Dynamic Multi-Species Size Spectrum Modelling
Get growth curves giving weight as a function of age
Deprecated function to get interaction matrix
Match numbers to observations
Helper function to assure validity of species argument
Check validity of gear parameters and set defaults
Calibrate the model scale to match total observed number
Create empty MizerParams object of the right size
Size spectra at end of simulation
Values of other ecosystem components at end of simulation
Determine reproduction rate needed for initial egg abundance
Get critical feeding level
Get reproduction level
Add new species
Calculate age at maturity from von Bertalanffy growth parameters
Calculate age at maturity
Deprecated functions for getting resource parameters
Animation of the abundance spectra
Beverton Holt function to calculate density-dependent reproduction rat...
Box predation kernel
Calculate selectivity from gear parameters
Calibrate the model scale to match total observed biomass
Set up parameters for a general multispecies model
Calibrate the model scale to match total observed yield
Compare two MizerParams objects and print out differences
Alias for validSpeciesParams()
Helper function to keep other components constant
Choose egg production to keep egg density constant
Give constant reproduction rate
Set up parameters for a single species in a power-law background
Replace a mizer function with a custom version
Set defaults for predation kernel parameters
Default editions
Check whether two objects are different
Measure distance between current and previous state in terms of RDI
Measure distance between current and previous state in terms of fish a...
Length based double-sigmoid selectivity function
Gear parameters
Get default value for f0
Get default value for gamma
Get default value for h
Calculate initial population abundances
Get default value for ks
Get values from feeding kernel function
Get size range array
Get_time_elements
Calculate the total biomass of each species within a size range at eac...
Calculate the slope of the community abundance
Get information about other ecosystem components
Get diet of predator at size, resolved by prey species
Fishing effort used in simulation
Get energy rate available for growth
Get encounter rate
Get energy rate available for reproduction
Get energy rate available for reproduction and growth
Alias for getERepro()
Get feeding level
Get the total fishing mortality rate from all fishing gears by time, s...
Get the fishing mortality by time, gear, species and size
Alias for getPredMort()
Alias for getResourceMort()
Calculate the mean maximum weight of the community
Calculate the mean weight of the community
Set up parameters for a trait-based multispecies model
Get total mortality rate
Calculate the number of individuals within a size range
Extract the parameter object underlying a simulation
Get available energy
Get total predation mortality rate
Give density-independent reproduction rate
Get predation rate
Calculate the proportion of large fish
Get all rates
Get density dependent reproduction rate
Get density independent rate of egg production
Get predation mortality rate for resource
Calculate the SSB of species
Times for which simulation results are available
Calculate the rate at which biomass of each species is fished
Calculate the rate at which biomass of each species is fished by each ...
Alias for getMort()
Description of indicator functions
Initial fishing effort
Initial values for fish spectra
Initial values for other ecosystem components
Initial value for resource spectrum
Weight based knife-edge selectivity function
Time series of other components
Length-weight conversion
Helper function to produce nice breaks on logarithmic axes
Lognormal predation kernel
Match biomasses to observations
Adjust model to produce observed growth
Match yields to observations
mizer: Multi-species size-based modelling in R
Get energy rate available for growth needed to project standard mizer ...
Get encounter rate needed to project standard mizer model
Get energy rate available for reproduction needed to project standard ...
Get energy rate available for reproduction and growth needed to projec...
Get feeding level needed to project standard mizer model
Get the total fishing mortality rate from all fishing gears
Get the fishing mortality needed to project standard mizer model
Get total mortality rate needed to project standard mizer model
A class to hold the parameters for a size based model.
Summary plot for MizerParams objects
Alias for set_multispecies_model()
Get total predation mortality rate needed to project standard mizer mo...
Get predation rate needed to project standard mizer model
Get all rates needed to project standard mizer model
Weight based sigmoidal selectivity function
Get density-independent rate of reproduction needed to project standar...
Get predation mortality rate for resource needed to project standard m...
A class to hold the results of a simulation
Constructor for the MizerSim class
Time series of size spectra
Determine whether a MizerParams or MizerSim object needs to be upgrade...
Set up parameters for a community-type model
Plot the biomass of species through time
Plotting observed vs. model biomass data
Make a plot from a data frame
Plot diet, resolved by prey species, as function of predator at size.
Plot the feeding level of species by size
Species parameters
Plot total fishing mortality of each species by size
Plot growth curves
Alias for plotPredMort()
Summary plot for MizerSim objects
Plot predation mortality rate of each species against size
Plot the abundance spectra
Description of the plotting functions
Upgrade MizerParams object from earlier mizer versions
Plot the total yield of species through time
Plot the total yield of each species by gear through time
Plotting observed vs. model yields
Power-law predation kernel
Upgrade MizerSim object from earlier mizer versions
Project abundances by a given number of time steps into the future
Project size spectrum forward in time
Project to steady state
Objects exported from other packages
Remove species
Rename species
Keep resource abundance constant
Helper function to assure validity of gears argument
Project resource using logistic model
Resource parameters
Project resource using semichemostat model
Ricker function to calculate density-dependent reproduction rate
Save a MizerParams object to file, and restore it
Change scale of the model
Deprecated function for setting up parameters for a community-type mod...
Deprecated obsolete function for setting up multispecies parameters
Set a species parameter to a default value
Deprecated function for setting up parameters for a trait-based model
Set Beverton-Holt reproduction without changing the steady state
Set line colours and line types to be used in mizer plots
Add a dynamical ecosystem component
Set external encounter rate
Set external mortality rate
Set fishing parameters
Set initial values to values from a simulation
Set species interaction matrix
Set maximum intake rate
Set metabolic rate
Set metadata for a model
Set or change any model parameters
Set predation kernel
Set own rate function to replace mizer rate function
Set reproduction parameters
Set resource dynamics
Alias for setBevertonHolt()
Set search volume
Sheperd function to calculate density-dependent reproduction rate
Length based sigmoid selectivity function
Set initial values to a steady state for the model
Set initial abundances to single-species steady state abundances
Description of summary functions
Summarize MizerParams object
Summarize MizerSim object
Truncated lognormal predation kernel
Validate MizerParams object and upgrade if necessary
Validate MizerSim object and upgrade if necessary
Validate species parameter data frame
Size bins
A set of classes and methods to set up and run multi-species, trait based and community size spectrum ecological models, focused on the marine environment.
Useful links