mizer: Multi-species sIZE spectrum modelling in R

A set of classes and methods to set up and run multispecies, trait based and community size spectrum ecological models, focussed on the marine environment.

AuthorFinlay Scott (JRC, IT) and Julia Blanchard (Sheffield University, UK) and Ken Andersen (DTU Aqua, Copenhagen, DK)
Date of publication2014-04-16 22:29:02
MaintainerFinlay Scott <finlay.scott@jrc.ec.europa.eu>
LicenseGPL-3
Version0.2

View on CRAN

Man pages

getBiomass-methods: Calculate the total biomass of each species within a size...

getCommunitySlope-methods: Calculate the slope of the community abundance

getEGrowth-methods: getEGrowth method for the size based model

getEReproAndGrowth-methods: getEReproAndGrowth method for the size based model

getESpawning-methods: getESpawning method for the size based model

getFeedingLevel-methods: getFeedingLevel method for the size based model

getFMortGear-methods: Get the fishing mortality by time, gear, species and size

getFMort-methods: Get the total fishing mortality from all fishing gears by...

get_initial_n: Calculate initial population abundances for the community...

getM2Background-methods: getM2Background method for the size based model

getM2-methods: getM2 method for the size based model

getMeanMaxWeight-methods: Calculate the mean maximum weight of the community

getMeanWeight-methods: Calculate the mean weight of the community

getN-methods: Calculate the total abundance in terms of numbers of species...

getPhiPrey-methods: getPhiPrey method for the size based model

getPredRate-methods: getPredRate method for the size based model

getProportionOfLargeFish-methods: Calculate the proportion of large fish

getRDD-methods: getRDD method for the size based model

getRDI-methods: getRDI method for the size based model

getSSB-methods: Calculate the SSB of species

getYieldGear-methods: Calculate the total yield per gear and species

getYield-methods: Calculate the total yield of each species

getZ-methods: getZ method for the size based model

inter: Sample interaction data set

knife_edge: Size based knife-edge selectivity function

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

MizerParams-class: MizerParams

MizerParams-methods: Constructors for objects of 'MizerParams' class

MizerSim-class: MizerSim

MizerSim-methods: Constructor for the 'MizerSim' class

NS_species_params: Example parameters data sets

plotBiomass-methods: Plot the biomass of each species through time

plotFeedingLevel-methods: Plot the feeding level of each species by size

plotFMort-methods: Plot total fishing mortality of each species by size

plotM2-methods: Plot M2 of each species by size

plot-methods: Summary plot for 'MizerSim' objects

plotSpectra-methods: Plot the abundance spectra of each species and the background...

plotYieldGear-methods: Plot the total yield of each species by gear through time

plotYield-methods: Plot the total yield of each species through time

project-methods: project method for the size based modelling

set_community_model: Sets up parameters for a community-type model

set_trait_model: Sets up parameters for a trait-based model

sigmoid_length: Length based sigmoid selectivity function

summary-methods: Summary method

Files in this package

mizer
mizer/inst
mizer/inst/examples
mizer/inst/examples/supplementary_material.R
mizer/inst/tests
mizer/inst/tests/test-MizerSim.r
mizer/inst/tests/test-single_species.R
mizer/inst/tests/test-MizerParams.r
mizer/inst/tests/test-wrapper_functions.R
mizer/inst/tests/test-plots.r
mizer/inst/tests/test-summary_methods.r
mizer/inst/tests/test-project.r
mizer/inst/tests/test-selectivity.r
mizer/inst/tests/test-project_methods.r
mizer/inst/doc
mizer/inst/doc/inter.csv
mizer/inst/doc/mizer_vignette.pdf
mizer/inst/doc/mizer_vignette.R
mizer/inst/doc/NS_species_params.csv
mizer/inst/doc/mizer_vignette.Rnw
mizer/inst/doc/NS_f_history.csv
mizer/tests
mizer/tests/run-all.r
mizer/NAMESPACE
mizer/NEWS
mizer/data
mizer/data/NS_species_params.RData
mizer/data/inter.RData
mizer/data/NS_species_params_gears.RData
mizer/R
mizer/R/wrapper_functions.R
mizer/R/project.r
mizer/R/NS_species_params-data.R
mizer/R/MizerParams-class.r
mizer/R/help.r
mizer/R/project_methods.r
mizer/R/MizerSim-class.r
mizer/R/summary_methods.r
mizer/R/selectivity_funcs.r
mizer/R/plots.r
mizer/vignettes
mizer/vignettes/inter.csv
mizer/vignettes/.install_extras
mizer/vignettes/NS_species_params.csv
mizer/vignettes/recruitment.pdf
mizer/vignettes/Growth_curve.pdf
mizer/vignettes/reflib.bib
mizer/vignettes/Spectrum.eps
mizer/vignettes/mizer_vignette.Rnw
mizer/vignettes/NS_f_history.csv
mizer/README.md
mizer/MD5
mizer/build
mizer/build/vignette.rds
mizer/DESCRIPTION
mizer/man
mizer/man/summary-methods.Rd mizer/man/plotYield-methods.Rd mizer/man/getRDI-methods.Rd mizer/man/getZ-methods.Rd mizer/man/plotSpectra-methods.Rd mizer/man/getN-methods.Rd mizer/man/getFeedingLevel-methods.Rd mizer/man/getSSB-methods.Rd mizer/man/plot-methods.Rd mizer/man/getProportionOfLargeFish-methods.Rd mizer/man/sigmoid_length.Rd mizer/man/MizerSim-methods.Rd mizer/man/getM2Background-methods.Rd mizer/man/set_community_model.Rd mizer/man/plotBiomass-methods.Rd mizer/man/plotM2-methods.Rd mizer/man/plotFeedingLevel-methods.Rd mizer/man/MizerSim-class.Rd mizer/man/getEReproAndGrowth-methods.Rd mizer/man/getFMort-methods.Rd mizer/man/get_initial_n.Rd mizer/man/MizerParams-methods.Rd mizer/man/project-methods.Rd mizer/man/getCommunitySlope-methods.Rd mizer/man/getPredRate-methods.Rd mizer/man/plotYieldGear-methods.Rd mizer/man/getMeanWeight-methods.Rd mizer/man/getM2-methods.Rd mizer/man/set_trait_model.Rd mizer/man/getFMortGear-methods.Rd mizer/man/MizerParams-class.Rd mizer/man/getBiomass-methods.Rd mizer/man/getESpawning-methods.Rd mizer/man/inter.Rd mizer/man/NS_species_params.Rd mizer/man/getYieldGear-methods.Rd mizer/man/getEGrowth-methods.Rd mizer/man/mizer.Rd mizer/man/getMeanMaxWeight-methods.Rd mizer/man/getPhiPrey-methods.Rd mizer/man/getRDD-methods.Rd mizer/man/plotFMort-methods.Rd mizer/man/getYield-methods.Rd mizer/man/knife_edge.Rd

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