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.

Install the latest version of this package by entering the following in R:
install.packages("mizer")
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

Functions

getBiomass Man page
getBiomass-method Man page
getBiomass,MizerSim-method Man page
getCommunitySlope Man page
getCommunitySlope-method Man page
getCommunitySlope,MizerSim-method Man page
getEGrowth Man page
getEGrowth-method Man page
getEGrowth,MizerParams,matrix,numeric,matrix,matrix-method Man page
getEGrowth,MizerParams,matrix,numeric,missing,missing-method Man page
getEReproAndGrowth Man page
getEReproAndGrowth-method Man page
getEReproAndGrowth,MizerParams,matrix,numeric,matrix-method Man page
getEReproAndGrowth,MizerParams,matrix,numeric,missing-method Man page
getESpawning Man page
getESpawning-method Man page
getESpawning,MizerParams,matrix,numeric,matrix-method Man page
getESpawning,MizerParams,matrix,numeric,missing-method Man page
getFeedingLevel Man page
getFeedingLevel-method Man page
getFeedingLevel,MizerParams,matrix,numeric,matrix-method Man page
getFeedingLevel,MizerParams,matrix,numeric,missing-method Man page
getFeedingLevel,MizerSim,missing,missing,missing-method Man page
getFMort Man page
getFMortGear Man page
getFMortGear-method Man page
getFMortGear,MizerParams,matrix-method Man page
getFMortGear,MizerParams,numeric-method Man page
getFMortGear,MizerSim,missing-method Man page
getFMort-method Man page
getFMort,MizerParams,matrix-method Man page
getFMort,MizerParams,numeric-method Man page
getFMort,MizerSim,missing-method Man page
get_initial_n Man page
getM2 Man page
getM2Background Man page
getM2Background-method Man page
getM2Background,MizerParams,matrix,numeric,array-method Man page
getM2Background,MizerParams,matrix,numeric,missing-method Man page
getM2-method Man page
getM2,MizerParams,matrix,numeric,array-method Man page
getM2,MizerParams,matrix,numeric,missing-method Man page
getM2,MizerSim,missing,missing,missing-method Man page
getMeanMaxWeight Man page
getMeanMaxWeight-method Man page
getMeanMaxWeight,MizerSim-method Man page
getMeanWeight Man page
getMeanWeight-method Man page
getMeanWeight,MizerSim-method Man page
getN Man page
getN-method Man page
getN,MizerSim-method Man page
getPhiPrey Man page
getPhiPrey-method Man page
getPhiPrey,MizerParams,matrix,numeric-method Man page
getPredRate Man page
getPredRate-method Man page
getPredRate,MizerParams,matrix,numeric,matrix-method Man page
getPredRate,MizerParams,matrix,numeric,missing-method Man page
getProportionOfLargeFish Man page
getProportionOfLargeFish-method Man page
getProportionOfLargeFish,MizerSim-method Man page
getRDD Man page
getRDD-method Man page
getRDD,MizerParams,matrix,numeric,matrix-method Man page
getRDD,MizerParams,matrix,numeric,missing-method Man page
getRDI Man page
getRDI-method Man page
getRDI,MizerParams,matrix,numeric,matrix-method Man page
getRDI,MizerParams,matrix,numeric,missing-method Man page
getSSB Man page
getSSB-method Man page
getSSB,MizerSim-method Man page
getYield Man page
getYieldGear Man page
getYieldGear-method Man page
getYieldGear,MizerSim-method Man page
getYield-method Man page
getYield,MizerSim-method Man page
getZ Man page
getZ-method Man page
getZ,MizerParams,matrix,numeric,numeric,matrix-method Man page
getZ,MizerParams,matrix,numeric,numeric,missing-method Man page
inter Man page
knife_edge Man page
mizer Man page
mizer, Man page
mizer-package Man page
MizerParams Man page
MizerParams-class Man page
MizerParams,data.frame,matrix-method Man page
MizerParams,data.frame,missing-method Man page
MizerParams-method Man page
MizerParams,numeric,missing-method Man page
MizerSim Man page
MizerSim-class Man page
MizerSim-method Man page
MizerSim,MizerParams-method Man page
NS_species_params Man page
NS_species_params_gears Man page
plot Man page
plotBiomass Man page
plotBiomass-method Man page
plotBiomass,MizerSim-method Man page
plotFeedingLevel Man page
plotFeedingLevel-method Man page
plotFeedingLevel,MizerSim-method Man page
plotFMort Man page
plotFMort-method Man page
plotFMort,MizerSim-method Man page
plotM2 Man page
plotM2-method Man page
plotM2,MizerSim-method Man page
plot,MizerSim,missing-method Man page
plotSpectra Man page
plotSpectra-method Man page
plotSpectra,MizerSim-method Man page
plotYield Man page
plotYieldGear Man page
plotYieldGear-method Man page
plotYieldGear,MizerSim-method Man page
plotYield-method Man page
plotYield,MizerSim-method Man page
project Man page
project-method Man page
project,MizerParams,array-method Man page
project,MizerParams,missing-method Man page
project,MizerParams,numeric-method Man page
set_community_model Man page
set_trait_model Man page
sigmoid_length Man page
summary Man page
summary,MizerParams-method Man page
summary,MizerSim-method Man page

Files

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.