mkdocs.yml

site_name: Epiworld
site_description: A general framework for epidemiologic simulation
site_url: https://UofUEpi.github.io/epiworld

repo_name: UofUEpiBio/epiworld
repo_url: https://github.com/UofUEpiBio/epiworld

docs_dir: docs
site_dir: site

theme:
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  logo: assets/branding/epiworld.png
  favicon: assets/branding/epiworld.png
  palette:
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      toggle:
        icon: material/brightness-7
        name: Switch to dark mode
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      scheme: slate
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        name: Switch to light mode
  font:
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    code: JetBrains Mono
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  features:
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    - navigation.tabs
    - navigation.sections
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nav:
  - Home: README.md
  - Models:
    - Overview: epiworld/modules.md
    - Basic Compartmental Models:
        - SIS: epiworld/classModelSIS.md
        - SIR: epiworld/classModelSIR.md
        - SEIR: epiworld/classModelSEIR.md
    - Models with Death Compartment:
        - SIRD: epiworld/classModelSIRD.md
        - SISD: epiworld/classModelSISD.md
        - SEIRD: epiworld/classModelSEIRD.md
    - Connected Population Models:
        - SIR Connected: epiworld/classModelSIRCONN.md
        - SEIR Connected: epiworld/classModelSEIRCONN.md
        - SIRD Connected: epiworld/classModelSIRDCONN.md
        - SEIRD Connected: epiworld/classModelSEIRDCONN.md
    - Population Mixing Models:
        - SEIR Mixing: epiworld/classModelSEIRMixing.md
        - SIR Mixing: epiworld/classModelSIRMixing.md
        - SEIR Mixing Quarantine: epiworld/classModelSEIRMixingQuarantine.md
    - Disease-Specific Models:
        - Measles School: epiworld/classModelMeaslesSchool.md
        - Measles Mixing: epiworld/classModelMeaslesMixing.md
        - Measles Mixing Risk Quarantine: epiworld/classModelMeaslesMixingRiskQuarantine.md
    - Specialized Models:
        - SIR Logit: epiworld/classModelSIRLogit.md
        - Diffusion Network: epiworld/classModelDiffNet.md
        - Surveillance: epiworld/classModelSURV.md
  - Examples:
    - Overview: examples/index.md
    - Hello World: examples/00-hello-world.md
    - SEIR Model: examples/01-seir.md
    - SIR Model: examples/01-sir.md
    - SIS Model: examples/01-sis.md
    - "SIR: Multiple Runs": examples/02-sir_multiple_runs.md
    - "SIR: Multiple Runs with Plotting": examples/02b-sir_multiple_runs.md
    - Simple SIR: examples/03-simple-sir.md
    - User Data: examples/05-user-data.md
    - SIR with OpenMP: examples/06-sir-omp.md
    - SIR with OpenMP (Callbacks): examples/06b-sir-omp.md
    - Surveillance Model: examples/07-surveillance.md
    - Likelihood-Free MCMC: examples/10-likelihood-free-mcmc.md
    - Entities: examples/11-entities.md
    - Generation Interval: examples/13-genint.md
    - Community and Hospital: examples/14-community-hosp.md
    - SEIRD Transitions: examples/15-seird-transitions.md
    - Stochastic Block Model: examples/16-sbm.md
    - SBM Scalability Benchmark: examples/17-sbm-scalability.md
    - SEIR Quarantine Benchmark: examples/18-seir-network-quarantine-benchmark.md
    - "Poisson vs. Binomial Sampling": examples/19-poisson-approximation-binomial.md
  - Implementation:
    - Overview: impl/index.md
    - Library Architecture: impl/library-architecture.md
    - Performance Optimization: impl/performance-optimization.md
    - Extending the Library: impl/extending-the-library.md
    - Extending the Library with Models: impl/extending-the-library-with-models.md
    - Core Simulation Models: impl/core-simulation-models.md
    - Queueing System: impl/queueing-system.md
    - Data Collection and Analysis: impl/data-collection-and-analysis.md
    - Random Number Generation and Statistical Functions: impl/random-number-generation.md
    - Reproducibility and run_multiple: impl/reproducibility-and-run-multiple.md
    - Mixing and Entity Distribution: impl/mixing-and-entity-distribution.md
    - Virus and Tool Distribution Functions: impl/virus-and-tool-distribution.md
    - Generation Interval and Reproductive Number Calculation: impl/generation-interval-and-reproductive-number.md
    - Events and Multi-Event Handling: impl/events-and-multi-event-handling.md
    - Quarantine, Isolation, and Contact Tracing: impl/quarantine-isolation-and-contact-tracing.md
    - Sampling Contacts: impl/sampling-contacts.md
  - API Reference:
    - Overview: api/index.md
    - Classes: epiworld/annotated.md
    - Files: epiworld/files.md
    - Namespaces: epiworld/namespaces.md

hooks:
  - script/mkdocs_hooks.py

plugins:
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  - mkdoxy:
      projects:
        epiworld:
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          full-doc: true
          doxy-cfg:
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            RECURSIVE: YES
            EXTRACT_ALL: YES

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extra_css:
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extra_javascript:
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  - javascripts/network-hero.js
  - javascripts/compiler.js
  - https://unpkg.com/mathjax@3/es5/tex-mml-chtml.js

validation:
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    not_found: warn
    absolute_links: warn
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    unrecognized_links: warn