_pkgdown.yml

# This is the configuration for the mizer website using the pkgdown package.

url: https://sizespectrum.org/mizer

authors:
  Julia Blanchard:
    href: http://www.utas.edu.au/profiles/staff/imas/julia-blanchard
  Ken Andersen:
    href: https://ken.haste.dk/
  Gustav Delius:
    href: https://www.york.ac.uk/maths/staff/gustav-delius/

template:
  params:
    bootswatch: cerulean
    docsearch:
      api_key: 96e9641255d3fff35a4fd16d1a1bf70c
      index_name: sizespectrum_mizer

development:
  mode: auto

toc: 
  depth: 3

navbar:
  structure:
    left: [home, intro, reference, articles, publications, news]
    right: [github]
  components:
    publications:
      text: Publications
      href: articles/publications.html

articles:
- title: User Guide
  navbar: ~
  contents:
  - mizer
  - model_description
  - community_model
  - trait_model
  - multispecies_model
  - running_a_simulation
  - exploring_the_simulation_results
  - a_multispecies_model_of_the_north_sea
  - plotting
- title: Developer Guide
  navbar: For developers
  contents:
  - developer_vignette
  - working_with_git
  - developer_FAQ
  - editing_website


reference:
- title: Creating a new model
  description: Mizer allows the easy set-up of three different types of models, 
    of increasing levels of complexity. See
    https://sizespectrum.org/mizer/dev/articles/mizer.html#size-spectrum-models
    for a description of these model types.
  contents:
  - newCommunityParams
  - newTraitParams
  - newMultispeciesParams
- title: Model parameters
  description: Even after you have created a model, you can still make changes
    with the following functions. This is useful while tuning the model and for
    investigating the impact of changes in parameters.
  contents:
  - species_params
  - gear_params
  - setParams
  - setPredKernel
  - getPredKernel
  - setSearchVolume
  - setInteraction
  - setMaxIntakeRate
  - setMetabolicRate
  - setExtMort
  - setReproduction
  - setFishing
  - setResource
  - resource_params
  - setInitialValues
  - setBevertonHolt
- title: Running simulations
  contents:
  - project
  - initialN
  - initialNResource
  - setInitialValues
  - steady
- title: Accessing results
  contents:
  - "N"
  - NResource
  - finalN
  - idxFinalT
  - getEffort
  - getTimes
- title: Analysing results
  contents:
  - summary_functions
  - getDiet
  - getBiomass
  - getN
  - getSSB
  - getYield
  - getYieldGear
  - getGrowthCurves
- title: Calculating indicators
  contents:
  - indicator_functions
  - getProportionOfLargeFish
  - getCommunitySlope
  - getMeanWeight
  - getMeanMaxWeight
- title: Plotting results
  contents:
  - plotting_functions
  - starts_with("plot")
  - -plotM2
  - setColours
  - setLinetypes
- title: Calculating rates
  contents:
  - getRates
  - getEncounter
  - getEGrowth
  - getERepro
  - getEReproAndGrowth
  - getFMort
  - getFMortGear
  - getFeedingLevel
  - getCriticalFeedingLevel
  - getMort
  - getResourceMort
  - getPredMort
  - getPredRate
  - getRDD
  - getRDI
- title: Extending Mizer
  contents:
  - setRateFunction
  - setComponent
  - getComponent
  - initialNOther
  - NOther
  - finalNOther
- title: Predation kernels
  contents:
  - lognormal_pred_kernel
  - box_pred_kernel
  - power_law_pred_kernel
  - truncated_lognormal_pred_kernel
- title: Fishing selectivity functions
  contents:
  - knife_edge
  - sigmoid_length
  - sigmoid_weight
  - double_sigmoid_length
- title: Resource dynamics
  contents:
  - resource_semichemostat
  - resource_constant
- title: Density-dependent reproduction
  contents:
  - BevertonHoltRDD
  - RickerRDD
  - SheperdRDD
  - noRDD
  - constantRDD
- title: Internal rate functions
  description: These functions are used by project() to calculate 
    instantaneous rates at each time step. You should use the get...() 
    functions instead of the mizer...() functions.
  contents:
  - mizerRates
  - starts_with("mizer")
  - -mizer
- title: Internal helper functions
  contents:
    # The following should list all functions with @concept helper
    # but instead lists all functions. A bug in pkgdown?
    #  - has_concept("helper")
  - validSpeciesParams
  - validGearParams
  - set_species_param_default
  - get_h_default
  - get_gamma_default
  - get_ks_default
  - get_phi
  - log_breaks
  - get_initial_n
  - retune_erepro
  - get_required_reproduction
  - emptyParams
  - project_simple
- title: Classes
  contents:
  - MizerParams-class
  - summary,MizerParams-method
  - "w"
  - validParams
  - upgradeParams
  - MizerSim-class
  - summary,MizerSim-method
  - upgradeSim
  - MizerSim
  - getParams
- title: Example parameter sets
  contents:
  - NS_params
  - NS_species_params
  - NS_species_params_gears
  - inter
- title: Deprecated
  desc: These functions are available for backwards compatibility with earlier
    versions of mizer
  contents:
  - set_multispecies_model
  - set_community_model
  - set_trait_model
  - MizerParams
  - getESpawning
  - getPhiPrey
  - getM2
  - getM2Background
  - getZ
  - plotM2