maturity from von Bertalanffy growth parameters | age_mat_vB |
Animation of the abundance spectra | animateSpectra |
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 |
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 |
Size spectra at end of simulation | finalN finalNResource idxFinalT |
Values of other ecosystem components at end of simulation | finalNOther |
Gear parameters | gear_params gear_params<- |
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 |
Determine reproduction rate needed for initial egg abundance | get_required_reproduction |
Get size range array | get_size_range_array |
Get_time_elements | 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 information about other ecosystem components | getComponent |
Get critical feeding level | getCriticalFeedingLevel |
Get diet of predator at size, resolved by prey species | getDiet |
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 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 parameter object underlying 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 reproduction level | getReproductionLevel |
Get predation mortality rate for resource | getResourceMort |
Calculate the SSB of species | getSSB |
Times for which simulation results are available | getTimes |
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<- validEffortVector |
Initial values for fish spectra | initialN initialN<- |
Initial values for other ecosystem components | initialNOther initialNOther<- |
Initial value for resource spectrum | initialNResource initialNResource<- |
Alias for 'NS_interaction' | inter |
Weight based knife-edge selectivity function | knife_edge |
Length-weight conversion | l2w w2l |
Lognormal predation kernel | lognormal_pred_kernel |
Match biomasses to observations | matchBiomasses |
Adjust model to produce observed growth | matchGrowth |
Match numbers to observations | matchNumbers |
Match yields to observations | matchYields |
Get energy rate available for growth needed to project standard mizer model | mizerEGrowth |
Get encounter rate needed to project standard mizer model | mizerEncounter |
Get energy rate available for reproduction needed to project standard mizer model | mizerERepro |
Get energy rate available for reproduction and growth needed to project standard mizer model | mizerEReproAndGrowth |
Get feeding level needed to project standard mizer model | mizerFeedingLevel |
Get the total fishing mortality rate from all fishing gears | mizerFMort |
Get the fishing mortality needed to project standard mizer model | mizerFMortGear |
Get total mortality rate needed to project standard mizer model | mizerMort |
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 |
Get predation rate needed to project standard mizer model | mizerPredRate |
Get all rates needed to project standard mizer model | mizerRates |
Get density-independent rate of reproduction needed to project standard mizer model | mizerRDI |
Get predation mortality rate for resource needed to project standard mizer model | mizerResourceMort |
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 | 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 |
Summary plot for 'MizerParams' objects | plot,MizerParams,missing-method |
Summary plot for 'MizerSim' objects | plot,MizerSim,missing-method |
Plot the biomass of species through time | plotBiomass plotlyBiomass |
Plotting observed vs. model biomass data | plotBiomassObservedVsModel plotlyBiomassObservedVsModel |
Plot diet, resolved by prey species, as function of predator at size. | plotDiet |
Plot the feeding level of species by size | plotFeedingLevel plotlyFeedingLevel |
Plot total fishing mortality of each species by size | plotFMort plotlyFMort |
Plot growth curves | plotGrowthCurves plotlyGrowthCurves |
Alias for 'plotPredMort()' | plotM2 |
Plot predation mortality rate of each species against size | plotlyPredMort plotPredMort |
Plot the abundance spectra | plotlySpectra plotSpectra |
Description of the plotting functions | plotting_functions |
Plot the total yield of species through time | plotlyYield plotYield |
Plot the total yield of each species by gear through time | plotlyYieldGear plotYieldGear |
Plotting observed vs. model yields | plotlyYieldObservedVsModel plotYieldObservedVsModel |
Power-law predation kernel | power_law_pred_kernel |
Project size spectrum forward in time | project |
Project abundances by a given number of time steps into the future | project_simple |
Project to steady state | projectToSteady |
Remove species | removeSpecies |
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 a MizerParams object to file, and restore it | readParams saveParams |
Change scale of the model | scaleModel |
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 | removeComponent setComponent |
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<- 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<- species_params species_params<- |
Set initial values to a steady state for the model | steady |
Set initial abundances to single-species steady state abundances | steadySingleSpecies |
Description of summary functions | summary_functions |
Summarize MizerParams object | summary,MizerParams-method |
Summarize MizerSim object | summary,MizerSim-method |
Truncated lognormal predation kernel | truncated_lognormal_pred_kernel |
Helper function to assure validity of gears argument | valid_gears_arg |
Helper function to assure validity of species argument | valid_species_arg |
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 |