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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.

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

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Version

Install

install.packages('mizer')

Monthly Downloads

397

Version

0.4

License

GPL-3

Maintainer

Gustav Delius

Last Published

December 14th, 2017

Functions in mizer (0.4)

getEGrowth

getEGrowth method for the size based model
MizerParams-class

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

getEReproAndGrowth method for the size based model
NS_species_params

Example parameter set based on the North Sea
MizerParams

Constructors for objects of MizerParams class
NS_species_params_gears

Example parameter set based on the North Sea with different gears
MizerSim-class

MizerSim
getBiomass

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

getFeedingLevel method for the size based model
MizerSim

Constructor for the MizerSim class
get_initial_n

Calculate initial population abundances for the community populations
getCommunitySlope

Calculate the slope of the community abundance
inter

Example interaction matrix for the North Sea example
getPhiPrey

getPhiPrey method for the size based model
getMeanMaxWeight

Calculate the mean maximum weight of the community
getSSB

Calculate the SSB of species
getFMortGear

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

Calculate the total yield of each species
getN

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

getRDD method for the size based model
getESpawning

getESpawning method for the size based model
getRDI

getRDI method for the size based model
getM2

getM2 method for the size based model
plot,MizerSim,missing-method

Summary plot for MizerSim objects
getM2Background

getM2Background method for the size based model
plotSpectra

Plot the abundance spectra of each species and the background population
getFMort

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

Size based knife-edge selectivity function
mizer

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

getPredRate method for the size based model
getYieldGear

Calculate the total yield per gear and species
getProportionOfLargeFish

Calculate the proportion of large fish
getZ

getZ method for the size based model
plotBiomass

Plot the biomass of each species through time
getMeanWeight

Calculate the mean weight of the community
plotFMort

Plot total fishing mortality of each species by size
plotYield

Plot the total yield of each species through time
set_community_model

Sets up parameters for a community-type model
plotYieldGear

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

Sets up parameters for a trait-based model
plotFeedingLevel

Plot the feeding level of each species by size
summary,MizerSim-method

Summarize MizerSim object
plotM2

Plot M2 of each species by size
project

project method for the size based modelling
sigmoid_length

Length based sigmoid selectivity function
summary,MizerParams-method

Summarize MizerParams object
project_methods

Methods used for projecting