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/rhub.yaml
.github/workflows/test-coverage.yaml
.lintr
.nojekyll
.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/validSpeciesParams.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/mizer_vignette.html
docs/articles/mizer_vignette_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-1.2.1/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/htmltools-fill-0.5.8.1/fill.css
docs/articles/plotting_files/htmlwidgets-1.6.4/htmlwidgets.js
docs/articles/plotting_files/plotly-binding-4.10.4/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/MathJax-3.2.2/MathJax_AMS-Regular.woff
docs/deps/MathJax-3.2.2/MathJax_Main-Regular.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_AMS-Regular.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Caligraphic-Bold.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Caligraphic-Regular.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Fraktur-Bold.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Fraktur-Regular.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Main-Bold.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Main-Italic.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Main-Regular.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Math-BoldItalic.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Math-Italic.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Math-Regular.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_SansSerif-Bold.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_SansSerif-Italic.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_SansSerif-Regular.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Script-Regular.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Size1-Regular.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Size2-Regular.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Size3-Regular.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Size4-Regular.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Typewriter-Regular.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Vector-Bold.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Vector-Regular.woff
docs/deps/MathJax-3.2.2/output/chtml/fonts/woff-v2/MathJax_Zero.woff
docs/deps/MathJax-3.2.2/tex-chtml.min.js
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/bootstrap-toc-1.0.1/bootstrap-toc.min.js
docs/deps/clipboard.js-2.0.11/clipboard.min.js
docs/deps/data-deps.txt
docs/deps/font-awesome-6.4.2/css/all.css
docs/deps/font-awesome-6.4.2/css/all.min.css
docs/deps/font-awesome-6.4.2/css/v4-shims.css
docs/deps/font-awesome-6.4.2/css/v4-shims.min.css
docs/deps/font-awesome-6.4.2/webfonts/fa-brands-400.ttf
docs/deps/font-awesome-6.4.2/webfonts/fa-brands-400.woff2
docs/deps/font-awesome-6.4.2/webfonts/fa-regular-400.ttf
docs/deps/font-awesome-6.4.2/webfonts/fa-regular-400.woff2
docs/deps/font-awesome-6.4.2/webfonts/fa-solid-900.ttf
docs/deps/font-awesome-6.4.2/webfonts/fa-solid-900.woff2
docs/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.ttf
docs/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.woff2
docs/deps/headroom-0.11.0/headroom.min.js
docs/deps/headroom-0.11.0/jQuery.headroom.min.js
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/deps/search-1.0.0/autocomplete.jquery.min.js
docs/deps/search-1.0.0/fuse.min.js
docs/deps/search-1.0.0/mark.min.js
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/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-1.2.1/css/crosstalk.min.css
docs/dev/articles/plotting_files/crosstalk-1.2.1/js/crosstalk.js
docs/dev/articles/plotting_files/crosstalk-1.2.1/js/crosstalk.js.map
docs/dev/articles/plotting_files/crosstalk-1.2.1/js/crosstalk.min.js
docs/dev/articles/plotting_files/crosstalk-1.2.1/js/crosstalk.min.js.map
docs/dev/articles/plotting_files/crosstalk-1.2.1/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/htmltools-fill-0.5.8.1/fill.css
docs/dev/articles/plotting_files/htmlwidgets-1.6.4/htmlwidgets.js
docs/dev/articles/plotting_files/plotly-binding-4.10.4/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/vignette_images/cheat_sheet_preview.png
docs/dev/articles/working_with_git.html
docs/dev/authors.html
docs/dev/deps/bootstrap-5.3.1/bootstrap.bundle.min.js
docs/dev/deps/bootstrap-5.3.1/bootstrap.bundle.min.js.map
docs/dev/deps/bootstrap-5.3.1/bootstrap.min.css
docs/dev/deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js
docs/dev/deps/clipboard.js-2.0.11/clipboard.min.js
docs/dev/deps/data-deps.txt
docs/dev/deps/font-awesome-6.4.2/css/all.css
docs/dev/deps/font-awesome-6.4.2/css/all.min.css
docs/dev/deps/font-awesome-6.4.2/css/v4-shims.css
docs/dev/deps/font-awesome-6.4.2/css/v4-shims.min.css
docs/dev/deps/font-awesome-6.4.2/webfonts/fa-brands-400.ttf
docs/dev/deps/font-awesome-6.4.2/webfonts/fa-brands-400.woff2
docs/dev/deps/font-awesome-6.4.2/webfonts/fa-regular-400.ttf
docs/dev/deps/font-awesome-6.4.2/webfonts/fa-regular-400.woff2
docs/dev/deps/font-awesome-6.4.2/webfonts/fa-solid-900.ttf
docs/dev/deps/font-awesome-6.4.2/webfonts/fa-solid-900.woff2
docs/dev/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.ttf
docs/dev/deps/font-awesome-6.4.2/webfonts/fa-v4compatibility.woff2
docs/dev/deps/headroom-0.11.0/headroom.min.js
docs/dev/deps/headroom-0.11.0/jQuery.headroom.min.js
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/deps/search-1.0.0/autocomplete.jquery.min.js
docs/dev/deps/search-1.0.0/fuse.min.js
docs/dev/deps/search-1.0.0/mark.min.js
docs/dev/favicon-16x16.png
docs/dev/favicon-32x32.png
docs/dev/favicon.ico
docs/dev/index.html
docs/dev/katex-auto.js
docs/dev/lightswitch.js
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/NResource.html
docs/dev/reference/NS_interaction.html
docs/dev/reference/NS_params-1.png
docs/dev/reference/NS_params.html
docs/dev/reference/NS_sim-1.png
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/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/calc_selectivity.html
docs/dev/reference/calculated_species_params.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/catchability.html
docs/dev/reference/compareParams.html
docs/dev/reference/completeSpeciesParams.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/dw.html
docs/dev/reference/dw_full.html
docs/dev/reference/emptyParams.html
docs/dev/reference/ext_encounter.html
docs/dev/reference/ext_mort.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/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/finalNResource.html
docs/dev/reference/gear_params.html
docs/dev/reference/getBiomass.html
docs/dev/reference/getCatchability.html
docs/dev/reference/getColours.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/getExtEncounter.html
docs/dev/reference/getExtMort.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/getInitialEffort.html
docs/dev/reference/getInteraction.html
docs/dev/reference/getLinetypes.html
docs/dev/reference/getM2.html
docs/dev/reference/getM2Background.html
docs/dev/reference/getMaturityProportion.html
docs/dev/reference/getMaxIntakeRate.html
docs/dev/reference/getMeanMaxWeight.html
docs/dev/reference/getMeanWeight.html
docs/dev/reference/getMetabolicRate.html
docs/dev/reference/getMetadata.html
docs/dev/reference/getMort.html
docs/dev/reference/getN.html
docs/dev/reference/getParams.html
docs/dev/reference/getPhiPrey.html
docs/dev/reference/getPredKernel.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/getRateFunction.html
docs/dev/reference/getRates.html
docs/dev/reference/getReproductionLevel.html
docs/dev/reference/getReproductionProportion.html
docs/dev/reference/getResourceCapacity.html
docs/dev/reference/getResourceDynamics.html
docs/dev/reference/getResourceLevel.html
docs/dev/reference/getResourceMort.html
docs/dev/reference/getResourceRate.html
docs/dev/reference/getSSB.html
docs/dev/reference/getSearchVolume.html
docs/dev/reference/getSelectivity.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/given_species_params.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/initialN.html
docs/dev/reference/initialNOther-set.html
docs/dev/reference/initialNOther.html
docs/dev/reference/initialNResource-set.html
docs/dev/reference/initialNResource.html
docs/dev/reference/initial_effort.html
docs/dev/reference/intake_max.html
docs/dev/reference/inter.html
docs/dev/reference/interaction_matrix.html
docs/dev/reference/knife_edge.html
docs/dev/reference/l2w.html
docs/dev/reference/libs/crosstalk-1.2.1/css/crosstalk.min.css
docs/dev/reference/libs/crosstalk-1.2.1/js/crosstalk.js
docs/dev/reference/libs/crosstalk-1.2.1/js/crosstalk.js.map
docs/dev/reference/libs/crosstalk-1.2.1/js/crosstalk.min.js
docs/dev/reference/libs/crosstalk-1.2.1/js/crosstalk.min.js.map
docs/dev/reference/libs/crosstalk-1.2.1/scss/crosstalk.scss
docs/dev/reference/libs/htmlwidgets-1.6.4/htmlwidgets.js
docs/dev/reference/libs/plotly-binding-4.10.4/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/maturity.html
docs/dev/reference/melt.html
docs/dev/reference/metab.html
docs/dev/reference/mizer-package.html
docs/dev/reference/mizer.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/other_params.html
docs/dev/reference/plot,MizerParams,missing-method.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.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.html
docs/dev/reference/plotlyBiomass.html
docs/dev/reference/plotlyBiomassObservedVsModel.html
docs/dev/reference/plotlyFMort.html
docs/dev/reference/plotlyFeedingLevel.html
docs/dev/reference/plotlyGrowthCurves.html
docs/dev/reference/plotlyPredMort.html
docs/dev/reference/plotlySpectra.html
docs/dev/reference/plotlyYield.html
docs/dev/reference/plotlyYieldGear.html
docs/dev/reference/plotlyYieldObservedVsModel.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/pred_kernel.html
docs/dev/reference/project.html
docs/dev/reference/projectToSteady.html
docs/dev/reference/project_simple.html
docs/dev/reference/readParams.html
docs/dev/reference/reexports.html
docs/dev/reference/removeComponent.html
docs/dev/reference/removeSpecies.html
docs/dev/reference/renameSpecies.html
docs/dev/reference/repro_prop.html
docs/dev/reference/resource_capacity.html
docs/dev/reference/resource_constant.html
docs/dev/reference/resource_dynamics.html
docs/dev/reference/resource_level.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/search_vol.html
docs/dev/reference/selectivity.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/setExtEncounter.html
docs/dev/reference/setExtMort.html
docs/dev/reference/setFishing.html
docs/dev/reference/setInitialValues.html
docs/dev/reference/setInteraction.html
docs/dev/reference/setLinetypes.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-1.png
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/setRmax.html
docs/dev/reference/setSearchVolume.html
docs/dev/reference/set_community_model-1.png
docs/dev/reference/set_community_model-2.png
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-1.png
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/validEffortVector.html
docs/dev/reference/validGearParams.html
docs/dev/reference/validParams.html
docs/dev/reference/validSpeciesParams.html
docs/dev/reference/valid_gears_arg.html
docs/dev/reference/valid_species_arg.html
docs/dev/reference/w.html
docs/dev/reference/w2l.html
docs/dev/reference/w_full.html
docs/dev/search.json
docs/dev/sitemap.xml
docs/favicon-16x16.png
docs/favicon-32x32.png
docs/favicon.ico
docs/index.html
docs/katex-auto.js
docs/lightswitch.js
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/NResource.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/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-1.png
docs/reference/box_pred_kernel.html
docs/reference/calc_selectivity.html
docs/reference/calculated_species_params.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/catchability.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/dw.html
docs/reference/dw_full.html
docs/reference/emptyParams.html
docs/reference/ext_encounter.html
docs/reference/ext_mort.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/finalNResource.html
docs/reference/gear_params.html
docs/reference/getBiomass.html
docs/reference/getCatchability.html
docs/reference/getColours.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/getExtEncounter.html
docs/reference/getExtMort.html
docs/reference/getFMort.html
docs/reference/getFMortGear.html
docs/reference/getFeedingLevel.html
docs/reference/getGrowthCurves-1.png
docs/reference/getGrowthCurves.html
docs/reference/getInitialEffort.html
docs/reference/getInteraction.html
docs/reference/getLinetypes.html
docs/reference/getM2.html
docs/reference/getM2Background.html
docs/reference/getMaturityProportion.html
docs/reference/getMaxIntakeRate.html
docs/reference/getMeanMaxWeight.html
docs/reference/getMeanWeight.html
docs/reference/getMetabolicRate.html
docs/reference/getMetadata.html
docs/reference/getMort.html
docs/reference/getN.html
docs/reference/getParams.html
docs/reference/getPhiPrey.html
docs/reference/getPredKernel.html
docs/reference/getPredMort.html
docs/reference/getPredRate.html
docs/reference/getProportionOfLargeFish.html
docs/reference/getRDD.html
docs/reference/getRDI.html
docs/reference/getRateFunction.html
docs/reference/getRates.html
docs/reference/getReproductionLevel.html
docs/reference/getReproductionProportion.html
docs/reference/getResourceCapacity.html
docs/reference/getResourceDynamics.html
docs/reference/getResourceLevel.html
docs/reference/getResourceMort.html
docs/reference/getResourceRate.html
docs/reference/getSSB.html
docs/reference/getSearchVolume.html
docs/reference/getSelectivity.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/given_species_params.html
docs/reference/idxFinalT.html
docs/reference/index.html
docs/reference/indicator_functions.html
docs/reference/initialN-set.html
docs/reference/initialN.html
docs/reference/initialNOther-set.html
docs/reference/initialNOther.html
docs/reference/initialNResource-set.html
docs/reference/initialNResource.html
docs/reference/initial_effort.html
docs/reference/intake_max.html
docs/reference/inter.html
docs/reference/interaction_matrix.html
docs/reference/knife_edge.html
docs/reference/l2w.html
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-1.6.4/htmlwidgets.js
docs/reference/libs/plotly-binding-4.10.4/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-1.png
docs/reference/lognormal_pred_kernel-2.png
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/maturity.html
docs/reference/melt.html
docs/reference/metab.html
docs/reference/mizer-package.html
docs/reference/mizer.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/other_params.html
docs/reference/plot,MizerParams,missing-method.html
docs/reference/plot-MizerParams-missing-method-1.png
docs/reference/plot-MizerParams-missing-method.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/plotlyBiomass.html
docs/reference/plotlyBiomassObservedVsModel.html
docs/reference/plotlyFMort.html
docs/reference/plotlyFeedingLevel.html
docs/reference/plotlyGrowthCurves.html
docs/reference/plotlyPredMort.html
docs/reference/plotlySpectra.html
docs/reference/plotlyYield.html
docs/reference/plotlyYieldGear.html
docs/reference/plotlyYieldObservedVsModel.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-1.png
docs/reference/power_law_pred_kernel.html
docs/reference/pred_kernel.html
docs/reference/project.html
docs/reference/projectToSteady.html
docs/reference/project_simple.html
docs/reference/readParams.html
docs/reference/reexports.html
docs/reference/removeComponent.html
docs/reference/removeSpecies.html
docs/reference/renameSpecies.html
docs/reference/repro_prop.html
docs/reference/resource_capacity.html
docs/reference/resource_constant.html
docs/reference/resource_dynamics.html
docs/reference/resource_level.html
docs/reference/resource_logistic.html
docs/reference/resource_params.html
docs/reference/resource_rate.html
docs/reference/resource_semichemostat.html
docs/reference/saveParams.html
docs/reference/scaleModel.html
docs/reference/search_vol.html
docs/reference/selectivity.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/setLinetypes.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-1.png
docs/reference/truncated_lognormal_pred_kernel.html
docs/reference/upgradeParams.html
docs/reference/upgradeSim.html
docs/reference/validEffortVector.html
docs/reference/validGearParams.html
docs/reference/validGivenSpeciesParams.html
docs/reference/validParams.html
docs/reference/validSim.html
docs/reference/validSpeciesParams.html
docs/reference/valid_gears_arg.html
docs/reference/valid_species_arg.html
docs/reference/w.html
docs/reference/w2l.html
docs/reference/w_full.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/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/plot-MizerParams-missing-method.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/validSim.Rd
man/validSpeciesParams.Rd
man/valid_gears_arg.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-validSpeciesParams.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.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
