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A B C D E F G I K L M N O P R S T U V W
| mizer-package | mizer: Multi-species size-based modelling in R |
| addSpecies | Add new species |
| animateSpectra | Animation of the abundance spectra |
| BevertonHoltRDD | Beverton Holt function to calculate density-dependent reproduction rate |
| box_pred_kernel | Box predation kernel |
| calibrateBiomass | Calibrate the model scale to match total observed biomass |
| calibrateYield | Calibrate the model scale to match total observed yield |
| catchability | Set fishing parameters |
| catchability<- | Set fishing parameters |
| compareParams | Compare two MizerParams objects and print out differences |
| constantEggRDI | Choose egg production to keep egg density constant |
| constantRDD | Give constant reproduction rate |
| constant_other | Helper function to keep other components constant |
| customFunction | Replace a mizer function with a custom version |
| default_pred_kernel_params | Set defaults for predation kernel parameters |
| different | Check whether two objects are different |
| distanceMaxRelRDI | Measure distance between current and previous state in terms of RDI |
| distanceSSLogN | Measure distance between current and previous state in terms of fish abundances |
| double_sigmoid_length | Length based double-sigmoid selectivity function |
| dw | Size bins |
| dw_full | Size bins |
| emptyParams | Create empty MizerParams object of the right size |
| ext_mort | Set external mortality rate |
| ext_mort<- | Set external mortality rate |
| finalN | Size spectra at end of simulation |
| finalNOther | Values of other ecosystem components at end of simulation |
| finalNResource | Size spectra at end of simulation |
| gear_params | Gear parameters |
| gear_params<- | Gear parameters |
| getBiomass | Calculate the total biomass of each species within a size range at each time step. |
| getCatchability | Set fishing parameters |
| getColours | Set line colours and line types to be used in mizer plots |
| getCommunitySlope | Calculate the slope of the community abundance |
| getComponent | Get information about other ecosystem components |
| getCriticalFeedingLevel | Get critical feeding level |
| getDiet | Get diet of predator at size, resolved by prey species |
| getEffort | Fishing effort used in simulation |
| getEGrowth | Get energy rate available for growth |
| getEncounter | Get encounter rate |
| getERepro | Get energy rate available for reproduction |
| getEReproAndGrowth | Get energy rate available for reproduction and growth |
| getESpawning | Alias for 'getERepro()' |
| getExtMort | Set external mortality rate |
| getFeedingLevel | Get feeding level |
| getFMort | Get the total fishing mortality rate from all fishing gears by time, species and size. |
| getFMortGear | Get the fishing mortality by time, gear, species and size |
| getGrowthCurves | Get growth curves giving weight as a function of age |
| getInitialEffort | Set fishing parameters |
| getInteraction | Set species interaction matrix |
| getLinetypes | Set line colours and line types to be used in mizer plots |
| getM2 | Alias for 'getPredMort()' |
| getM2Background | Alias for 'getResourceMort()' |
| getMaturityProportion | Set reproduction parameters |
| getMaxIntakeRate | Set maximum intake rate |
| getMeanMaxWeight | Calculate the mean maximum weight of the community |
| getMeanWeight | Calculate the mean weight of the community |
| getMetabolicRate | Set metabolic rate |
| getMetadata | Set metadata for a model |
| getMort | Get total mortality rate |
| getN | Calculate the number of individuals within a size range |
| getParams | Extract the parameter object underlying a simulation |
| getPhiPrey | Get available energy |
| getPredKernel | Set predation kernel |
| getPredMort | Get total predation mortality rate |
| getPredRate | Get predation rate |
| getProportionOfLargeFish | Calculate the proportion of large fish |
| getRateFunction | Set own rate function to replace mizer rate function |
| getRates | Get all rates |
| getRDD | Get density dependent reproduction rate |
| getRDI | Get density independent rate of egg production |
| getReproductionLevel | Get reproduction level |
| getReproductionProportion | Set reproduction parameters |
| getResourceCapacity | Set up resource |
| getResourceDynamics | Set up resource |
| getResourceMort | Get predation mortality rate for resource |
| getResourceRate | Set up resource |
| getSearchVolume | Set search volume |
| getSelectivity | Set fishing parameters |
| getSSB | Calculate the SSB of species |
| getTimes | Times for which simulation results are available |
| getYield | Calculate the yearly yield for each species |
| getYieldGear | Calculate the yearly yield per gear and species |
| getZ | Alias for 'getMort()' |
| get_f0_default | Get default value for f0 |
| get_gamma_default | Get default value for gamma |
| get_initial_n | Calculate initial population abundances for the community populations |
| get_ks_default | Get default value for 'ks' |
| get_phi | Get values from feeding kernel function |
| get_required_reproduction | Determine reproduction rate needed for initial egg abundance |
| get_size_range_array | Get size range array |
| get_time_elements | Get_time_elements |
| idxFinalT | Time index at end of simulation |
| indicator_functions | Description of indicator functions |
| initialN | Initial values for fish spectra |
| initialN<- | Initial values for fish spectra |
| initialNOther | Initial values for other ecosystem components |
| initialNOther<- | Initial values for other ecosystem components |
| initialNResource | Initial value for resource spectrum |
| initialNResource<- | Initial value for resource spectrum |
| initial_effort | Initial fishing effort |
| initial_effort<- | Initial fishing effort |
| intake_max | Set maximum intake rate |
| intake_max<- | Set maximum intake rate |
| inter | Alias for 'NS_interaction' |
| knife_edge | Weight based knife-edge selectivity function |
| lognormal_pred_kernel | Lognormal predation kernel |
| matchBiomasses | Match biomasses to observations |
| matchYields | Match yields to observations |
| maturity | Set reproduction parameters |
| maturity<- | Set reproduction parameters |
| metab | Set metabolic rate |
| metab<- | Set metabolic rate |
| mizer | mizer: Multi-species size-based modelling in R |
| mizerEGrowth | Get energy rate available for growth needed to project standard mizer model |
| mizerEncounter | Get encounter rate needed to project standard mizer model |
| mizerERepro | Get energy rate available for reproduction needed to project standard mizer model |
| mizerEReproAndGrowth | Get energy rate available for reproduction and growth needed to project standard mizer model |
| mizerFeedingLevel | Get feeding level needed to project standard mizer model |
| mizerFMort | Get the total fishing mortality rate from all fishing gears |
| mizerFMortGear | Get the fishing mortality needed to project standard mizer model |
| mizerMort | Get total mortality rate needed to project standard mizer model |
| MizerParams | Alias for 'set_multispecies_model()' |
| MizerParams-class | A class to hold the parameters for a size based model. |
| mizerPredMort | Get total predation mortality rate needed to project standard mizer model |
| mizerPredRate | Get predation rate needed to project standard mizer model |
| mizerRates | Get all rates needed to project standard mizer model |
| mizerRDI | Get density-independent rate of reproduction needed to project standard mizer model |
| mizerResourceMort | Get predation mortality rate for resource needed to project standard mizer model |
| MizerSim | Constructor for the 'MizerSim' class |
| MizerSim-class | A class to hold the results of a simulation |
| N | Time series of size spectra |
| newCommunityParams | Set up parameters for a community-type model |
| newMultispeciesParams | Set up parameters for a general multispecies model |
| newSingleSpeciesParams | Set up parameters for a single species in a power-law background |
| newTraitParams | Set up parameters for a trait-based multispecies model |
| noRDD | Give density-independent reproduction rate |
| NOther | Time series of other components |
| NResource | Time series of size spectra |
| NS_interaction | Example interaction matrix for the North Sea example |
| NS_params | Example MizerParams object for the North Sea example |
| NS_sim | Example MizerSim object for the North Sea example |
| NS_species_params | Example species parameter set based on the North Sea |
| NS_species_params_gears | Example species parameter set based on the North Sea with different gears |
| other_params | Set own rate function to replace mizer rate function |
| other_params<- | Set own rate function to replace mizer rate function |
| plot-method | Summary plot for 'MizerSim' objects |
| plotBiomass | Plot the biomass of species through time |
| plotBiomassObservedVsModel | Plotting observed vs. model biomass data |
| plotDiet | Plot diet, resolved by prey species, as function of predator at size. |
| plotFeedingLevel | Plot the feeding level of species by size |
| plotFMort | Plot total fishing mortality of each species by size |
| plotGrowthCurves | Plot growth curves giving weight as a function of age |
| plotlyBiomass | Plot the biomass of species through time |
| plotlyBiomassObservedVsModel | Plotting observed vs. model biomass data |
| plotlyFeedingLevel | Plot the feeding level of species by size |
| plotlyFMort | Plot total fishing mortality of each species by size |
| plotlyGrowthCurves | Plot growth curves giving weight as a function of age |
| plotlyPredMort | Plot predation mortality rate of each species against size |
| plotlySpectra | Plot the abundance spectra |
| plotlyYield | Plot the total yield of species through time |
| plotlyYieldGear | Plot the total yield of each species by gear through time |
| plotlyYieldObservedVsModel | Plotting observed vs. model yields |
| plotM2 | Alias for 'plotPredMort()' |
| plotPredMort | Plot predation mortality rate of each species against size |
| plotSpectra | Plot the abundance spectra |
| plotting_functions | Description of the plotting functions |
| plotYield | Plot the total yield of species through time |
| plotYieldGear | Plot the total yield of each species by gear through time |
| plotYieldObservedVsModel | Plotting observed vs. model yields |
| power_law_pred_kernel | Power-law predation kernel |
| pred_kernel | Set predation kernel |
| pred_kernel<- | Set predation kernel |
| project | Project size spectrum forward in time |
| projectToSteady | Project to steady state |
| project_simple | Project abundances by a given number of time steps into the future |
| readParams | Save a MizerParams object to file, and restore it |
| removeComponent | Add a dynamical ecosystem component |
| removeSpecies | Remove species |
| renameSpecies | Rename species |
| repro_prop | Set reproduction parameters |
| repro_prop<- | Set reproduction parameters |
| resource_capacity | Set up resource |
| resource_capacity<- | Set up resource |
| resource_constant | Keep resource abundance constant |
| resource_dynamics | Set up resource |
| resource_dynamics<- | Set up resource |
| resource_params | Resource parameters |
| resource_params<- | Resource parameters |
| resource_rate | Set up resource |
| resource_rate<- | Set up resource |
| resource_semichemostat | Project resource using semichemostat model |
| RickerRDD | Ricker function to calculate density-dependent reproduction rate |
| saveParams | Save a MizerParams object to file, and restore it |
| scaleModel | Change scale of the model |
| search_vol | Set search volume |
| search_vol<- | Set search volume |
| selectivity | Set fishing parameters |
| selectivity<- | Set fishing parameters |
| setBevertonHolt | Set Beverton-Holt density dependence |
| setColours | Set line colours and line types to be used in mizer plots |
| setComponent | Add a dynamical ecosystem component |
| setExtMort | Set external mortality rate |
| setFishing | Set fishing parameters |
| setInitialValues | Set initial values to final values of a simulation |
| setInteraction | Set species interaction matrix |
| setLinetypes | Set line colours and line types to be used in mizer plots |
| setMaxIntakeRate | Set maximum intake rate |
| setMetabolicRate | Set metabolic rate |
| setMetadata | Set metadata for a model |
| setParams | Set or change any model parameters |
| setPredKernel | Set predation kernel |
| setRateFunction | Set own rate function to replace mizer rate function |
| setReproduction | Set reproduction parameters |
| setResource | Set up resource |
| setRmax | Alias for 'setBevertonHolt()' |
| setSearchVolume | Set search volume |
| set_community_model | Deprecated function for setting up parameters for a community-type model |
| set_multispecies_model | Deprecated obsolete function for setting up multispecies parameters |
| set_species_param_default | Set a species parameter to a default value |
| set_trait_model | Deprecated function for setting up parameters for a trait-based model |
| SheperdRDD | Sheperd function to calculate density-dependent reproduction rate |
| sigmoid_length | Length based sigmoid selectivity function |
| sigmoid_weight | Weight based sigmoidal selectivity function |
| species_params | Species parameters |
| species_params<- | Species parameters |
| steady | Set initial values to a steady state for the model |
| summary-method | Summarize MizerParams object |
| summary-method | Summarize MizerSim object |
| summary_functions | Description of summary functions |
| truncated_lognormal_pred_kernel | Truncated lognormal predation kernel |
| upgradeParams | Upgrade MizerParams object from earlier mizer versions |
| upgradeSim | Upgrade MizerSim object from earlier mizer versions |
| validEffortVector | Initial fishing effort |
| validGearParams | Check validity of gear parameters and set defaults |
| validParams | Validate MizerParams object and upgrade if necessary |
| validSpeciesParams | Validate species parameter data frame |
| valid_species_arg | Helper function to assure validity of species argument |
| w | Size bins |
| w_full | Size bins |