_site.yml

name: doc
output:
  html_document:
    theme: yeti
    highlight: textmate
output_dir: docs
navbar:
  left:
    - text: "FLR"
      icon: fa-home
      href: http://flr-project.org
    - text: "Home"
      icon: fa-info
      href: index.html
    - text: "Intro"
      icon: fa-play-circle-o
      menu:
        - text: "A quick introduction to FLR"
          href: A_quick_introduction_to_FLR.html
        - text: "An overview of the FLCore classes"
          href: An_overview_of_the_FLCore_classes.html
    - text: "Input"
      icon: fa-database
      menu:
        - text: "Loading your data into FLR"
          href: Loading_your_data_into_FLR.html
    - text: "Modelling"
      icon: fa-magic
      menu:
        - text: "Modelling stock recruitment with FLSR"
          href: Modelling_stock_recruitment_with_FLSR.html
        - text: "Statistical catch at age models in FLa4a"
          href: Statistical_catch_at_age_models_in_FLa4a.html
        - text: "Modelling growth and its uncertainty in FLa4a"
          href: Modelling_growth_and_its_uncertainty_in_FLa4a.html
        - text: "Natural mortality modelling in FLa4a"
          href: Natural_mortality_modelling_in_FLa4a.html
        - text: "Stock assessment using eXtended Survivors Analysis with FLXSA"
          href: Stock_assessment_using_eXtended_Survivors_Analysis_with_FLXSA.html
        - text: "Using information on Life History relationships"
          href: Using_information_on_life_history_relationships.html
        - text: "Life history relationships"
          href: Life_history_relationships.html
    - text: "Advice"
      icon: fa-tachometer
      menu:
        - text: "Running Medium Term Forecasts with FLash"
          href: Running_Medium_Term_Forecasts_with_FLash.html
        - text: "Short Term Forecasting for advice using FLash"
          href: Short_Term_Forecasting_for_advice_using_FLash.html
        - text: "Forecasting on the Medium Term for advice using FLasher"
          href: Forecasting_on_the_Medium_Term_for_advice_using_FLasher.html
        - text: "Reference points for fisheries management with FLBRP"
          href: Reference_points_for_fisheries_management_with_FLBRP.html
    - text: "MSE"
      icon: fa-cogs
      menu:
        - text: "An introduction to MSE using FLR"
          href: An_introduction_to_MSE_using_FLR.html
        - text: "Biomass Dynamic Management Procedures"
          href: Management_procedure_biomass_dynamic.html
    - text: "FLBEIA"
      icon: fa-cogs
      menu:
        - text: "An introduction to MSE using FLR"
          href: An_introduction_to_MSE_using_FLR.html
        - text: "Conditioning FLBEIA using Smart Conditioning Functions"
          href: FLBEIA_Conditioning.html
        - text: "A simple example on how to use FLBEIA"
          href: FLBEIA_A_Simple_Example.html
        - text: "A simple example with multiple dimensions in FLBEIA"
          href: FLBEIA_An_Example_with_multiple_dimensions.html
        - text: "Checking FLBEIA inputs"
          href: FLBEIA_Checking_inputs.html
        - text: "Using Stock Assessment models in the Management procedure of FLBEIA"
          href: FLBEIA_Using_Assessment_models_in_the_MP.html
        - text: "Including SS3 assessment within the Management Procedure of FLBEIA"
          href: FLBEIA_Incorporating_SS3assessment_MP.html
        - text: "Testing different Management Strategies in FLBEIA"
          href: FLBEIA_Testing_Management_Strategies.html
        - text: "Data Limited MSE in FLBEIA"
          href: FLBEIA_Data_Poor_MSE.html
        - text: "Smart Conditioning II"
          href: FLBEIA_Smart_Conditioning_II.html
        - text: "ICES Mixed Fisheries Advice using FLBEIA"
          href: FLBEIA_Mixed_Fisheries_Tutorial.html
        - text: "Bio-Economic simulation using FLBEIA"
          href: FLBEIA_Bio_Economic_Tutorial.html
    - text: "Plotting"
      icon: fa-area-chart
      menu:
        - text: "ggplotFL, plotting FLR objects with ggplot2"
          href: ggplotFL_plotting_FLR_objects_with_ggplot2.html
        - text: "Plotting FLR objects using lattice"
          href: Plotting_FLR_objects_using_lattice.html
    - text: "Internals"
      icon: fa-puzzle-piece
      menu:
        - text: "Units of measurement in FLR objects"
          href: Units_of_measurement_in_FLR_objects.html
  right:
    - icon: fa-question fa-lg
      href: http://github.com/flr/doc/issues