Dynamic Multi-Species Size Spectrum Modelling

Documentation for package ‘mizer’ version 3.0.0

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mizer: Multi-species size-based modelling in R

-- A --

addPlot	Add lines to an existing plot
addPlot.ArraySpeciesBySize	Add lines to an existing plot
addPlot.ArrayTimeBySpecies	Add lines to an existing plot
addSpecies	Add new species
age_mat	Calculate age at maturity
age_mat_vB	Calculate age at maturity from von Bertalanffy growth parameters
age_mat_vB.data.frame	Calculate age at maturity from von Bertalanffy growth parameters
age_mat_vB.default	Calculate age at maturity from von Bertalanffy growth parameters
age_mat_vB.MizerParams	Calculate age at maturity from von Bertalanffy growth parameters
animate	Animate size-dependent quantities through time
animate.ArrayTimeBySpeciesBySize	Animate size-dependent quantities through time
animate.MizerSim	Animate size-dependent quantities through time
animateSpectra	Animate size-dependent quantities through time
ArraySpeciesBySize	S3 class for species x size rate arrays
ArrayTimeBySpecies	S3 class for time x species arrays
ArrayTimeBySpeciesBySize	S3 class for time x species x size arrays
as.data.frame	Convert mizer arrays to data frames
as.data.frame.ArraySpeciesBySize	Convert mizer arrays to data frames
as.data.frame.ArrayTimeBySpecies	Convert mizer arrays to data frames
as.data.frame.ArrayTimeBySpeciesBySize	Convert mizer arrays to data frames

-- B --

balance_resource_logistic	Project resource using logistic model
balance_resource_semichemostat	Project resource using semichemostat model
BevertonHoltRDD	Beverton Holt function to calculate density-dependent reproduction rate
box_pred_kernel	Box predation kernel

-- C --

calculated_species_params	Species parameters
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
catchability	Set fishing parameters
catchability<-	Set fishing parameters
clearExtensionChain	Clear the registered extension chain
coerceToExtensionClass	Coerce a mizer object to its registered extension class
compareParams	Compare two MizerParams objects and print out differences
completeSpeciesParams	Alias for 'validSpeciesParams()'
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

-- D --

defaults_edition	Default editions
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

-- E --

emptyParams	Create empty MizerParams object of the right size
expandSizeGrid	Expand the size grid
expandSizeGrid.MizerParams	Expand the size grid
ext_diffusion	Set external diffusion rate
ext_diffusion<-	Set external diffusion rate
ext_encounter	Set external encounter rate
ext_encounter<-	Set external encounter rate
ext_mort	Set external mortality rate
ext_mort<-	Set external mortality rate

-- F --

finalN	Size spectra at end of simulation
finalNOther	Time series of other components
finalNResource	Size spectra at end of simulation
finalParams	Extract the final state from a simulation

-- G --

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	Add a dynamical ecosystem component
getCriticalFeedingLevel	Get critical feeding level
getDiet	Get diet of predator at size, resolved by prey species
getDiffusion	Get diffusion rate from predation
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()'
getExtEncounter	Set external encounter rate
getExtMort	Set external mortality rate
getFeedingLevel	Get feeding level
getFlux	Get flux into size bins
getFlux.MizerParams	Get flux into size bins
getFlux.MizerSim	Get flux into size bins
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
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 model state from 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
getRegisteredExtensions	Get the registered mizer extension chain
getReproductionLevel	Get reproduction level
getReproductionProportion	Set reproduction parameters
getRequiredRDD	Determine reproduction rate needed for initial egg abundance
getResourceMort	Get predation mortality rate for resource
getSearchVolume	Set search volume
getSelectivity	Set fishing parameters
getSimParams	Extract the projection parameters used to produce a simulation
getSSB	Calculate the SSB of species
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 by each gear
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
get_ks_default	Get default value for 'ks'
get_phi	Get values from feeding kernel function
get_size_range_array	Get size range array
get_steady_state_n	Calculate steady state abundance
get_time_elements	Get array indices for a time range in a MizerSim object
given_species_params	Species parameters
given_species_params<-	Species parameters

-- I --

idxFinalT	Size spectra at end of simulation
indicator_functions	Description of indicator functions
initialN	Initial values for fish spectra
initialN.MizerParams	Initial values for fish spectra
initialN.MizerSim	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.MizerParams	Initial value for resource spectrum
initialNResource.MizerSim	Initial value for resource spectrum
initialNResource<-	Initial value for resource spectrum
initialParams	Extract the initial state from a simulation
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'
interaction_matrix	Set species interaction matrix
interaction_matrix<-	Set species interaction matrix
is.ArraySpeciesBySize	Test if an object is a ArraySpeciesBySize
is.ArrayTimeBySpecies	Test if an object is a ArrayTimeBySpecies
is.ArrayTimeBySpeciesBySize	Test if an object is an ArrayTimeBySpeciesBySize

-- K --

knife_edge

Weight based knife-edge selectivity function

-- L --

l2w	Length-weight conversion
lognormal_pred_kernel	Lognormal predation kernel

-- M --

markBackground	Designate species as background species
matchBiomasses	Match biomasses to observations
matchGrowth	Adjust model to produce observed growth
matchNumbers	Match numbers 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
mizerDiffusion	Calculate diffusion rate
mizerEGrowth	Get energy rate available for growth needed to project standard mizer model
mizerEncounter	Get encounter rate during projection
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 --

N	Time series of size spectra
needs_upgrading	Determine whether a MizerParams or MizerSim object needs to be upgraded
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

-- O --

other_params	Set own rate function to replace mizer rate function
other_params<-	Set own rate function to replace mizer rate function

-- P --

plot	Plot mizer arrays
plot.ArraySpeciesBySize	Plot mizer arrays
plot.ArrayTimeBySpecies	Plot mizer arrays
plot.ArrayTimeBySpeciesBySize	Plot mizer arrays
plot.MizerParams	Summary plot for 'MizerParams' objects
plot.MizerSim	Summary plot for 'MizerSim' objects
plot2	Compare two mizer arrays in a single plot
plot2.ArraySpeciesBySize	Compare two mizer arrays in a single plot
plot2.ArrayTimeBySpecies	Compare two mizer arrays in a single plot
plot2.ArrayTimeBySpeciesBySize	Compare two mizer arrays in a single plot
plotBiomass	Plot the biomass of species through time
plotBiomass.MizerSim	Plot the biomass of species through time
plotBiomassObservedVsModel	Plotting observed vs. model biomass data
plotCDF	Plot cumulative abundance or biomass distributions
plotCDF.MizerParams	Plot cumulative abundance or biomass distributions
plotCDF.MizerSim	Plot cumulative abundance or biomass distributions
plotCDF2	Compare cumulative abundance or biomass distributions from two objects
plotDiet	Plot diet, resolved by prey species, as function of predator at size.
plotDiet.MizerParams	Plot diet, resolved by prey species, as function of predator at size.
plotDiet.MizerSim	Plot diet, resolved by prey species, as function of predator at size.
plotFeedingLevel	Plot the feeding level of species by size
plotFeedingLevel.MizerParams	Plot the feeding level of species by size
plotFeedingLevel.MizerSim	Plot the feeding level of species by size
plotFMort	Plot total fishing mortality of each species by size
plotFMort.MizerParams	Plot total fishing mortality of each species by size
plotFMort.MizerSim	Plot total fishing mortality of each species by size
plotGrowthCurves	Plot growth curves
plotGrowthCurves.MizerParams	Plot growth curves
plotGrowthCurves.MizerSim	Plot growth curves
plotHover	Create a hover-enabled plotly plot from a mizer object
plotHover.ArraySpeciesBySize	Create a hover-enabled plotly plot from a mizer object
plotHover.ArrayTimeBySpecies	Create a hover-enabled plotly plot from a mizer object
plotHover.ArrayTimeBySpeciesBySize	Create a hover-enabled plotly plot from a mizer object
plotHover.mizer_plot	Create a hover-enabled plotly plot from a mizer object
plotlyBiomass	Plot the biomass of species through time
plotlyBiomassObservedVsModel	Plotting observed vs. model biomass data
plotlyCDF	Plot cumulative abundance or biomass distributions
plotlyCDF2	Compare cumulative abundance or biomass distributions from two objects
plotlyDiet	Plot diet, resolved by prey species, as function of predator at size.
plotlyFeedingLevel	Plot the feeding level of species by size
plotlyFMort	Plot total fishing mortality of each species by size
plotlyGrowthCurves	Plot growth curves
plotlyPredMort	Plot predation mortality rate of each species against size
plotlySpectra	Plot abundance and biomass spectra
plotlySpectra2	Compare abundance and biomass spectra from two objects
plotlySpectraRelative	Plot relative difference between 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()'
plotMizerParams	Summary plot for 'MizerParams' objects
plotMizerSim	Summary plot for 'MizerSim' objects
plotPredMort	Plot predation mortality rate of each species against size
plotPredMort.MizerParams	Plot predation mortality rate of each species against size
plotPredMort.MizerSim	Plot predation mortality rate of each species against size
plotRelative	Plot relative difference between two mizer arrays
plotRelative.ArraySpeciesBySize	Plot relative difference between two mizer arrays
plotRelative.ArrayTimeBySpecies	Plot relative difference between two mizer arrays
plotRelative.ArrayTimeBySpeciesBySize	Plot relative difference between two mizer arrays
plotSpectra	Plot abundance and biomass spectra
plotSpectra.MizerParams	Plot abundance and biomass spectra
plotSpectra.MizerSim	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
plotYield.MizerSim	Plot the total yield of species through time
plotYieldGear	Plot the total yield of each species by gear through time
plotYieldGear.MizerSim	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
print	Print mizer objects
print.ArraySpeciesBySize	Print mizer objects
print.ArrayTimeBySpecies	Print mizer objects
print.ArrayTimeBySpeciesBySize	Print mizer objects
print.summary.ArraySpeciesBySize	Print mizer objects
print.summary.ArrayTimeBySpecies	Print mizer objects
print.summary.ArrayTimeBySpeciesBySize	Print mizer objects
project	Project size spectrum forward in time
project.MizerParams	Project size spectrum forward in time
project.MizerSim	Project size spectrum forward in time
projectDiffusion	Calculate diffusion rate
projectDiffusion.MizerParams	Calculate diffusion rate
projectEGrowth	Get energy rate available for growth needed to project standard mizer model
projectEGrowth.MizerParams	Get energy rate available for growth needed to project standard mizer model
projectEncounter	Get encounter rate during projection
projectEncounter.MizerParams	Get encounter rate during projection
projectERepro	Get energy rate available for reproduction needed to project standard mizer model
projectERepro.MizerParams	Get energy rate available for reproduction needed to project standard mizer model
projectEReproAndGrowth	Get energy rate available for reproduction and growth needed to project standard mizer model
projectEReproAndGrowth.MizerParams	Get energy rate available for reproduction and growth needed to project standard mizer model
projectFeedingLevel	Get feeding level needed to project standard mizer model
projectFeedingLevel.MizerParams	Get feeding level needed to project standard mizer model
projectFMort	Get the total fishing mortality rate from all fishing gears
projectFMort.MizerParams	Get the total fishing mortality rate from all fishing gears
projectMort	Get total mortality rate needed to project standard mizer model
projectMort.MizerParams	Get total mortality rate needed to project standard mizer model
projectPredMort	Get total predation mortality rate needed to project standard mizer model
projectPredMort.MizerParams	Get total predation mortality rate needed to project standard mizer model
projectPredRate	Get predation rate needed to project standard mizer model
projectPredRate.MizerParams	Get predation rate needed to project standard mizer model
projectRates	Get all rates needed to project standard mizer model
projectRDD	Get density-dependent reproduction rate during projection
projectRDD.MizerParams	Get density-dependent reproduction rate during projection
projectRDI	Get density-independent rate of reproduction needed to project standard mizer model
projectRDI.MizerParams	Get density-independent rate of reproduction needed to project standard mizer model
projectResourceMort	Get predation mortality rate for resource needed to project standard mizer model
projectResourceMort.MizerParams	Get predation mortality rate for resource needed to project standard mizer model
projectToSteady	Project to steady state
project_n	Project values for first time step of Euler method
project_n_2	Project values with a predictor-corrector method
project_n_no_diffusion	Project values for first time step of Euler method
project_simple	Project abundances by a given number of time steps into the future
psi	Set reproduction parameters

-- R --

readParams	Save and restore mizer objects
readSim	Save and restore mizer objects
registerExtension	Register a single mizer extension for this R session
registerExtensions	Register mizer extensions for this R session
removeBackgroundSpecies	Remove all background species
removeComponent	Add a dynamical ecosystem component
removeSpecies	Remove species
renameGear	Rename gears
renameSpecies	Rename species
repro_prop	Set reproduction parameters
repro_prop<-	Set reproduction parameters
resource_capacity	Set resource dynamics
resource_capacity<-	Set resource dynamics
resource_constant	Keep resource abundance constant
resource_dynamics	Set resource dynamics
resource_dynamics<-	Set resource dynamics
resource_level	Set resource dynamics
resource_level<-	Set resource dynamics
resource_logistic	Project resource using logistic model
resource_params	Resource parameters
resource_params<-	Resource parameters
resource_rate	Set resource dynamics
resource_rate<-	Set resource dynamics
resource_semichemostat	Project resource using semichemostat model
RickerRDD	Ricker function to calculate density-dependent reproduction rate

-- S --

saveParams	Save and restore mizer objects
saveSim	Save and restore mizer objects
scaleModel	Change scale of the model
scaleRates	Rescale all rates in a mizer model
search_vol	Set search volume
search_vol<-	Set search volume
selectivity	Set fishing parameters
selectivity<-	Set fishing parameters
setBevertonHolt	Set Beverton-Holt reproduction without changing the steady state
setColours	Set line colours and line types to be used in mizer plots
setComponent	Add a dynamical ecosystem component
setExtDiffusion	Set external diffusion rate
setExtDiffusion.MizerParams	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
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 resource dynamics
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
steadySingleSpecies	Set initial abundances to solution of steady-state equation with current rates
str	Display the structure of mizer objects
str.ArraySpeciesBySize	Display the structure of mizer objects
str.ArrayTimeBySpecies	Display the structure of mizer objects
str.ArrayTimeBySpeciesBySize	Display the structure of mizer objects
str.MizerParams	Display structure of MizerParams object
str.MizerSim	Display structure of MizerSim object
summary	Summarise mizer objects
summary.ArraySpeciesBySize	Summarise mizer objects
summary.ArrayTimeBySpecies	Summarise mizer objects
summary.ArrayTimeBySpeciesBySize	Summarise mizer objects
summary.MizerParams	Summarize MizerParams object
summary.MizerSim	Summarize MizerSim object
summary_functions	Description of summary functions

-- T --

truncated_lognormal_pred_kernel

Truncated lognormal predation kernel

-- U --

use_predation_diffusion	Get or set the use_predation_diffusion flag
use_predation_diffusion<-	Get or set the use_predation_diffusion flag

-- V --

validEffortVector	Make a valid effort vector
validGearParams	Check validity of gear parameters and set defaults
validGivenSpeciesParams	Validate species parameter data frame
validParams	Validate MizerParams object and upgrade if necessary
validSim	Validate MizerSim object and upgrade if necessary
validSpeciesParams	Validate species parameter data frame
valid_gears_arg	Helper function to assure validity of gears argument
valid_species_arg	Helper function to assure validity of species argument

-- W --

w	Size bins
w2l	Length-weight conversion
w_full	Size bins