Files in mizer

Dynamic Multi-Species Size Spectrum Modelling

NEWS.md README.md R/RcppExports.R R/extension.R R/setColours.R R/setMetadata.R R/newSingleSpeciesParams.R R/calibrate.R R/MizerParams-class.R R/defaults_edition.R R/age_mat.R R/setSearchVolume.R R/setBevertonHolt.R R/steadySingleSpecies.R R/rate_functions.R R/newMultispeciesParams.R R/animateSpectra.R R/customFunction.R R/resource_dynamics.R R/setInitialValues.R R/resource_semichemostat.R R/wrapper_functions.R R/setMaxIntakeRate.R R/get_initial_n.R R/data.R R/validSpeciesParams.R R/pred_kernel_funcs.R R/project_methods.R R/setPredKernel.R R/plotYieldObservedVsModel.R R/selectivity_funcs.R R/deprecated.R R/manipulate_species.R R/upgrade.R R/setExtEncounter.R R/setMetabolicRate.R R/saveParams.R R/setReproduction.R R/setFishing.R R/setInteraction.R R/MizerSim-class.R R/plots.R R/matchGrowth.R R/reproduction.R R/mizer-package.R R/resource_logistic.R R/compareParams.R R/setExtMort.R R/steady.R R/setResource.R R/summary_methods.R R/species_params.R R/match.R R/helpers.R R/plotBiomassObservedVsModel.R R/project.R inst/doc/mizer_vignette.R inst/doc/mizer_vignette.pdf inst/doc/mizer_vignette.Rmd inst/shiny/selectivity_effects/app.R inst/examples/supplementary_material.R tests/testthat.R tests/spelling.R tests/testthat/test-matchGrowth.R tests/testthat/test-MizerParams-class.R tests/testthat/test-steady.R tests/testthat/test-setSearchVolume.R tests/testthat/test-MizerSim-class.R tests/testthat/test-resource_logistic.R tests/testthat/test-backwards_compatibility.R tests/testthat/test-setMetabolicRate.R tests/testthat/test-extension.R tests/testthat/test-validSpeciesParams.R tests/testthat/test-get_initial_n.R tests/testthat/test-steadySingleSpecies.R tests/testthat/test-setResource.R tests/testthat/test-compareParams.R tests/testthat/test-selectivity_funcs.R tests/testthat/test-setExtMort.R tests/testthat/test-reproduction.R tests/testthat/test-plotYieldObservedVsModel.R tests/testthat/test-age_mat.R tests/testthat/test-plotBiomassObservedVsModel.R tests/testthat/test-rate_functions.R tests/testthat/test-newMultispeciesParams.R tests/testthat/test-data.R tests/testthat/test-setMetadata.R tests/testthat/test-setMaxIntakeRate.R tests/testthat/test-plots.R tests/testthat/test-setFishing.R tests/testthat/test-setColours.R tests/testthat/test-setExtEncounter.R tests/testthat/test-pred_kernel_funcs.R tests/testthat/test-single_species.R tests/testthat/test-setBevertonHolt.R tests/testthat/test-newSingleSpeciesParams.R tests/testthat/helper.R tests/testthat/Rplots.pdf tests/testthat/test-helpers.R tests/testthat/test-calibrate.R tests/testthat/test-resource_semichemostat.R tests/testthat/test-setReproduction.R tests/testthat/test-setInitialValues.R tests/testthat/test-resource_dynamics.R tests/testthat/test-setInteraction.R tests/testthat/test-match.R tests/testthat/test-upgrade.R tests/testthat/test-manipulate_species.R tests/testthat/test-summary_methods.R tests/testthat/test-customFunction.R tests/testthat/test-animateSpectra.R tests/testthat/test-project_methods.R tests/testthat/test-analytic_results.R tests/testthat/test-wrapper_functions.R tests/testthat/test-species_params.R tests/testthat/test-project.R tests/testthat/test-setPredKernel.R tests/testthat/_snaps/backwards_compatibility.md tests/testthat/_snaps/project.md tests/testthat/_snaps/steady.md tests/testthat/_snaps/summary_methods.md tests/testthat/_snaps/project_methods.md tests/testthat/_snaps/age_mat.md vignettes/mizer_vignette.Rmd vignettes/mizer.R man/NS_params.Rd man/renameSpecies.Rd man/plotSpectra.Rd man/setInteraction.Rd man/animateSpectra.Rd man/mizerEReproAndGrowth.Rd man/setSearchVolume.Rd man/MizerSim.Rd man/w.Rd man/getFMortGear.Rd man/saveParams.Rd man/setRmax.Rd man/summary-MizerSim-method.Rd man/finalN.Rd man/species_params.Rd man/matchYields.Rd man/finalNOther.Rd man/setBevertonHolt.Rd man/NS_species_params_gears.Rd man/reexports.Rd man/mizerMort.Rd man/setRateFunction.Rd man/get_time_elements.Rd man/age_mat_vB.Rd man/newMultispeciesParams.Rd man/projectToSteady.Rd man/log_breaks.Rd man/setParams.Rd man/getComponent.Rd man/getResourceDynamics.Rd man/get_required_reproduction.Rd man/addSpecies.Rd man/getRDD.Rd man/getZ.Rd man/getResourceMort.Rd man/resource_params.Rd man/initialN-set.Rd man/validSpeciesParams.Rd man/truncated_lognormal_pred_kernel.Rd man/mizer-package.Rd man/plotM2.Rd man/plotFeedingLevel.Rd man/getPredMort.Rd man/getMeanWeight.Rd man/get_f0_default.Rd man/removeSpecies.Rd man/setComponent.Rd man/getEReproAndGrowth.Rd man/steadySingleSpecies.Rd man/NS_species_params.Rd man/calibrateNumber.Rd man/scaleModel.Rd man/plot-MizerParams-missing-method.Rd man/setResource.Rd man/getFMort.Rd man/getYield.Rd man/mizerFeedingLevel.Rd man/noRDD.Rd man/set_species_param_default.Rd man/getEGrowth.Rd man/plotFMort.Rd man/getRDI.Rd man/mizerERepro.Rd man/mizerEGrowth.Rd man/newTraitParams.Rd man/get_size_range_array.Rd man/MizerSim-class.Rd man/setMaxIntakeRate.Rd man/sigmoid_length.Rd man/getCommunitySlope.Rd man/getM2Background.Rd man/validSim.Rd man/get_gamma_default.Rd man/NS_interaction.Rd man/power_law_pred_kernel.Rd man/getYieldGear.Rd man/mizerFMortGear.Rd man/validGearParams.Rd man/constant_other.Rd man/getProportionOfLargeFish.Rd man/get_h_default.Rd man/MizerParams.Rd man/inter.Rd man/getParams.Rd man/setInitialValues.Rd man/mizerRDI.Rd man/getEffort.Rd man/upgradeSim.Rd man/customFunction.Rd man/setMetadata.Rd man/gear_params.Rd man/setPredKernel.Rd man/getCriticalFeedingLevel.Rd man/matchBiomasses.Rd man/matchNumbers.Rd man/getM2.Rd man/needs_upgrading.Rd man/calibrateBiomass.Rd man/default_pred_kernel_params.Rd man/setMetabolicRate.Rd man/lognormal_pred_kernel.Rd man/mizerFMort.Rd man/indicator_functions.Rd man/double_sigmoid_length.Rd man/getSSB.Rd man/different.Rd man/get_initial_n.Rd man/box_pred_kernel.Rd man/newCommunityParams.Rd man/mizerResourceMort.Rd man/mizerPredRate.Rd man/plotDataFrame.Rd man/setReproduction.Rd man/matchGrowth.Rd man/emptyParams.Rd man/plotBiomassObservedVsModel.Rd man/plotGrowthCurves.Rd man/getPhiPrey.Rd man/getTimes.Rd man/initialNOther-set.Rd man/compareParams.Rd man/mizerPredMort.Rd man/distanceSSLogN.Rd man/l2w.Rd man/plotYieldGear.Rd man/getGrowthCurves.Rd man/constantEggRDI.Rd man/newSingleSpeciesParams.Rd man/project.Rd man/constantRDD.Rd man/getPredRate.Rd man/set_trait_model.Rd man/getESpawning.Rd man/get_phi.Rd man/setExtMort.Rd man/initial_effort.Rd man/NS_sim.Rd man/getMeanMaxWeight.Rd man/valid_species_arg.Rd man/defaults_edition.Rd man/validParams.Rd man/knife_edge.Rd man/plotting_functions.Rd man/mizerRates.Rd man/project_simple.Rd man/getInteraction.Rd man/calc_selectivity.Rd man/mizerEncounter.Rd man/getDiet.Rd man/summary_functions.Rd man/summary-MizerParams-method.Rd man/resource_semichemostat.Rd man/getMort.Rd man/set_multispecies_model.Rd man/resource_logistic.Rd man/BevertonHoltRDD.Rd man/setFishing.Rd man/upgradeParams.Rd man/plotDiet.Rd man/N.Rd man/plotYield.Rd man/RickerRDD.Rd man/getERepro.Rd man/getReproductionLevel.Rd man/resource_constant.Rd man/valid_gears_arg.Rd man/getFeedingLevel.Rd man/getRates.Rd man/getEncounter.Rd man/get_ks_default.Rd man/initialNResource-set.Rd man/set_community_model.Rd man/plotYieldObservedVsModel.Rd man/age_mat.Rd man/setColours.Rd man/plotPredMort.Rd man/calibrateYield.Rd man/sigmoid_weight.Rd man/distanceMaxRelRDI.Rd man/setExtEncounter.Rd man/plotBiomass.Rd man/steady.Rd man/completeSpeciesParams.Rd man/getN.Rd man/plotMizerSim.Rd man/NOther.Rd man/MizerParams-class.Rd man/SheperdRDD.Rd man/getBiomass.Rd