Man pages for mizer
Dynamic Multi-Species Size Spectrum Modelling
| addSpecies | Add new species |
| age_mat | Calculate age at maturity |
| age_mat_vB | Calculate age at maturity from von Bertalanffy growth... |
| animateSpectra | Animation of the abundance spectra |
| BevertonHoltRDD | Beverton Holt function to calculate density-dependent... |
| box_pred_kernel | Box predation kernel |
| calc_selectivity | Calculate selectivity from gear parameters |
| calibrateBiomass | Calibrate the model scale to match total observed biomass |
| calibrateNumber | Calibrate the model scale to match total observed number |
| calibrateYield | Calibrate the model scale to match total observed yield |
| compareParams | Compare two MizerParams objects and print out differences |
| completeSpeciesParams | Alias for 'validSpeciesParams()' |
| constantEggRDI | Choose egg production to keep egg density constant |
| constant_other | Helper function to keep other components constant |
| constantRDD | Give constant reproduction rate |
| customFunction | Replace a mizer function with a custom version |
| default_pred_kernel_params | Set defaults for predation kernel parameters |
| defaults_edition | Default editions |
| different | Check whether two objects are different |
| distanceMaxRelRDI | Measure distance between current and previous state in terms... |
| distanceSSLogN | Measure distance between current and previous state in terms... |
| double_sigmoid_length | Length based double-sigmoid selectivity function |
| emptyParams | Create empty MizerParams object of the right size |
| finalN | Size spectra at end of simulation |
| finalNOther | Values of other ecosystem components at end of simulation |
| gear_params | Gear parameters |
| getBiomass | Calculate the total biomass of each species within a size... |
| 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()' |
| get_f0_default | Get default value for f0 |
| getFeedingLevel | Get feeding level |
| getFMort | Get the total fishing mortality rate from all fishing gears... |
| getFMortGear | Get the fishing mortality by time, gear, species and size |
| get_gamma_default | Get default value for gamma |
| getGrowthCurves | Get growth curves giving weight as a function of age |
| get_h_default | Get default value for h |
| get_initial_n | Calculate initial population abundances |
| getInteraction | Deprecated function to get interaction matrix |
| get_ks_default | Get default value for 'ks' |
| getM2 | Alias for 'getPredMort()' |
| getM2Background | Alias for 'getResourceMort()' |
| getMeanMaxWeight | Calculate the mean maximum weight of the community |
| getMeanWeight | Calculate the mean weight of the community |
| getMort | Get total mortality rate |
| getN | Calculate the number of individuals within a size range |
| getParams | Extract the parameter object underlying a simulation |
| get_phi | Get values from feeding kernel function |
| getPhiPrey | Get available energy |
| getPredMort | Get total predation mortality rate |
| getPredRate | Get predation rate |
| getProportionOfLargeFish | Calculate the proportion of large fish |
| getRates | Get all rates |
| getRDD | Get density dependent reproduction rate |
| getRDI | Get density independent rate of egg production |
| getReproductionLevel | Get reproduction level |
| get_required_reproduction | Determine reproduction rate needed for initial egg abundance |
| getResourceDynamics | Deprecated functions for getting resource parameters |
| getResourceMort | Get predation mortality rate for resource |
| get_size_range_array | Get size range array |
| getSSB | Calculate the SSB of species |
| get_time_elements | Get_time_elements |
| getTimes | Times for which simulation results are available |
| getYield | Calculate the rate at which biomass of each species is fished |
| getYieldGear | Calculate the rate at which biomass of each species is fished... |
| getZ | Alias for 'getMort()' |
| indicator_functions | Description of indicator functions |
| initial_effort | Initial fishing effort |
| initialNOther-set | Initial values for other ecosystem components |
| initialNResource-set | Initial value for resource spectrum |
| initialN-set | Initial values for fish spectra |
| inter | Alias for 'NS_interaction' |
| knife_edge | Weight based knife-edge selectivity function |
| l2w | Length-weight conversion |
| log_breaks | Helper function to produce nice breaks on logarithmic axes |
| lognormal_pred_kernel | Lognormal predation kernel |
| matchBiomasses | Match biomasses to observations |
| matchGrowth | Adjust model to produce observed growth |
| matchNumbers | Match numbers to observations |
| matchYields | Match yields to observations |
| mizerEGrowth | Get energy rate available for growth needed to project... |
| mizerEncounter | Get encounter rate needed to project standard mizer model |
| mizerERepro | Get energy rate available for reproduction needed to project... |
| mizerEReproAndGrowth | Get energy rate available for reproduction and growth needed... |
| 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... |
| mizerMort | Get total mortality rate needed to project standard mizer... |
| mizer-package | mizer: Multi-species size-based modelling in R |
| 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... |
| 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... |
| mizerResourceMort | Get predation mortality rate for resource needed to project... |
| MizerSim | Constructor for the 'MizerSim' class |
| MizerSim-class | A class to hold the results of a simulation |
| N | Time series of size spectra |
| needs_upgrading | Determine whether a MizerParams or MizerSim object needs to... |
| 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... |
| newTraitParams | Set up parameters for a trait-based multispecies model |
| noRDD | Give density-independent reproduction rate |
| NOther | Time series of other components |
| 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... |
| plotBiomass | Plot the biomass of species through time |
| plotBiomassObservedVsModel | Plotting observed vs. model biomass data |
| plotDataFrame | Make a plot from a data frame |
| plotDiet | Plot diet, resolved by prey species, as function of predator... |
| plotFeedingLevel | Plot the feeding level of species by size |
| plotFMort | Plot total fishing mortality of each species by size |
| plotGrowthCurves | Plot growth curves |
| plotM2 | Alias for 'plotPredMort()' |
| plot-MizerParams-missing-method | Summary plot for 'MizerParams' objects |
| plotMizerSim | Summary plot for 'MizerSim' objects |
| 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 |
| project | Project size spectrum forward in time |
| project_simple | Project abundances by a given number of time steps into the... |
| projectToSteady | Project to steady state |
| reexports | Objects exported from other packages |
| removeSpecies | Remove species |
| renameSpecies | Rename species |
| resource_constant | Keep resource abundance constant |
| resource_logistic | Project resource using logistic model |
| resource_params | Resource parameters |
| resource_semichemostat | Project resource using semichemostat model |
| RickerRDD | Ricker function to calculate density-dependent reproduction... |
| saveParams | Save a MizerParams object to file, and restore it |
| scaleModel | Change scale of the model |
| setBevertonHolt | Set Beverton-Holt reproduction without changing the steady... |
| setColours | Set line colours and line types to be used in mizer plots |
| set_community_model | Deprecated function for setting up parameters for a... |
| setComponent | Add a dynamical ecosystem component |
| setExtEncounter | Set external encounter rate |
| setExtMort | Set external mortality rate |
| setFishing | Set fishing parameters |
| setInitialValues | Set initial values to values from a simulation |
| setInteraction | Set species interaction matrix |
| setMaxIntakeRate | Set maximum intake rate |
| setMetabolicRate | Set metabolic rate |
| setMetadata | Set metadata for a model |
| set_multispecies_model | Deprecated obsolete function for setting up multispecies... |
| 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 resource dynamics |
| setRmax | Alias for 'setBevertonHolt()' |
| setSearchVolume | Set search volume |
| set_species_param_default | Set a species parameter to a default value |
| set_trait_model | Deprecated function for setting up parameters for a... |
| SheperdRDD | Sheperd function to calculate density-dependent reproduction... |
| sigmoid_length | Length based sigmoid selectivity function |
| sigmoid_weight | Weight based sigmoidal selectivity function |
| species_params | Species parameters |
| steady | Set initial values to a steady state for the model |
| steadySingleSpecies | Set initial abundances to single-species steady state... |
| summary_functions | Description of summary functions |
| summary-MizerParams-method | Summarize MizerParams object |
| summary-MizerSim-method | Summarize MizerSim object |
| truncated_lognormal_pred_kernel | Truncated lognormal predation kernel |
| upgradeParams | Upgrade MizerParams object from earlier mizer versions |
| upgradeSim | Upgrade MizerSim object from earlier mizer versions |
| validGearParams | Check validity of gear parameters and set defaults |
| valid_gears_arg | Helper function to assure validity of gears argument |
| validParams | Validate MizerParams object and upgrade if necessary |
| validSim | Validate MizerSim object and upgrade if necessary |
| valid_species_arg | Helper function to assure validity of species argument |
| validSpeciesParams | Validate species parameter data frame |
| w | Size bins |
