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mizer

mizer is a package that implements size-based ecological models. The package has been developed to model marine ecosystems that are subject to fishing. However, it may also be appropriate for other ecosystems.

The package contains routines and methods to allow users to set up the model community, and then project it through time under different fishing strategies.

Methods are included to explore the results, including plots and calculation of community indicators such as the slope of the size spectrum. Size-based models can be complicated so mizer contains many default options that can be easily changed by the user.

The package is on CRAN and therefore available from R's build-it package manager.

See the accompanying vignette for more details on how the package works, including detailed examples.

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Version

Install

install.packages('mizer')

Monthly Downloads

353

Version

1.0.1

License

GPL-3

Maintainer

Gustav Delius

Last Published

January 27th, 2019

Functions in mizer (1.0.1)

getFMort

Get the total fishing mortality rate from all fishing gears by time, species and size.
get_initial_n

Calculate initial population abundances for the community populations
inter

Example interaction matrix for the North Sea example
plot,MizerSim,missing-method

Summary plot for MizerSim objects
getFeedingLevel

Get feeding level
plotSpectra

Plot the abundance spectra
getM2

getM2 method for the size based model
getM2Background

Get predation mortality rate for plankton
display_frames

Display frames
getMeanMaxWeight

Calculate the mean maximum weight of the community
getRDI

Get density independent recruitment
getProportionOfLargeFish

Calculate the proportion of large fish
getRDD

Get density dependent recruitment
getPredRate

Get predation rate
getEReproAndGrowth

Get energy after metabolism and movement
getCommunitySlope

Calculate the slope of the community abundance
getESpawning

Get energy rate available for reproduction
getPhiPrey

Get available energy
plotGrowthCurves

Plot growth curves giving weight as a function of age
getEGrowth

Get energy rate available for growth
log_breaks

Helper function to produce nice breaks on logarithmic axes
knife_edge

Size based knife-edge selectivity function
getN

Calculate the total abundance in terms of numbers of species within a size range
getMeanWeight

Calculate the mean weight of the community
getFMortGear

Get the fishing mortality by time, gear, species and size
getSSB

Calculate the SSB of species
mizer

mizer: Multi-species size-based modelling in R
plotBiomass

Plot the biomass of species through time
plotM2

Plot predation mortality rate of each species against size
getSSBFrame

Get data frame of spawning stock biomass of species through time, ready for ggplot2
plotYield

Plot the total yield of species through time
getYield

Calculate the total yield of each species
plotFeedingLevel

Plot the feeding level of species by size
plotFMort

Plot total fishing mortality of each species by size
wrapper_functions

Functions used for setting up models
summary,MizerSim-method

Summarize MizerSim object
plotYieldGear

Plot the total yield of each species by gear through time
project

project method for the size based modelling
getYieldGear

Calculate the total yield per gear and species
sigmoid_length

Length based sigmoid selectivity function
set_trait_model

Sets up parameters for a trait-based model
set_scaling_model

Sets up parameters for a scale free trait-based model
project_methods

Methods used for projecting
set_community_model

Sets up parameters for a community-type model
steady

Tune params object to be at steady state
retune_abundance

Retunes abundance of background species.
setBackground

Designate species as background species
getZ

Get total mortality rate
summary,MizerParams-method

Summarize MizerParams object
MizerParams-class

A class to hold the parameters for a size based model.
MizerSim-class

MizerSim
getBiomassFrame

Get data frame of biomass of species through time, ready for ggplot2
NS_species_params

Example parameter set based on the North Sea
NS_species_params_gears

Example parameter set based on the North Sea with different gears
getBiomass

Calculate the total biomass of each species within a size range at each time step.
addSpecies

Add more species into an ecosystem with background species.
MizerParams

Constructors for objects of MizerParams class
MizerSim

Constructor for the MizerSim class