mizer: Multi-species sIZE spectrum modelling in R

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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.

Author
Finlay Scott (JRC, IT) and Julia Blanchard (Sheffield University, UK) and Ken Andersen (DTU Aqua, Copenhagen, DK)
Date of publication
2014-04-16 22:29:02
Maintainer
Finlay Scott <finlay.scott@jrc.ec.europa.eu>
License
GPL-3
Version
0.2

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