Files in sizespectrum/mizer
Dynamic Multi-Species Size Spectrum Modelling

.Rbuildignore
.github/.gitignore
.github/CONTRIBUTING.md
.github/workflows/check-standard.yaml
.github/workflows/lint.yaml
.github/workflows/pkgdown.yaml
.github/workflows/test-coverage.yaml
.lintr
.travis.yml
CITATION.cff
DESCRIPTION
NAMESPACE
NEWS.md R/MizerParams-class.R R/MizerSim-class.R R/RcppExports.R R/age_mat.R R/animateSpectra.R R/calibrate.R R/compareParams.R R/customFunction.R R/data.R R/defaults_edition.R R/deprecated.R R/extension.R R/get_initial_n.R R/helpers.R R/manipulate_species.R R/match.R R/matchGrowth.R R/mizer-package.R R/newMultispeciesParams.R R/newSingleSpeciesParams.R R/plotBiomassObservedVsModel.R R/plotYieldObservedVsModel.R R/plots.R R/pred_kernel_funcs.R R/project.R R/project_methods.R R/rate_functions.R R/reproduction.R R/resource_dynamics.R R/resource_logistic.R R/resource_semichemostat.R R/saveParams.R R/selectivity_funcs.R R/setBevertonHolt.R R/setColours.R R/setExtEncounter.R R/setExtMort.R R/setFishing.R R/setInitialValues.R R/setInteraction.R R/setMaxIntakeRate.R R/setMetabolicRate.R R/setMetadata.R R/setPredKernel.R R/setReproduction.R R/setResource.R R/setSearchVolume.R R/species_params.R R/steady.R R/steadySingleSpecies.R R/summary_methods.R R/upgrade.R R/wrapper_functions.R README.Rmd README.md
codecov.yml
cran-comments.md
data/NS_interaction.RData
data/NS_params.rda
data/NS_sim.rda
data/NS_species_params.rda
data/NS_species_params_gears.rda
data/inter.RData
dev_scripts.R
docs/404.html
docs/CONTRIBUTING.html
docs/apple-touch-icon-120x120.png
docs/apple-touch-icon-152x152.png
docs/apple-touch-icon-180x180.png
docs/apple-touch-icon-60x60.png
docs/apple-touch-icon-76x76.png
docs/apple-touch-icon.png
docs/articles/a_multispecies_model_of_the_north_sea.html
docs/articles/a_multispecies_model_of_the_north_sea_files/figure-html/plot_ns_biomass-1.png
docs/articles/a_multispecies_model_of_the_north_sea_files/figure-html/plot_ns_indicators-1.png
docs/articles/a_multispecies_model_of_the_north_sea_files/figure-html/projected_ssb_ns-1.png
docs/articles/community_model.html
docs/articles/community_model_files/figure-html/plot_comm_biomass_sigma1-1.png
docs/articles/community_model_files/figure-html/plot_relative_comm_abund-1.png
docs/articles/community_model_files/figure-html/print_plot_comm_fmort-1.png
docs/articles/community_model_files/figure-html/print_plot_comm_m2-1.png
docs/articles/community_model_files/figure-html/print_plot_comm_sim-1.png
docs/articles/community_model_files/figure-html/unnamed-chunk-4-1.png
docs/articles/developer_FAQ.html
docs/articles/developer_vignette.html
docs/articles/editing_website.html
docs/articles/exploring_the_simulation_results.html
docs/articles/exploring_the_simulation_results_files/figure-html/demo_summary_plot-1.png
docs/articles/exploring_the_simulation_results_files/figure-html/plotBiomass-1.png
docs/articles/exploring_the_simulation_results_files/figure-html/plotSpectra_example-1.png
docs/articles/images/build.png
docs/articles/images/build_tools.png
docs/articles/images/cheat_sheet.pdf
docs/articles/images/cheat_sheet_preview.png
docs/articles/images/commit.png
docs/articles/images/commit_button.png
docs/articles/images/fork.png
docs/articles/images/git.png
docs/articles/images/new_branch_button.png
docs/articles/images/new_project.png
docs/articles/images/outline.png
docs/articles/images/recently_pushed.png
docs/articles/images/repository.png
docs/articles/images/repro_url.png
docs/articles/images/roxygen.png
docs/articles/images/tabs.png
docs/articles/images/tick.png
docs/articles/images/version_control.png
docs/articles/index.html
docs/articles/mizer.html
docs/articles/mizer_files/figure-html/unnamed-chunk-8-1.png
docs/articles/model_description.html
docs/articles/model_description_files/figure-html/unnamed-chunk-1-1.png
docs/articles/multispecies_model.html
docs/articles/plotting.html
docs/articles/plotting_files/crosstalk-1.2.0/css/crosstalk.min.css
docs/articles/plotting_files/crosstalk-1.2.0/js/crosstalk.js
docs/articles/plotting_files/crosstalk-1.2.0/js/crosstalk.js.map
docs/articles/plotting_files/crosstalk-1.2.0/js/crosstalk.min.js
docs/articles/plotting_files/crosstalk-1.2.0/js/crosstalk.min.js.map
docs/articles/plotting_files/crosstalk-1.2.0/scss/crosstalk.scss
docs/articles/plotting_files/crosstalk-1.2.1/css/crosstalk.min.css
docs/articles/plotting_files/crosstalk-1.2.1/js/crosstalk.js
docs/articles/plotting_files/crosstalk-1.2.1/js/crosstalk.js.map
docs/articles/plotting_files/crosstalk-1.2.1/js/crosstalk.min.js
docs/articles/plotting_files/crosstalk-1.2.1/js/crosstalk.min.js.map
docs/articles/plotting_files/crosstalk-1.2.1/scss/crosstalk.scss
docs/articles/plotting_files/figure-html/unnamed-chunk-12-1.png
docs/articles/plotting_files/figure-html/unnamed-chunk-13-1.png
docs/articles/plotting_files/figure-html/unnamed-chunk-15-1.png
docs/articles/plotting_files/figure-html/unnamed-chunk-22-1.png
docs/articles/plotting_files/figure-html/unnamed-chunk-27-1.png
docs/articles/plotting_files/figure-html/unnamed-chunk-28-1.png
docs/articles/plotting_files/figure-html/unnamed-chunk-29-1.png
docs/articles/plotting_files/figure-html/unnamed-chunk-34-1.png
docs/articles/plotting_files/figure-html/unnamed-chunk-36-1.png
docs/articles/plotting_files/figure-html/unnamed-chunk-37-1.png
docs/articles/plotting_files/figure-html/unnamed-chunk-39-1.png
docs/articles/plotting_files/figure-html/unnamed-chunk-40-1.png
docs/articles/plotting_files/figure-html/unnamed-chunk-7-1.png
docs/articles/plotting_files/figure-html/unnamed-chunk-9-1.png
docs/articles/plotting_files/htmlwidgets-1.6.0/htmlwidgets.js
docs/articles/plotting_files/htmlwidgets-1.6.2/htmlwidgets.js
docs/articles/plotting_files/htmlwidgets-1.6.4/htmlwidgets.js
docs/articles/plotting_files/plotly-binding-4.10.1/plotly.js
docs/articles/plotting_files/plotly-binding-4.10.3/plotly.js
docs/articles/plotting_files/plotly-htmlwidgets-css-2.11.1/plotly-htmlwidgets.css
docs/articles/plotting_files/plotly-main-2.11.1/plotly-latest.min.js
docs/articles/plotting_files/typedarray-0.1/typedarray.min.js
docs/articles/publications.html
docs/articles/running_a_simulation.html
docs/articles/running_a_simulation_files/figure-html/plotFMort-1.png
docs/articles/running_a_simulation_files/figure-html/plot_basic_ms_sim-1.png
docs/articles/single_species_size-spectrum_dynamics.html
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-11-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-12-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-20-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-25-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-27-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-31-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-36-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-39-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-4-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-40-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-42-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-47-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-48-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-5-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-51-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-54-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-55-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-56-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-57-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-60-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-61-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-62-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-63-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-64-1.png
docs/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-67-1.png
docs/articles/trait_model.html
docs/articles/trait_model_files/figure-html/plot_comm_sim_2-1.png
docs/articles/trait_model_files/figure-html/plot_multi_gear_trait-1.png
docs/articles/trait_model_files/figure-html/plot_multi_gear_trait_single_effort-1.png
docs/articles/trait_model_files/figure-html/plot_relative_comm_abund2-1.png
docs/articles/trait_model_files/figure-html/plot_relative_comm_abund_industrial-1.png
docs/articles/trait_model_files/figure-html/plot_relative_trait_m2-1.png
docs/articles/trait_model_files/figure-html/plot_trait_fmort-1.png
docs/articles/working_with_git.html
docs/authors.html
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.2.2/bootstrap.min.css
docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js
docs/deps/bootstrap-5.3.1/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.3.1/bootstrap.min.css
docs/deps/data-deps.txt
docs/deps/jquery-3.6.0/jquery-3.6.0.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.map
docs/dev/CONTRIBUTING.html
docs/dev/apple-touch-icon-120x120.png
docs/dev/apple-touch-icon-152x152.png
docs/dev/apple-touch-icon-180x180.png
docs/dev/apple-touch-icon-60x60.png
docs/dev/apple-touch-icon-76x76.png
docs/dev/apple-touch-icon.png
docs/dev/articles/a_multispecies_model_of_the_north_sea.html
docs/dev/articles/a_multispecies_model_of_the_north_sea_files/figure-html/plot_ns_biomass-1.png
docs/dev/articles/a_multispecies_model_of_the_north_sea_files/figure-html/plot_ns_indicators-1.png
docs/dev/articles/a_multispecies_model_of_the_north_sea_files/figure-html/projected_ssb_ns-1.png
docs/dev/articles/community_model.html
docs/dev/articles/community_model_files/figure-html/plot_comm_biomass_sigma1-1.png
docs/dev/articles/community_model_files/figure-html/plot_relative_comm_abund-1.png
docs/dev/articles/community_model_files/figure-html/print_plot_comm_fmort-1.png
docs/dev/articles/community_model_files/figure-html/print_plot_comm_m2-1.png
docs/dev/articles/community_model_files/figure-html/print_plot_comm_sim-1.png
docs/dev/articles/community_model_files/figure-html/unnamed-chunk-4-1.png
docs/dev/articles/developer_FAQ.html
docs/dev/articles/developer_vignette.html
docs/dev/articles/editing_website.html
docs/dev/articles/exploring_the_simulation_results.html
docs/dev/articles/exploring_the_simulation_results_files/figure-html/demo_summary_plot-1.png
docs/dev/articles/exploring_the_simulation_results_files/figure-html/plotBiomass-1.png
docs/dev/articles/exploring_the_simulation_results_files/figure-html/plotSpectra_example-1.png
docs/dev/articles/images/build.png
docs/dev/articles/images/build_tools.png
docs/dev/articles/images/cheat_sheet.pdf
docs/dev/articles/images/cheat_sheet_preview.png
docs/dev/articles/images/commit.png
docs/dev/articles/images/commit_button.png
docs/dev/articles/images/fork.png
docs/dev/articles/images/git.png
docs/dev/articles/images/new_branch_button.png
docs/dev/articles/images/new_project.png
docs/dev/articles/images/outline.png
docs/dev/articles/images/recently_pushed.png
docs/dev/articles/images/repository.png
docs/dev/articles/images/repro_url.png
docs/dev/articles/images/roxygen.png
docs/dev/articles/images/tabs.png
docs/dev/articles/images/tick.png
docs/dev/articles/images/version_control.png
docs/dev/articles/index.html
docs/dev/articles/mizer.html
docs/dev/articles/mizer_files/figure-html/unnamed-chunk-8-1.png
docs/dev/articles/model_description.html
docs/dev/articles/model_description_files/figure-html/unnamed-chunk-1-1.png
docs/dev/articles/multispecies_model.html
docs/dev/articles/plotting.html
docs/dev/articles/plotting_files/crosstalk-1.2.0/css/crosstalk.min.css
docs/dev/articles/plotting_files/crosstalk-1.2.0/js/crosstalk.js
docs/dev/articles/plotting_files/crosstalk-1.2.0/js/crosstalk.js.map
docs/dev/articles/plotting_files/crosstalk-1.2.0/js/crosstalk.min.js
docs/dev/articles/plotting_files/crosstalk-1.2.0/js/crosstalk.min.js.map
docs/dev/articles/plotting_files/crosstalk-1.2.0/scss/crosstalk.scss
docs/dev/articles/plotting_files/figure-html/unnamed-chunk-12-1.png
docs/dev/articles/plotting_files/figure-html/unnamed-chunk-13-1.png
docs/dev/articles/plotting_files/figure-html/unnamed-chunk-15-1.png
docs/dev/articles/plotting_files/figure-html/unnamed-chunk-22-1.png
docs/dev/articles/plotting_files/figure-html/unnamed-chunk-27-1.png
docs/dev/articles/plotting_files/figure-html/unnamed-chunk-28-1.png
docs/dev/articles/plotting_files/figure-html/unnamed-chunk-29-1.png
docs/dev/articles/plotting_files/figure-html/unnamed-chunk-34-1.png
docs/dev/articles/plotting_files/figure-html/unnamed-chunk-36-1.png
docs/dev/articles/plotting_files/figure-html/unnamed-chunk-37-1.png
docs/dev/articles/plotting_files/figure-html/unnamed-chunk-39-1.png
docs/dev/articles/plotting_files/figure-html/unnamed-chunk-40-1.png
docs/dev/articles/plotting_files/figure-html/unnamed-chunk-7-1.png
docs/dev/articles/plotting_files/figure-html/unnamed-chunk-9-1.png
docs/dev/articles/plotting_files/htmlwidgets-1.5.4/htmlwidgets.js
docs/dev/articles/plotting_files/htmlwidgets-1.6.0/htmlwidgets.js
docs/dev/articles/plotting_files/plotly-binding-4.10.1/plotly.js
docs/dev/articles/plotting_files/plotly-htmlwidgets-css-2.11.1/plotly-htmlwidgets.css
docs/dev/articles/plotting_files/plotly-main-2.11.1/plotly-latest.min.js
docs/dev/articles/plotting_files/typedarray-0.1/typedarray.min.js
docs/dev/articles/publications.html
docs/dev/articles/running_a_simulation.html
docs/dev/articles/running_a_simulation_files/figure-html/plotFMort-1.png
docs/dev/articles/running_a_simulation_files/figure-html/plot_basic_ms_sim-1.png
docs/dev/articles/single_species_size-spectrum_dynamics.html
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-11-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-12-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-20-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-25-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-27-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-31-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-36-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-39-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-4-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-40-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-42-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-47-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-48-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-5-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-51-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-54-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-55-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-56-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-57-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-60-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-61-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-62-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-63-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-64-1.png
docs/dev/articles/single_species_size-spectrum_dynamics_files/figure-html/unnamed-chunk-67-1.png
docs/dev/articles/trait_model.html
docs/dev/articles/trait_model_files/figure-html/plot_comm_sim_2-1.png
docs/dev/articles/trait_model_files/figure-html/plot_multi_gear_trait-1.png
docs/dev/articles/trait_model_files/figure-html/plot_multi_gear_trait_single_effort-1.png
docs/dev/articles/trait_model_files/figure-html/plot_relative_comm_abund2-1.png
docs/dev/articles/trait_model_files/figure-html/plot_relative_comm_abund_industrial-1.png
docs/dev/articles/trait_model_files/figure-html/plot_relative_trait_m2-1.png
docs/dev/articles/trait_model_files/figure-html/plot_trait_fmort-1.png
docs/dev/articles/working_with_git.html
docs/dev/authors.html
docs/dev/deps/bootstrap-5.1.3/bootstrap.bundle.min.js
docs/dev/deps/bootstrap-5.1.3/bootstrap.bundle.min.js.map
docs/dev/deps/bootstrap-5.1.3/bootstrap.min.css
docs/dev/deps/bootstrap-5.2.2/bootstrap.bundle.min.js
docs/dev/deps/bootstrap-5.2.2/bootstrap.bundle.min.js.map
docs/dev/deps/bootstrap-5.2.2/bootstrap.min.css
docs/dev/deps/data-deps.txt
docs/dev/deps/jquery-3.6.0/jquery-3.6.0.js
docs/dev/deps/jquery-3.6.0/jquery-3.6.0.min.js
docs/dev/deps/jquery-3.6.0/jquery-3.6.0.min.map
docs/dev/favicon-16x16.png
docs/dev/favicon-32x32.png
docs/dev/favicon.ico
docs/dev/index.html
docs/dev/link.svg
docs/dev/logo.png
docs/dev/news/index.html
docs/dev/pkgdown.js
docs/dev/pkgdown.yml
docs/dev/reference/BevertonHoltRDD.html
docs/dev/reference/MizerParams-class.html
docs/dev/reference/MizerParams.html
docs/dev/reference/MizerSim-class.html
docs/dev/reference/MizerSim.html
docs/dev/reference/N.html
docs/dev/reference/NOther.html
docs/dev/reference/NS_interaction.html
docs/dev/reference/NS_params.html
docs/dev/reference/NS_sim.html
docs/dev/reference/NS_species_params.html
docs/dev/reference/NS_species_params_gears.html
docs/dev/reference/RickerRDD.html
docs/dev/reference/Rplot001.png
docs/dev/reference/Rplot002.png
docs/dev/reference/Rplot003.png
docs/dev/reference/Rplot004.png
docs/dev/reference/Rplot005.png
docs/dev/reference/Rplot006.png
docs/dev/reference/SheperdRDD.html
docs/dev/reference/addSpecies-1.png
docs/dev/reference/addSpecies.html
docs/dev/reference/age_mat.html
docs/dev/reference/age_mat_vB.html
docs/dev/reference/animateSpectra.html
docs/dev/reference/balance_resource_logistic.html
docs/dev/reference/balance_resource_semichemostat.html
docs/dev/reference/box_pred_kernel.html
docs/dev/reference/calibrateBiomass-1.png
docs/dev/reference/calibrateBiomass.html
docs/dev/reference/calibrateNumber.html
docs/dev/reference/calibrateYield-1.png
docs/dev/reference/calibrateYield.html
docs/dev/reference/compareParams.html
docs/dev/reference/constantEggRDI.html
docs/dev/reference/constantRDD.html
docs/dev/reference/constant_other.html
docs/dev/reference/customFunction.html
docs/dev/reference/default_pred_kernel_params.html
docs/dev/reference/defaults_edition.html
docs/dev/reference/different.html
docs/dev/reference/distanceMaxRelRDI.html
docs/dev/reference/distanceSSLogN.html
docs/dev/reference/double_sigmoid_length.html
docs/dev/reference/emptyParams.html
docs/dev/reference/figures/Beverton-Holt-plot-1.png
docs/dev/reference/figures/lifecycle-archived.svg
docs/dev/reference/figures/lifecycle-defunct.svg
docs/dev/reference/figures/lifecycle-deprecated.svg
docs/dev/reference/figures/lifecycle-experimental.svg
docs/dev/reference/figures/lifecycle-maturing.svg
docs/dev/reference/figures/lifecycle-questioning.svg
docs/dev/reference/figures/lifecycle-soft-deprecated.svg
docs/dev/reference/figures/lifecycle-stable.svg
docs/dev/reference/figures/lifecycle-superseded.svg
docs/dev/reference/figures/logo.png
docs/dev/reference/figures/mizer.png
docs/dev/reference/figures/mizer_twitter.jpeg
docs/dev/reference/figures/unnamed-chunk-4-1.png
docs/dev/reference/finalN.html
docs/dev/reference/finalNOther.html
docs/dev/reference/gear_params.html
docs/dev/reference/getBiomass.html
docs/dev/reference/getCommunitySlope.html
docs/dev/reference/getComponent.html
docs/dev/reference/getCriticalFeedingLevel.html
docs/dev/reference/getDiet.html
docs/dev/reference/getEGrowth.html
docs/dev/reference/getERepro.html
docs/dev/reference/getEReproAndGrowth.html
docs/dev/reference/getESpawning.html
docs/dev/reference/getEffort.html
docs/dev/reference/getEncounter.html
docs/dev/reference/getFMort.html
docs/dev/reference/getFMortGear.html
docs/dev/reference/getFeedingLevel.html
docs/dev/reference/getGrowthCurves-1.png
docs/dev/reference/getGrowthCurves.html
docs/dev/reference/getInteraction.html
docs/dev/reference/getM2.html
docs/dev/reference/getM2Background.html
docs/dev/reference/getMeanMaxWeight.html
docs/dev/reference/getMeanWeight.html
docs/dev/reference/getMort.html
docs/dev/reference/getN.html
docs/dev/reference/getParams.html
docs/dev/reference/getPhiPrey.html
docs/dev/reference/getPredMort.html
docs/dev/reference/getPredRate.html
docs/dev/reference/getProportionOfLargeFish.html
docs/dev/reference/getRDD.html
docs/dev/reference/getRDI.html
docs/dev/reference/getRates.html
docs/dev/reference/getReproductionLevel.html
docs/dev/reference/getResourceDynamics.html
docs/dev/reference/getResourceMort.html
docs/dev/reference/getSSB.html
docs/dev/reference/getTimes.html
docs/dev/reference/getYield.html
docs/dev/reference/getYieldGear.html
docs/dev/reference/getZ.html
docs/dev/reference/get_f0_default.html
docs/dev/reference/get_gamma_default.html
docs/dev/reference/get_h_default.html
docs/dev/reference/get_initial_n.html
docs/dev/reference/get_ks_default.html
docs/dev/reference/get_phi.html
docs/dev/reference/get_required_reproduction.html
docs/dev/reference/get_size_range_array.html
docs/dev/reference/get_time_elements.html
docs/dev/reference/idxFinalT.html
docs/dev/reference/index.html
docs/dev/reference/indicator_functions.html
docs/dev/reference/initialN-set.html
docs/dev/reference/initialNOther-set.html
docs/dev/reference/initialNResource-set.html
docs/dev/reference/initial_effort.html
docs/dev/reference/inter.html
docs/dev/reference/knife_edge.html
docs/dev/reference/l2w.html
docs/dev/reference/libs/crosstalk-1.2.0/css/crosstalk.min.css
docs/dev/reference/libs/crosstalk-1.2.0/js/crosstalk.js
docs/dev/reference/libs/crosstalk-1.2.0/js/crosstalk.js.map
docs/dev/reference/libs/crosstalk-1.2.0/js/crosstalk.min.js
docs/dev/reference/libs/crosstalk-1.2.0/js/crosstalk.min.js.map
docs/dev/reference/libs/crosstalk-1.2.0/scss/crosstalk.scss
docs/dev/reference/libs/htmlwidgets-1.5.4/htmlwidgets.js
docs/dev/reference/libs/htmlwidgets-1.6.0/htmlwidgets.js
docs/dev/reference/libs/plotly-binding-4.10.1/plotly.js
docs/dev/reference/libs/plotly-htmlwidgets-css-2.11.1/plotly-htmlwidgets.css
docs/dev/reference/libs/plotly-main-2.11.1/plotly-latest.min.js
docs/dev/reference/libs/typedarray-0.1/typedarray.min.js
docs/dev/reference/log_breaks.html
docs/dev/reference/lognormal_pred_kernel.html
docs/dev/reference/matchBiomasses-1.png
docs/dev/reference/matchBiomasses.html
docs/dev/reference/matchGrowth.html
docs/dev/reference/matchNumbers.html
docs/dev/reference/matchYields-1.png
docs/dev/reference/matchYields.html
docs/dev/reference/mizer-package.html
docs/dev/reference/mizerEGrowth.html
docs/dev/reference/mizerERepro.html
docs/dev/reference/mizerEReproAndGrowth.html
docs/dev/reference/mizerEncounter.html
docs/dev/reference/mizerFMort.html
docs/dev/reference/mizerFMortGear.html
docs/dev/reference/mizerFeedingLevel.html
docs/dev/reference/mizerMort.html
docs/dev/reference/mizerPredMort.html
docs/dev/reference/mizerPredRate.html
docs/dev/reference/mizerRDI.html
docs/dev/reference/mizerRates.html
docs/dev/reference/mizerResourceMort.html
docs/dev/reference/needs_upgrading.html
docs/dev/reference/newCommunityParams-1.png
docs/dev/reference/newCommunityParams-2.png
docs/dev/reference/newCommunityParams-3.png
docs/dev/reference/newCommunityParams-4.png
docs/dev/reference/newCommunityParams.html
docs/dev/reference/newMultispeciesParams.html
docs/dev/reference/newSingleSpeciesParams-1.png
docs/dev/reference/newSingleSpeciesParams.html
docs/dev/reference/newTraitParams-1.png
docs/dev/reference/newTraitParams.html
docs/dev/reference/noRDD.html
docs/dev/reference/plotBiomass-1.png
docs/dev/reference/plotBiomass-2.png
docs/dev/reference/plotBiomass-3.png
docs/dev/reference/plotBiomass.html
docs/dev/reference/plotBiomassObservedVsModel-1.png
docs/dev/reference/plotBiomassObservedVsModel-2.png
docs/dev/reference/plotBiomassObservedVsModel-3.png
docs/dev/reference/plotBiomassObservedVsModel-4.png
docs/dev/reference/plotBiomassObservedVsModel-5.png
docs/dev/reference/plotBiomassObservedVsModel-6.png
docs/dev/reference/plotBiomassObservedVsModel.html
docs/dev/reference/plotDataFrame.html
docs/dev/reference/plotDiet-1.png
docs/dev/reference/plotDiet-2.png
docs/dev/reference/plotDiet.html
docs/dev/reference/plotFMort-1.png
docs/dev/reference/plotFMort-2.png
docs/dev/reference/plotFMort.html
docs/dev/reference/plotFeedingLevel-1.png
docs/dev/reference/plotFeedingLevel-2.png
docs/dev/reference/plotFeedingLevel.html
docs/dev/reference/plotGrowthCurves-1.png
docs/dev/reference/plotGrowthCurves-2.png
docs/dev/reference/plotGrowthCurves-3.png
docs/dev/reference/plotGrowthCurves.html
docs/dev/reference/plotM2-1.png
docs/dev/reference/plotM2-2.png
docs/dev/reference/plotM2.html
docs/dev/reference/plotMizerSim-1.png
docs/dev/reference/plotMizerSim-2.png
docs/dev/reference/plotMizerSim-3.png
docs/dev/reference/plotMizerSim-4.png
docs/dev/reference/plotMizerSim-5.png
docs/dev/reference/plotMizerSim.html
docs/dev/reference/plotPredMort-1.png
docs/dev/reference/plotPredMort-2.png
docs/dev/reference/plotPredMort.html
docs/dev/reference/plotSpectra-1.png
docs/dev/reference/plotSpectra-2.png
docs/dev/reference/plotSpectra-3.png
docs/dev/reference/plotSpectra-4.png
docs/dev/reference/plotSpectra-5.png
docs/dev/reference/plotSpectra.html
docs/dev/reference/plotYield-1.png
docs/dev/reference/plotYield-2.png
docs/dev/reference/plotYield-3.png
docs/dev/reference/plotYield.html
docs/dev/reference/plotYieldGear-1.png
docs/dev/reference/plotYieldGear-2.png
docs/dev/reference/plotYieldGear.html
docs/dev/reference/plotYieldObservedVsModel-1.png
docs/dev/reference/plotYieldObservedVsModel-2.png
docs/dev/reference/plotYieldObservedVsModel-3.png
docs/dev/reference/plotYieldObservedVsModel-4.png
docs/dev/reference/plotYieldObservedVsModel-5.png
docs/dev/reference/plotYieldObservedVsModel-6.png
docs/dev/reference/plotYieldObservedVsModel.html
docs/dev/reference/plotting_functions-1.png
docs/dev/reference/plotting_functions-2.png
docs/dev/reference/plotting_functions-3.png
docs/dev/reference/plotting_functions-4.png
docs/dev/reference/plotting_functions.html
docs/dev/reference/power_law_pred_kernel.html
docs/dev/reference/project.html
docs/dev/reference/projectToSteady.html
docs/dev/reference/project_simple.html
docs/dev/reference/reexports.html
docs/dev/reference/removeSpecies.html
docs/dev/reference/renameSpecies.html
docs/dev/reference/resource_capacity.html
docs/dev/reference/resource_constant.html
docs/dev/reference/resource_dynamics.html
docs/dev/reference/resource_logistic.html
docs/dev/reference/resource_params.html
docs/dev/reference/resource_rate.html
docs/dev/reference/resource_semichemostat.html
docs/dev/reference/saveParams.html
docs/dev/reference/scaleModel.html
docs/dev/reference/setBevertonHolt.html
docs/dev/reference/setColours-1.png
docs/dev/reference/setColours.html
docs/dev/reference/setComponent.html
docs/dev/reference/setExtMort.html
docs/dev/reference/setFishing.html
docs/dev/reference/setInitialValues.html
docs/dev/reference/setInteraction.html
docs/dev/reference/setMaxIntakeRate.html
docs/dev/reference/setMetabolicRate.html
docs/dev/reference/setMetadata.html
docs/dev/reference/setParams.html
docs/dev/reference/setPredKernel.html
docs/dev/reference/setRateFunction.html
docs/dev/reference/setReproduction-1.png
docs/dev/reference/setReproduction.html
docs/dev/reference/setResource.html
docs/dev/reference/setResourceLogistic.html
docs/dev/reference/setResourceSemichemostat.html
docs/dev/reference/setRmax.html
docs/dev/reference/setSearchVolume.html
docs/dev/reference/set_community_model.html
docs/dev/reference/set_multispecies_model.html
docs/dev/reference/set_species_param_default.html
docs/dev/reference/set_trait_model.html
docs/dev/reference/sigmoid_length.html
docs/dev/reference/sigmoid_weight.html
docs/dev/reference/species_params.html
docs/dev/reference/steady.html
docs/dev/reference/steadySingleSpecies.html
docs/dev/reference/summary-MizerParams-method.html
docs/dev/reference/summary-MizerSim-method.html
docs/dev/reference/summary_functions.html
docs/dev/reference/truncated_lognormal_pred_kernel.html
docs/dev/reference/upgradeParams.html
docs/dev/reference/upgradeSim.html
docs/dev/reference/validGearParams.html
docs/dev/reference/validParams.html
docs/dev/reference/validSpeciesParams.html
docs/dev/reference/valid_species_arg.html
docs/dev/reference/w.html
docs/dev/search.json
docs/dev/sitemap.xml
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/news/index.html
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/BevertonHoltRDD.html
docs/reference/MizerParams-class.html
docs/reference/MizerParams.html
docs/reference/MizerSim-class.html
docs/reference/MizerSim.html
docs/reference/N.html
docs/reference/NOther.html
docs/reference/NS_interaction.html
docs/reference/NS_params-1.png
docs/reference/NS_params.html
docs/reference/NS_sim-1.png
docs/reference/NS_sim.html
docs/reference/NS_species_params.html
docs/reference/NS_species_params_gears.html
docs/reference/RickerRDD.html
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/Rplot003.png
docs/reference/Rplot004.png
docs/reference/Rplot005.png
docs/reference/SheperdRDD.html
docs/reference/addSpecies-1.png
docs/reference/addSpecies.html
docs/reference/age_mat.html
docs/reference/age_mat_vB.html
docs/reference/animateSpectra.html
docs/reference/balance_resource_logistic.html
docs/reference/balance_resource_semichemostat.html
docs/reference/box_pred_kernel.html
docs/reference/calibrateBiomass-1.png
docs/reference/calibrateBiomass.html
docs/reference/calibrateNumber.html
docs/reference/calibrateYield-1.png
docs/reference/calibrateYield.html
docs/reference/compareParams.html
docs/reference/completeSpeciesParams.html
docs/reference/constantEggRDI.html
docs/reference/constantRDD.html
docs/reference/constant_other.html
docs/reference/customFunction.html
docs/reference/default_pred_kernel_params.html
docs/reference/defaults_edition.html
docs/reference/different.html
docs/reference/distanceMaxRelRDI.html
docs/reference/distanceSSLogN.html
docs/reference/double_sigmoid_length.html
docs/reference/emptyParams.html
docs/reference/figures/Beverton-Holt-plot-1.png
docs/reference/figures/lifecycle-archived.svg
docs/reference/figures/lifecycle-defunct.svg
docs/reference/figures/lifecycle-deprecated.svg
docs/reference/figures/lifecycle-experimental.svg
docs/reference/figures/lifecycle-maturing.svg
docs/reference/figures/lifecycle-questioning.svg
docs/reference/figures/lifecycle-soft-deprecated.svg
docs/reference/figures/lifecycle-stable.svg
docs/reference/figures/logo.png
docs/reference/figures/mizer.png
docs/reference/figures/mizer_twitter.jpeg
docs/reference/figures/unnamed-chunk-4-1.png
docs/reference/finalN.html
docs/reference/finalNOther.html
docs/reference/gear_params.html
docs/reference/getBiomass.html
docs/reference/getCommunitySlope.html
docs/reference/getComponent.html
docs/reference/getCriticalFeedingLevel.html
docs/reference/getDiet.html
docs/reference/getEGrowth.html
docs/reference/getERepro.html
docs/reference/getEReproAndGrowth.html
docs/reference/getESpawning.html
docs/reference/getEffort.html
docs/reference/getEncounter.html
docs/reference/getFMort.html
docs/reference/getFMortGear.html
docs/reference/getFeedingLevel.html
docs/reference/getGrowthCurves-1.png
docs/reference/getGrowthCurves.html
docs/reference/getInteraction.html
docs/reference/getM2.html
docs/reference/getM2Background.html
docs/reference/getMeanMaxWeight.html
docs/reference/getMeanWeight.html
docs/reference/getMort.html
docs/reference/getN.html
docs/reference/getParams.html
docs/reference/getPhiPrey.html
docs/reference/getPredMort.html
docs/reference/getPredRate.html
docs/reference/getProportionOfLargeFish.html
docs/reference/getRDD.html
docs/reference/getRDI.html
docs/reference/getRates.html
docs/reference/getReproductionLevel.html
docs/reference/getResourceDynamics.html
docs/reference/getResourceMort.html
docs/reference/getSSB.html
docs/reference/getTimes.html
docs/reference/getYield.html
docs/reference/getYieldGear.html
docs/reference/getZ.html
docs/reference/get_f0_default.html
docs/reference/get_gamma_default.html
docs/reference/get_h_default.html
docs/reference/get_initial_n.html
docs/reference/get_ks_default.html
docs/reference/get_phi.html
docs/reference/get_required_reproduction.html
docs/reference/get_size_range_array.html
docs/reference/get_time_elements.html
docs/reference/idxFinalT.html
docs/reference/index.html
docs/reference/indicator_functions.html
docs/reference/initialN-set.html
docs/reference/initialNOther-set.html
docs/reference/initialNResource-set.html
docs/reference/initial_effort.html
docs/reference/inter.html
docs/reference/knife_edge.html
docs/reference/l2w.html
docs/reference/libs/crosstalk-1.2.0/css/crosstalk.min.css
docs/reference/libs/crosstalk-1.2.0/js/crosstalk.js
docs/reference/libs/crosstalk-1.2.0/js/crosstalk.js.map
docs/reference/libs/crosstalk-1.2.0/js/crosstalk.min.js
docs/reference/libs/crosstalk-1.2.0/js/crosstalk.min.js.map
docs/reference/libs/crosstalk-1.2.0/scss/crosstalk.scss
docs/reference/libs/crosstalk-1.2.1/css/crosstalk.min.css
docs/reference/libs/crosstalk-1.2.1/js/crosstalk.js
docs/reference/libs/crosstalk-1.2.1/js/crosstalk.js.map
docs/reference/libs/crosstalk-1.2.1/js/crosstalk.min.js
docs/reference/libs/crosstalk-1.2.1/js/crosstalk.min.js.map
docs/reference/libs/crosstalk-1.2.1/scss/crosstalk.scss
docs/reference/libs/htmlwidgets-1.6.0/htmlwidgets.js
docs/reference/libs/htmlwidgets-1.6.2/htmlwidgets.js
docs/reference/libs/htmlwidgets-1.6.4/htmlwidgets.js
docs/reference/libs/plotly-binding-4.10.1/plotly.js
docs/reference/libs/plotly-binding-4.10.3/plotly.js
docs/reference/libs/plotly-htmlwidgets-css-2.11.1/plotly-htmlwidgets.css
docs/reference/libs/plotly-main-2.11.1/plotly-latest.min.js
docs/reference/libs/typedarray-0.1/typedarray.min.js
docs/reference/log_breaks.html
docs/reference/lognormal_pred_kernel.html
docs/reference/matchBiomasses-1.png
docs/reference/matchBiomasses.html
docs/reference/matchGrowth.html
docs/reference/matchNumbers.html
docs/reference/matchYields-1.png
docs/reference/matchYields.html
docs/reference/mizer-package.html
docs/reference/mizerEGrowth.html
docs/reference/mizerERepro.html
docs/reference/mizerEReproAndGrowth.html
docs/reference/mizerEncounter.html
docs/reference/mizerFMort.html
docs/reference/mizerFMortGear.html
docs/reference/mizerFeedingLevel.html
docs/reference/mizerMort.html
docs/reference/mizerPredMort.html
docs/reference/mizerPredRate.html
docs/reference/mizerRDI.html
docs/reference/mizerRates.html
docs/reference/mizerResourceMort.html
docs/reference/needs_upgrading.html
docs/reference/newCommunityParams-1.png
docs/reference/newCommunityParams-2.png
docs/reference/newCommunityParams-3.png
docs/reference/newCommunityParams-4.png
docs/reference/newCommunityParams.html
docs/reference/newMultispeciesParams.html
docs/reference/newSingleSpeciesParams-1.png
docs/reference/newSingleSpeciesParams.html
docs/reference/newTraitParams-1.png
docs/reference/newTraitParams.html
docs/reference/noRDD.html
docs/reference/plotBiomass-1.png
docs/reference/plotBiomass-2.png
docs/reference/plotBiomass-3.png
docs/reference/plotBiomass.html
docs/reference/plotBiomassObservedVsModel-1.png
docs/reference/plotBiomassObservedVsModel-2.png
docs/reference/plotBiomassObservedVsModel-3.png
docs/reference/plotBiomassObservedVsModel.html
docs/reference/plotDataFrame.html
docs/reference/plotDiet-1.png
docs/reference/plotDiet-2.png
docs/reference/plotDiet.html
docs/reference/plotFMort-1.png
docs/reference/plotFMort-2.png
docs/reference/plotFMort.html
docs/reference/plotFeedingLevel-1.png
docs/reference/plotFeedingLevel-2.png
docs/reference/plotFeedingLevel.html
docs/reference/plotGrowthCurves-1.png
docs/reference/plotGrowthCurves-2.png
docs/reference/plotGrowthCurves-3.png
docs/reference/plotGrowthCurves.html
docs/reference/plotM2-1.png
docs/reference/plotM2-2.png
docs/reference/plotM2.html
docs/reference/plotMizerSim-1.png
docs/reference/plotMizerSim-2.png
docs/reference/plotMizerSim-3.png
docs/reference/plotMizerSim-4.png
docs/reference/plotMizerSim-5.png
docs/reference/plotMizerSim.html
docs/reference/plotPredMort-1.png
docs/reference/plotPredMort-2.png
docs/reference/plotPredMort.html
docs/reference/plotSpectra-1.png
docs/reference/plotSpectra-2.png
docs/reference/plotSpectra-3.png
docs/reference/plotSpectra-4.png
docs/reference/plotSpectra-5.png
docs/reference/plotSpectra.html
docs/reference/plotYield-1.png
docs/reference/plotYield-2.png
docs/reference/plotYield-3.png
docs/reference/plotYield.html
docs/reference/plotYieldGear-1.png
docs/reference/plotYieldGear-2.png
docs/reference/plotYieldGear.html
docs/reference/plotYieldObservedVsModel-1.png
docs/reference/plotYieldObservedVsModel-2.png
docs/reference/plotYieldObservedVsModel-3.png
docs/reference/plotYieldObservedVsModel.html
docs/reference/plotting_functions-1.png
docs/reference/plotting_functions-2.png
docs/reference/plotting_functions-3.png
docs/reference/plotting_functions-4.png
docs/reference/plotting_functions.html
docs/reference/power_law_pred_kernel.html
docs/reference/project.html
docs/reference/projectToSteady.html
docs/reference/project_simple.html
docs/reference/reexports.html
docs/reference/removeSpecies.html
docs/reference/renameSpecies.html
docs/reference/resource_constant.html
docs/reference/resource_logistic.html
docs/reference/resource_params.html
docs/reference/resource_semichemostat.html
docs/reference/saveParams.html
docs/reference/scaleModel.html
docs/reference/setBevertonHolt.html
docs/reference/setColours-1.png
docs/reference/setColours.html
docs/reference/setComponent.html
docs/reference/setExtEncounter.html
docs/reference/setExtMort.html
docs/reference/setFishing.html
docs/reference/setInitialValues.html
docs/reference/setInteraction.html
docs/reference/setMaxIntakeRate.html
docs/reference/setMetabolicRate.html
docs/reference/setMetadata.html
docs/reference/setParams.html
docs/reference/setPredKernel-1.png
docs/reference/setPredKernel.html
docs/reference/setRateFunction.html
docs/reference/setReproduction-1.png
docs/reference/setReproduction.html
docs/reference/setResource.html
docs/reference/setRmax.html
docs/reference/setSearchVolume.html
docs/reference/set_community_model-1.png
docs/reference/set_community_model-2.png
docs/reference/set_community_model.html
docs/reference/set_multispecies_model.html
docs/reference/set_species_param_default.html
docs/reference/set_trait_model.html
docs/reference/sigmoid_length.html
docs/reference/sigmoid_weight.html
docs/reference/species_params.html
docs/reference/steady-1.png
docs/reference/steady.html
docs/reference/steadySingleSpecies.html
docs/reference/summary-MizerParams-method.html
docs/reference/summary-MizerSim-method.html
docs/reference/summary_functions.html
docs/reference/truncated_lognormal_pred_kernel.html
docs/reference/upgradeParams.html
docs/reference/upgradeSim.html
docs/reference/validGearParams.html
docs/reference/validParams.html
docs/reference/validSpeciesParams.html
docs/reference/valid_species_arg.html
docs/reference/w.html
docs/search.json
docs/sitemap.xml
inst/WORDLIST
inst/examples/supplementary_material.R
inst/extdata/NS_f_history.csv
inst/extdata/NS_interaction.csv
inst/extdata/NS_species_params.csv
inst/shiny/selectivity_effects/app.R
inst/shiny/selectivity_effects/hake_mullet.RDS
inst/shiny/selectivity_effects/www/logo_minouw_blue.png
man/BevertonHoltRDD.Rd man/MizerParams-class.Rd man/MizerParams.Rd man/MizerSim-class.Rd man/MizerSim.Rd man/N.Rd man/NOther.Rd man/NS_interaction.Rd man/NS_params.Rd man/NS_sim.Rd man/NS_species_params.Rd man/NS_species_params_gears.Rd man/RickerRDD.Rd man/SheperdRDD.Rd man/addSpecies.Rd man/age_mat.Rd man/age_mat_vB.Rd man/animateSpectra.Rd man/box_pred_kernel.Rd man/calc_selectivity.Rd man/calibrateBiomass.Rd man/calibrateNumber.Rd man/calibrateYield.Rd man/compareParams.Rd man/completeSpeciesParams.Rd man/constantEggRDI.Rd man/constantRDD.Rd man/constant_other.Rd man/customFunction.Rd man/default_pred_kernel_params.Rd man/defaults_edition.Rd man/different.Rd man/distanceMaxRelRDI.Rd man/distanceSSLogN.Rd man/double_sigmoid_length.Rd man/emptyParams.Rd
man/figures/Beverton-Holt-plot-1.png
man/figures/lifecycle-archived.svg
man/figures/lifecycle-defunct.svg
man/figures/lifecycle-deprecated.svg
man/figures/lifecycle-experimental.svg
man/figures/lifecycle-maturing.svg
man/figures/lifecycle-questioning.svg
man/figures/lifecycle-soft-deprecated.svg
man/figures/lifecycle-stable.svg
man/figures/logo.png
man/figures/mizer.png
man/figures/mizer_twitter.jpeg
man/figures/unnamed-chunk-4-1.png
man/finalN.Rd man/finalNOther.Rd man/gear_params.Rd man/getBiomass.Rd man/getCommunitySlope.Rd man/getComponent.Rd man/getCriticalFeedingLevel.Rd man/getDiet.Rd man/getEGrowth.Rd man/getERepro.Rd man/getEReproAndGrowth.Rd man/getESpawning.Rd man/getEffort.Rd man/getEncounter.Rd man/getFMort.Rd man/getFMortGear.Rd man/getFeedingLevel.Rd man/getGrowthCurves.Rd man/getInteraction.Rd man/getM2.Rd man/getM2Background.Rd man/getMeanMaxWeight.Rd man/getMeanWeight.Rd man/getMort.Rd man/getN.Rd man/getParams.Rd man/getPhiPrey.Rd man/getPredMort.Rd man/getPredRate.Rd man/getProportionOfLargeFish.Rd man/getRDD.Rd man/getRDI.Rd man/getRates.Rd man/getReproductionLevel.Rd man/getResourceDynamics.Rd man/getResourceMort.Rd man/getSSB.Rd man/getTimes.Rd man/getYield.Rd man/getYieldGear.Rd man/getZ.Rd man/get_f0_default.Rd man/get_gamma_default.Rd man/get_h_default.Rd man/get_initial_n.Rd man/get_ks_default.Rd man/get_phi.Rd man/get_required_reproduction.Rd man/get_size_range_array.Rd man/get_time_elements.Rd man/idxFinalT.Rd man/indicator_functions.Rd man/initialN-set.Rd man/initialNOther-set.Rd man/initialNResource-set.Rd man/initial_effort.Rd man/inter.Rd man/knife_edge.Rd man/l2w.Rd man/log_breaks.Rd man/lognormal_pred_kernel.Rd man/matchBiomasses.Rd man/matchGrowth.Rd man/matchNumbers.Rd man/matchYields.Rd man/mizer-package.Rd man/mizerEGrowth.Rd man/mizerERepro.Rd man/mizerEReproAndGrowth.Rd man/mizerEncounter.Rd man/mizerFMort.Rd man/mizerFMortGear.Rd man/mizerFeedingLevel.Rd man/mizerMort.Rd man/mizerPredMort.Rd man/mizerPredRate.Rd man/mizerRDI.Rd man/mizerRates.Rd man/mizerResourceMort.Rd man/needs_upgrading.Rd man/newCommunityParams.Rd man/newMultispeciesParams.Rd man/newSingleSpeciesParams.Rd man/newTraitParams.Rd man/noRDD.Rd man/plotBiomass.Rd man/plotBiomassObservedVsModel.Rd man/plotDataFrame.Rd man/plotDiet.Rd man/plotFMort.Rd man/plotFeedingLevel.Rd man/plotGrowthCurves.Rd man/plotM2.Rd man/plotMizerSim.Rd man/plotPredMort.Rd man/plotSpectra.Rd man/plotYield.Rd man/plotYieldGear.Rd man/plotYieldObservedVsModel.Rd man/plotting_functions.Rd man/power_law_pred_kernel.Rd man/project.Rd man/projectToSteady.Rd man/project_simple.Rd man/reexports.Rd man/removeSpecies.Rd man/renameSpecies.Rd man/resource_constant.Rd man/resource_logistic.Rd man/resource_params.Rd man/resource_semichemostat.Rd man/saveParams.Rd man/scaleModel.Rd man/setBevertonHolt.Rd man/setColours.Rd man/setComponent.Rd man/setExtEncounter.Rd man/setExtMort.Rd man/setFishing.Rd man/setInitialValues.Rd man/setInteraction.Rd man/setMaxIntakeRate.Rd man/setMetabolicRate.Rd man/setMetadata.Rd man/setParams.Rd man/setPredKernel.Rd man/setRateFunction.Rd man/setReproduction.Rd man/setResource.Rd man/setRmax.Rd man/setSearchVolume.Rd man/set_community_model.Rd man/set_multispecies_model.Rd man/set_species_param_default.Rd man/set_trait_model.Rd man/sigmoid_length.Rd man/sigmoid_weight.Rd man/species_params.Rd man/steady.Rd man/steadySingleSpecies.Rd man/summary-MizerParams-method.Rd man/summary-MizerSim-method.Rd man/summary_functions.Rd man/truncated_lognormal_pred_kernel.Rd man/upgradeParams.Rd man/upgradeSim.Rd man/validGearParams.Rd man/validParams.Rd man/validSpeciesParams.Rd man/valid_species_arg.Rd man/w.Rd
pkgdown/_pkgdown.yml
pkgdown/favicon/apple-touch-icon-120x120.png
pkgdown/favicon/apple-touch-icon-152x152.png
pkgdown/favicon/apple-touch-icon-180x180.png
pkgdown/favicon/apple-touch-icon-60x60.png
pkgdown/favicon/apple-touch-icon-76x76.png
pkgdown/favicon/apple-touch-icon.png
pkgdown/favicon/favicon-16x16.png
pkgdown/favicon/favicon-32x32.png
pkgdown/favicon/favicon.ico
runtime.txt
src/.gitignore
src/RcppExports.cpp
src/inner_project_loop.cpp
tests/spelling.R tests/testthat.R tests/testthat/_snaps/age_mat.md tests/testthat/_snaps/backwards_compatibility.md
tests/testthat/_snaps/plotBiomassObservedVsModel/plotbiomassobservedvsmodel.svg
tests/testthat/_snaps/plotYieldObservedVsModel/plotyieldobservedvsmodel.svg
tests/testthat/_snaps/plots/plot-biomass.svg
tests/testthat/_snaps/plots/plot-diet.svg
tests/testthat/_snaps/plots/plot-feeding-level-critical.svg
tests/testthat/_snaps/plots/plot-feeding-level.svg
tests/testthat/_snaps/plots/plot-single-growth-curve.svg
tests/testthat/_snaps/plots/plot-spectra.svg
tests/testthat/_snaps/plots/plot-yield-by-gear.svg
tests/testthat/_snaps/plots/plot-yield.svg
tests/testthat/_snaps/plots/plotfishing-mortality.svg
tests/testthat/_snaps/plots/plotfmort-truncated.svg
tests/testthat/_snaps/plots/plotpredation-mortality.svg
tests/testthat/_snaps/project.md tests/testthat/_snaps/project_methods.md tests/testthat/_snaps/steady.md tests/testthat/_snaps/summary_methods.md
tests/testthat/assets/simc.0.4.rds
tests/testthat/assets/simc.1.0.rds
tests/testthat/helper.R tests/testthat/test-MizerParams-class.R tests/testthat/test-MizerSim-class.R tests/testthat/test-age_mat.R tests/testthat/test-analytic_results.R tests/testthat/test-animateSpectra.R tests/testthat/test-backwards_compatibility.R tests/testthat/test-calibrate.R tests/testthat/test-compareParams.R tests/testthat/test-customFunction.R tests/testthat/test-data.R tests/testthat/test-extension.R tests/testthat/test-get_initial_n.R tests/testthat/test-helpers.R tests/testthat/test-manipulate_species.R tests/testthat/test-match.R tests/testthat/test-matchGrowth.R tests/testthat/test-newMultispeciesParams.R tests/testthat/test-newSingleSpeciesParams.R tests/testthat/test-plotBiomassObservedVsModel.R tests/testthat/test-plotYieldObservedVsModel.R tests/testthat/test-plots.R tests/testthat/test-pred_kernel_funcs.R tests/testthat/test-project.R tests/testthat/test-project_methods.R tests/testthat/test-rate_functions.R tests/testthat/test-reproduction.R tests/testthat/test-resource_dynamics.R tests/testthat/test-resource_logistic.R tests/testthat/test-resource_semichemostat.R tests/testthat/test-selectivity_funcs.R tests/testthat/test-setBevertonHolt.R tests/testthat/test-setColours.R tests/testthat/test-setExtEncounter.R tests/testthat/test-setExtMort.R tests/testthat/test-setFishing.R tests/testthat/test-setInitialValues.R tests/testthat/test-setInteraction.R tests/testthat/test-setMaxIntakeRate.R tests/testthat/test-setMetabolicRate.R tests/testthat/test-setMetadata.R tests/testthat/test-setPredKernel.R tests/testthat/test-setReproduction.R tests/testthat/test-setResource.R tests/testthat/test-setSearchVolume.R tests/testthat/test-single_species.R tests/testthat/test-species_params.R tests/testthat/test-steady.R tests/testthat/test-steadySingleSpecies.R tests/testthat/test-summary_methods.R tests/testthat/test-upgrade.R tests/testthat/test-wrapper_functions.R
tests/testthat/values/getBiomass
tests/testthat/values/getCommunitySlope
tests/testthat/values/getDiet
tests/testthat/values/getEGrowth
tests/testthat/values/getERepro
tests/testthat/values/getEReproAndGrowth
tests/testthat/values/getFMort
tests/testthat/values/getFMortGear
tests/testthat/values/getFeedingLevel
tests/testthat/values/getMeanMaxWeight
tests/testthat/values/getMeanWeight
tests/testthat/values/getMort
tests/testthat/values/getN
tests/testthat/values/getPredMort
tests/testthat/values/getPredRate
tests/testthat/values/getProportionOfLargeFish
tests/testthat/values/getRDD
tests/testthat/values/getRDI
tests/testthat/values/getResourceMort
tests/testthat/values/getSSB
tests/testthat/values/getYield
tests/testthat/values/getYieldGear
tests/testthat/values/plotFMort
tests/testthat/values/projectn
tests/testthat/values/projectp
tests/testthat/values/set_community_model_cc_pp
tests/testthat/values/set_community_model_initial_n
tests/testthat/values/set_community_model_initial_n_pp
tests/testthat/values/set_community_model_intake_max
tests/testthat/values/set_community_model_metab
tests/testthat/values/set_community_model_mu_b
tests/testthat/values/set_community_model_pred_rate
tests/testthat/values/set_community_model_psi
tests/testthat/values/set_community_model_rr_pp
tests/testthat/values/set_community_model_search_vol
tests/testthat/values/set_community_phi_prey
tests/testthat/values/set_multispecies_model_cc_pp
tests/testthat/values/set_multispecies_model_initial_n
tests/testthat/values/set_multispecies_model_initial_n_pp
tests/testthat/values/set_multispecies_model_intake_max
tests/testthat/values/set_multispecies_model_maturity
tests/testthat/values/set_multispecies_model_metab
tests/testthat/values/set_multispecies_model_mu_b
tests/testthat/values/set_multispecies_model_phi_prey
tests/testthat/values/set_multispecies_model_pred_rate
tests/testthat/values/set_multispecies_model_psi
tests/testthat/values/set_multispecies_model_rr_pp
tests/testthat/values/set_multispecies_model_search_vol
tests/testthat/values/set_trait_model_cc_pp
tests/testthat/values/set_trait_model_initial_n
tests/testthat/values/set_trait_model_initial_n_pp
tests/testthat/values/set_trait_model_intake_max
tests/testthat/values/set_trait_model_metab
tests/testthat/values/set_trait_model_mu_b
tests/testthat/values/set_trait_model_pred_rate
tests/testthat/values/set_trait_model_psi
tests/testthat/values/set_trait_model_rr_pp
tests/testthat/values/set_trait_model_search_vol
tests/testthat/values/set_trait_phi_prey
tests/testthat/values/steady
vignettes/.gitignore
vignettes/.install_extras
vignettes/Growth_curve.pdf vignettes/Lysekil/_build_model_1.Rmd vignettes/Lysekil/_build_model_2.Rmd vignettes/Lysekil/_build_model_3.Rmd vignettes/_estimating_feeding_kernel_params.Rmd vignettes/a_multispecies_model_of_the_north_sea.Rmd vignettes/community_model.Rmd vignettes/developer_FAQ.Rmd vignettes/developer_vignette.Rmd vignettes/editing_website.Rmd vignettes/exploring_the_simulation_results.Rmd
vignettes/images/build.png
vignettes/images/build_tools.png
vignettes/images/cheat_sheet.pdf
vignettes/images/commit.png
vignettes/images/commit_button.png
vignettes/images/fork.png
vignettes/images/git.png
vignettes/images/new_branch_button.png
vignettes/images/new_project.png
vignettes/images/outline.png
vignettes/images/recently_pushed.png
vignettes/images/repository.png
vignettes/images/repro_url.png
vignettes/images/roxygen.png
vignettes/images/tabs.png
vignettes/images/tick.png
vignettes/images/version_control.png
vignettes/mizer.Rmd vignettes/mizer_vignette.pdf vignettes/model_description.Rmd vignettes/multispecies_model.Rmd vignettes/plotting.Rmd vignettes/publications.Rmd
vignettes/reflib.bib
vignettes/running_a_simulation.Rmd vignettes/single_species_size-spectrum_dynamics.Rmd vignettes/trait_model.Rmd
vignettes/vignette_images/cheat_sheet_preview.png
vignettes/working_with_git.Rmd
sizespectrum/mizer documentation built on April 14, 2024, 3:08 a.m.