Man pages for mizer
Dynamic Multi-Species Size Spectrum Modelling
| addPlot | Add lines to an existing plot |
| add_scan_annotations | Add the annotation layers to a MizerScan plot |
| addSpecies | Add new species |
| add_total_line | Add a total line to plotting data by summing over its series |
| adjustSizeGrid | Adjust the size grid |
| age_mat | Calculate age at maturity |
| age_mat_vB | Calculate age at maturity from von Bertalanffy growth... |
| animate | Animate size-dependent quantities through time |
| append_total_line | Convert the contributors to a total and append the total line |
| apply_wlim | Restrict plot data to a range of weights |
| array_density_wrt | The density measure of a mizer array |
| array_log_y | The logarithmic y axis an array's type calls for |
| ArrayResourceBySize | S3 class for resource size spectra |
| ArrayResourceBySize_plot_data | The complete plotting data of a resource-by-size array |
| ArraySpeciesBySize | S3 class for species x size rate arrays |
| ArraySpeciesBySize_plot_data | The complete plotting data of a species-by-size array |
| ArrayTimeByResourceBySize | S3 class for time x resource-size arrays |
| ArrayTimeBySpecies | S3 class for time x species arrays |
| ArrayTimeBySpeciesBySize | S3 class for time x species x size arrays |
| array_type | The type of a mizer array |
| array_types | Kinds of quantity a mizer array can hold |
| array_ylim | Y-axis limits an array's type calls for |
| as.data.frame | Convert mizer arrays to data frames |
| as_series_matrix | Bring what a value function returned into a time by series... |
| BevertonHoltRDD | Beverton Holt function to calculate density-dependent... |
| bin_average_weight | Bin-average the weight of a size-spectrum integral |
| bin_midpoints | Geometric bin centres of the size grid |
| box_pred_kernel | Box predation kernel |
| broadcast_dims | Expand an array to a larger set of labelled dimensions |
| 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 |
| calibrate_to | Calibrate the model scale to match a total observation |
| cdf_y_label | Y-axis label for a cumulative-distribution plot |
| check_band_vars | Check that a data frame has the variables a band style needs |
| check_finite | Check that the rate arrays hold only finite values |
| check_per_log_size | Check that 'per_log_size' applies to a mizer array |
| coerceToExtensionClass | Coerce a mizer object to its extension class |
| collect_dimnames | Assemble the dimnames of a broadcast array |
| 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 |
| convert_density_units | Restate the units of a density in a different density measure |
| convert_plot_density_axis | Express plotting data on the requested size axis |
| convert_plot_size_axis | Convert plotting data from weight to length |
| convert_plot_spectrum_axis | Convert a weight-based spectrum to a length-based spectrum |
| copy_scan_attributes | Copy the metadata of a MizerScan onto another object |
| customFunction | Replace a mizer function with a custom version |
| cutoff_min_w | The minimum weights given by a cutoff species parameter |
| default_info_level | The default level of information that mizer gives |
| default_pred_kernel_params | Set defaults for predation kernel parameters |
| defaults_edition | Default editions |
| density_measure_jacobian | Jacobian converting between two density measures |
| density_measures | Density measures a spectrum can be expressed in |
| density_measure_weight | Factor relating a density measure to a density with respect... |
| density_size_unit | The size unit appearing in the units of a density |
| density_target_measure | The density measure a plot calls for |
| different | Check whether two objects are different |
| dim_extents | Collect the extent of each labelled dimension |
| dim_from_labels | The dimensions of an array, given its labels |
| distanceMaxRelRDI | Measure distance between current and previous state in terms... |
| distanceSSLogN | Measure distance between current and previous state in terms... |
| dot-checkRateFunctionOutput | Check that a rate function returns the correct output... |
| dot-hasSlot | S4/S3 compatibility .hasSlot helper |
| double_sigmoid_length | Length based double-sigmoid selectivity function |
| emptyParams | Create empty MizerParams object of the right size |
| encounter_kernel | The predation kernel as used by the encounter quadrature |
| ensureExtensionNamespaces | Load (and optionally install) namespaces for all non-NA... |
| expand_kernel_offsets | Expand kernel weights indexed by grid offset into a full... |
| expandSizeGrid | Expand the size grid |
| extension_needs_upgrading | Whether any extension recorded on an object needs upgrading |
| extensionRequirements | Extract the requirement view of an extension chain |
| extensionVersion | Get the recorded version stamp for one extension on an object |
| extensionVersions | Extract the version stamps of an extension chain |
| filter_plot_length_limits | Filter plotting data to the requested length limits |
| finalN | Size spectra at end of simulation |
| findSteadyState | Find the steady state of a model |
| flux_from_rates | Assemble the flux matrix from growth, diffusion and... |
| flux_units | Units string for the flux returned by 'getFlux()' |
| free_gear_name | A gear name that the model is not already using |
| frozen_rate_params | Which parameters feed which frozen array |
| gaussian_mixture_pred_kernel | Gaussian-mixture predation kernel |
| gear_names | Every gear name a model uses |
| gear_params | Gear parameters |
| get_ArrayResourceBySize_w | Get the size grid for an ArrayResourceBySize object |
| get_ArraySpeciesBySize_w | Get the size grid for an ArraySpeciesBySize object |
| get_ArrayTimeBySpeciesBySize_w | Get the size grid for an ArrayTimeBySpeciesBySize object |
| getBiomass | Calculate the total biomass of each species within a size... |
| getCommunitySlope | Calculate the slope of the community abundance |
| getCriticalFeedingLevel | Get critical feeding level |
| getDiet | Get diet of predator at size, resolved by prey species |
| getDiffusion | Get diffusion rate from predation |
| getDiscreteStability | Analyse the stability of mizer's numerical time step |
| 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 |
| getFlux | Get flux into size bins |
| getFluxGradient | Get flux gradient |
| 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 |
| 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 size of the community |
| getMort | Get total mortality rate |
| getN | Calculate the number of individuals within a size range |
| getOscillationModeSim | Construct a MizerSim of the leading oscillatory mode |
| getParams | Extract the model state from 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 |
| getRequiredRDD | Determine reproduction rate needed for initial egg abundance |
| getResourceMort | Get predation mortality rate for resource |
| getSimParams | Extract the projection parameters used to produce a... |
| get_sim_rate_slice | Extract one saved simulation state for a rate calculation |
| get_sim_rate_time_elements | Get selected saved time steps for a simulation rate |
| get_size_range_array | Get size range array |
| get_species_size_rate_from_sim | Apply a species-by-size rate function over saved simulation... |
| get_species_time_rate_from_sim | Apply a species rate function over saved simulation times |
| getSSB | Calculate the SSB of species |
| getStability | Analyse the dynamic stability of a mizer steady state |
| getSteadyResidual | How far a model is from its steady state |
| get_steady_state_n | Calculate steady state abundance |
| get_time_elements | Get array indices for a time range in a MizerSim object |
| getTimes | Times for which simulation results are available |
| getTrophicLevel | Get trophic level of individuals at size |
| getTrophicLevelBySpecies | Get mean trophic level of each species |
| getYield | Calculate the rate at which biomass of each species is fished |
| getYieldGear | Calculate the rate at which biomass of each species is fished... |
| get_yield_observed | Observed yield of each species |
| 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 |
| install_tmp_gear | Add a gear that exerts the fishing mortality being scanned |
| inter | Alias for 'NS_interaction' |
| interpolate_in_log_size | Interpolate a series linearly in the logarithm of size |
| interpolate_relative_frames | Put two series on a common size grid before comparing them |
| isSteady | Check whether a model is at steady state |
| is_validated | Keep track of which MizerParams objects have been fully... |
| isVersionRequirement | Test whether a requirement string is a dotted version number |
| knife_edge | Weight based knife-edge selectivity function |
| knife_edge_length | Length based knife-edge selectivity function |
| l2w | Length-weight conversion |
| length_at_size | Length of an individual at each weight on the size grid |
| log_breaks | Helper function to produce nice breaks on logarithmic axes |
| lognormal_pred_kernel | Lognormal predation kernel |
| makeExtensions | Build a versioned extension list from requirements and... |
| make_linesize | Construct a named vector of line widths for a plot |
| make_mizer_plot | Tag a ggplot object as a mizer plot |
| markBackground | Designate species as background species |
| matchBiomasses | Match biomasses to observations |
| matchGrowth | Adjust model to produce observed growth |
| matchNumbers | Match numbers to observations |
| match_to | Match a quantity to observations species by species |
| measure_on_attractor | Measure a quantity on the attractor a projection settled on |
| merge_dim_labels | Merge two ordered sets of dimension labels |
| mizerDiffusion | Calculate diffusion rate |
| mizerEGrowth | Get energy rate available for growth needed to project... |
| mizerEncounter | Get encounter rate during projection |
| 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_needs_upgrading | Whether the core mizer slots of an object need upgrading |
| 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 |
| mizer_rates_subset | Calculate a selected subset of the rates |
| mizerRDI | Get density-independent rate of reproduction needed to... |
| mizerResourceMort | Get predation mortality rate for resource needed to project... |
| MizerScan | S3 class for the result of a parameter scan |
| MizerSim | Constructor for the 'MizerSim' class |
| MizerSim-class | A class to hold the results of a simulation |
| mizer_tooltip_vars | Determine the tooltip variables for a mizer plot |
| model_observation | The modelled counterpart of an observation |
| N | Time series of size spectra |
| needed_rates | Determine which rates must be calculated to obtain a set of... |
| 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... |
| objectExtensions | Get the extensions stored in a mizer object |
| observation_columns | The species parameter columns holding an observation |
| other_mort | Extra contributions to the mortality and encounter rates |
| params_as_sim | A MizerSim holding only the state stored in a MizerParams |
| parsePlotLog | Parse the log-axis arguments of a mizer plot function |
| plot | Plot mizer arrays |
| plot2 | Compare two mizer arrays in a single plot |
| plot.ArrayResourceBySize | Plot method for 'ArrayResourceBySize' objects |
| plot.ArraySpeciesBySize | Plot method for 'ArraySpeciesBySize' objects |
| plot.ArrayTimeByResourceBySize | Plot method for 'ArrayTimeByResourceBySize' objects |
| plot.ArrayTimeBySpecies | Plot method for 'ArrayTimeBySpecies' objects |
| plot.ArrayTimeBySpeciesBySize | Plot method for 'ArrayTimeBySpeciesBySize' objects |
| plotBiomass | Plot the biomass of species through time |
| plotBiomassObservedVsModel | Plotting observed vs. model biomass data |
| plot_cdf | Build the cumulative-distribution plot |
| plotCDF | Plot cumulative abundance or biomass distributions |
| plotCDF2 | Compare cumulative abundance or biomass distributions from... |
| plotComparisonDataFrame | Make a plot comparing two data frames |
| plotDataFrame | Make a plot from a data frame |
| plot_diet | Build the diet-composition plot |
| plotDiet | Plot diet, resolved by prey species, as function of predator... |
| plot_feeding_level | Build the feeding-level plot |
| plotFeedingLevel | Plot the feeding level of species by size |
| plotFMort | Plot total fishing mortality of each species by size |
| plot_growth_curves | Build the growth-curves plot |
| plotGrowthCurves | Plot growth curves |
| plotHover | Create a hover-enabled plotly plot from a mizer object |
| plot_length_params | The weight-length parameters to plot each row of plotting... |
| plotM2 | Alias for 'plotPredMort()' |
| plotMizerParams | Summary plot for 'MizerParams' objects |
| plot.MizerScan | Plot method for 'MizerScan' objects |
| plotMizerSim | Summary plot for 'MizerSim' objects |
| plotPredMort | Plot predation mortality rate of each species against size |
| plotRelative | Plot relative difference between two mizer arrays |
| plotRelativeDataFrame | Make a plot of the relative difference between two data... |
| plot_size_axis | Validate the size-axis argument |
| plot_size_tooltip | Assemble the tooltip variables for a size-axis plot |
| plot_size_xlab | Axis label for a given size axis |
| plot_size_xlim | Choose the x-axis limits for a given size axis |
| plot_size_x_var | Name of the x-variable for a given size axis |
| plot_spectra | Build the size-spectrum plot |
| plotSpectra | Plot abundance and biomass spectra |
| plotSpectra2 | Compare abundance and biomass spectra from two objects |
| plotSpectraRelative | Plot relative difference between 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 |
| plotYieldVsF | Plot the yield of a species against the fishing mortality on... |
| plot_y_is_log | Whether a plot's y axis is logarithmic |
| power_law_bin_average | Bin average of a power law over geometric bins |
| power_law_pred_kernel | Power-law predation kernel |
| prepare_ArrayTimeBySpecies_plot_data | The complete plotting data of a time-by-species array |
| prepare_MizerScan_plot_data | Prepare the data frame for plotting a MizerScan |
| prepare_spectra_cdf_data | Integrate spectra data into a cumulative distribution |
| Print mizer objects | |
| print.mizer_plot | Print a mizer plot |
| project | Project size spectrum forward in time |
| project_n | Project values for first time step of Euler method |
| project_n_2 | Project values with a predictor-corrector method |
| project_n_tr_bdf2 | Project values with the TR-BDF2 method |
| projectRDD | Get density-dependent reproduction rate during projection |
| project_simple | Project abundances by a given number of time steps into the... |
| projectUntilSettled | Project the dynamics until they settle |
| proportion_ylim | Y-axis limits for a plot of a proportion |
| reconcileSpeciesParams | Reconcile the species parameters with the given species... |
| recordExtension | Record an extension and its version stamp on a mizer object |
| record_given_species_params | Record the species parameters that have changed |
| reexports | Objects exported from other packages |
| relative_difference | Symmetric relative difference between two values |
| removeBackgroundSpecies | Remove all background species |
| removeSpecies | Remove species |
| renameGear | Rename gears |
| renameSpecies | Rename species |
| repair_params | Repair a MizerParams object |
| report_scan_convergence | Report the scan values that did not settle on a fixed point |
| resolve_array_type | Resolve the type of a mizer array |
| resolve_cdf_power | Resolve the power of weight for a cumulative distribution |
| resolve_second_order_w | Resolve a 'second_order_w' value against the default scheme |
| resolve_spectrum_power | Resolve the power of weight multiplying a spectrum |
| resource_constant | Keep resource abundance constant |
| resource_length_defaults | Default weight-length parameters for the resource |
| resource_length_params | The weight-length parameters of the resource |
| resource_logistic | Project resource using logistic model |
| resource_params | Resource parameters |
| resource_power_law | Construct the background resource power-law spectrum |
| resource_semichemostat | Project resource using semichemostat model |
| RickerRDD | Ricker function to calculate density-dependent reproduction... |
| runExtensionUpgrades | Run the registered extension upgrade methods on an object |
| saveParams | Save and restore mizer objects |
| scaleModel | Change scale of the model |
| scaleRates | Rescale all rates in a mizer model |
| scanEffort | Setters for scanning a model |
| scan_gear_installed | Has a fishing-mortality scan already been installed in this... |
| scanModel | Scan a model over a range of values |
| scan_plot_params | The params object to use when plotting a MizerScan |
| scan_x_var | The x and y variables of a MizerScan |
| scan_y_label | Axis labels for a MizerScan |
| second_order_w | Get or set the second_order_w flags |
| select_gear_rows | The gear params rows whose fishing mortality is to be varied |
| select_scan_series | Pick out some of the series of a scan |
| 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 |
| setExtDiffusion | Set external diffusion rate |
| 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()' |
| set_scan_maximum | Record where each series attains its maximum |
| 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 |
| signal_defaulted_length_weight | Report a selectivity built from a defaulted weight-length... |
| signal_frozen | Signal that a change the user made cannot take effect |
| signal_frozen_changes | Signal the changes to species parameters that cannot take... |
| signal_gear_params_changes | Signal a gear parameter changed through the given species... |
| signal_ignored_changes | Signal the changes that are ignored because another parameter... |
| signal_info | Signal information about a choice mizer made |
| signal_not_recalculated | Signal that a rate array was not recalculated because it is... |
| signal_removed_species_params | Signal that species parameter columns have been removed |
| simExtensionClass | Derive the MizerSim extension class name for a given... |
| sim_size_rate | Build a 'MizerSim' rate getter that resolves the rate... |
| sim_species_rate | Build a 'MizerSim' rate getter that resolves the rate... |
| size_dim_labels | Identify the dimensions of an array over the size grid |
| sizeIntegral | Integrate a quantity over the size spectrum |
| slot | S4/S3 compatibility slot access helper |
| slotNames | S4/S3 compatibility slotNames helper |
| slot-set | S4/S3 compatibility slot assignment helper |
| species_params | Species parameters |
| species_size_range_mask | Which size classes lie inside each species' own size range |
| spectra_bin_width | Look up the size-bin widths for spectra data |
| spectra_y_label | Y-axis label for a size-spectrum plot |
| spectrum_density_wrt | The density measure of a 'power'-based spectrum |
| steadySingleSpecies | Set initial abundances to solution of steady-state equation... |
| str | Display the structure of mizer objects |
| summary | Summarise mizer objects |
| summary_functions | Description of summary functions |
| superseded_accessors | Superseded 'get'-prefixed aliases for values stored in a... |
| superseded_steady | Superseded names for the steady-state finders |
| sweep_arms | The order in which to project the scan values |
| total_contributors | Assemble the contributors to the total of a species-by-size... |
| trapezoidal_bin_average | Trapezoidal bin-average of a per-bin weight |
| truncated_lognormal_pred_kernel | Truncated lognormal predation kernel |
| tuneSteadyState | Tune a model so that the state it is in becomes a steady... |
| upgrade.MizerParams | Upgrade the core slots of a MizerParams object |
| upgrade.MizerSim | Upgrade a MizerSim object from earlier versions |
| upgradeParams | Back-compatible wrapper for the core MizerParams upgrade |
| upgrade_s4_to_s3 | Convert an S4 MizerParams or MizerSim object to an S3 object |
| upgradeSim | Back-compatible wrapper for the MizerSim upgrade |
| use_predation_diffusion | Get or set the use_predation_diffusion flag |
| validate_array_type | Validate the type of a mizer array |
| validate_density_wrt | Validate a density measure |
| validateExtensionsVector | Validate and normalise an extensions named character vector |
| validate_second_order_w | Apply a 'second_order_w' value to the current slot list |
| validation_key | Fingerprint of the slots that determine the outcome of the... |
| validEffortVector | Make a valid effort vector |
| validGearParams | Check validity of gear parameters and set defaults |
| valid_gears_arg | Helper function to assure validity of gears argument |
| validObject | Validity checker compatibility helper |
| 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 |
| with_info_level | Collect and report the information signals raised while... |
