Implement Gallery Website

.github/workflows/publish.yml

@@ -0,0 +1,42 @@
+on:
+  push:
+    branches:
+      - main
+
+name: Build and Deploy Website
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: "pages"
+  cancel-in-progress: false
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: quarto-dev/quarto-actions/setup@v2
+
+      - name: Render Quarto Website
+        uses: quarto-dev/quarto-actions/render@v2
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: _site
+
+  deploy:
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

.gitignore

@@ -41,3 +41,11 @@ EpiModel-Gallery.Rproj
 
 renv/
 Rplots.pdf
+
+# Quarto
+_site/
+.quarto/
+
+/.quarto/
+
+**/*.quarto_ipynb

README.md

@@ -1,4 +1,4 @@
-# EpiModel-Gallery
+# EpiModel Gallery
 
 [![Test Gallery Models](https://github.com/EpiModel/EpiModel-Gallery/workflows/Test-Gallery-Models/badge.svg?branch=main)](https://github.com/EpiModel/EpiModel-Gallery/actions)
 
@@ -11,20 +11,20 @@ EpiModel provides built-in SIS/SIR models out of the box, but its module API sup
 
 | Example | Description |
 |---------|-------------|
-| [AddingAnExposedState](2018-08-AddingAnExposedState/) | SEIR/SEIRS: adding an exposed (latent) compartment, with optional waning immunity |
-| [ObservedNetworkData](2018-08-ObservedNetworkData/) | Epidemics over observed (census) dynamic networks without ERGM estimation |
-| [SIwithVitalDynamics](2018-08-SIwithVitalDynamics/) | SI with aging, births, deaths, and age-specific mortality |
-| [TestAndTreatIntervention](2018-08-TestAndTreatIntervention/) | SIS with screening and antibiotic treatment for bacterial STIs |
-| [CompetingStrains](2018-09-CompetingStrains/) | SIS with two pathogen strains differing in infectiousness and duration |
-| [SocialDiffusion](2018-09-SocialDiffusion/) | SI framework repurposed for social diffusion with threshold and dose-response contagion |
-| [SEIRwithAONVax](2018-10-SEIRwithAONVax/) | SEIR with all-or-nothing vaccination, vital dynamics, and herd immunity |
-| [Syphilis](2018-11-Syphilis/) | Multi-stage syphilis with diagnosis, treatment, and recovery |
-| [SEIRSwithLeakyVax](2018-12-SEIRSwithLeakyVax/) | SEIRS with leaky vaccination (reduced transmission probability) and vital dynamics |
-| [HIV](2019-03-HIV/) | HIV with acute/chronic/AIDS stages and antiretroviral therapy (ART) |
-| [CostEffectivenessAnalysis](2021-10-CostEffectivenessAnalysis/) | SI with cost-effectiveness analysis: costs, QALYs, discounting, and ICERs |
-| [Multinets](2022-12-Multinets/) | Multilayer networks with cross-layer dependency (e.g., main vs. casual partnerships) |
-
-Each example contains three files: `README.md` (model explanation), `model.R` (network estimation and simulation), and `module-fx.R` (custom module functions).
+| [SI with Vital Dynamics](examples/si-vital-dynamics/) | SI with aging, births, deaths, and age-specific mortality |
+| [Adding an Exposed State](examples/seir-exposed-state/) | SEIR/SEIRS: adding an exposed (latent) compartment, with optional waning immunity |
+| [Test and Treat](examples/sis-test-and-treat/) | SIS with screening and antibiotic treatment for bacterial STIs |
+| [Competing Strains](examples/sis-competing-strains/) | SIS with two pathogen strains differing in infectiousness and duration |
+| [Social Diffusion](examples/social-diffusion/) | SI framework repurposed for social diffusion with threshold and dose-response contagion |
+| [Syphilis](examples/syphilis/) | Multi-stage syphilis with diagnosis, treatment, and recovery |
+| [SEIR with AON Vaccination](examples/seir-aon-vaccination/) | SEIR with all-or-nothing vaccination, vital dynamics, and herd immunity |
+| [SEIRS with Leaky Vaccination](examples/seirs-leaky-vaccination/) | SEIRS with leaky vaccination (reduced transmission probability) and vital dynamics |
+| [HIV](examples/hiv/) | HIV with acute/chronic/AIDS stages and antiretroviral therapy (ART) |
+| [Cost-Effectiveness](examples/cost-effectiveness/) | SI with cost-effectiveness analysis: costs, QALYs, discounting, and ICERs |
+| [Observed Network Data](examples/observed-network-data/) | Epidemics over observed (census) dynamic networks without ERGM estimation |
+| [Multinets](examples/multinets/) | Multilayer networks with cross-layer dependency (e.g., main vs. casual partnerships) |
+
+Each example contains `model.R` (network estimation and simulation), `module-fx.R` (custom module functions), and `index.qmd` (annotated Quarto document).
 
 
 ## Getting Started
@@ -45,13 +45,13 @@ install.packages("EpiModel")
 Clone the repository, then run any example from the project root:
 
 ```r
-source("2018-08-AddingAnExposedState/model.R")
+source("examples/si-vital-dynamics/model.R")
 ```
 
 Or from the command line:
 
 ```bash
-Rscript 2018-08-AddingAnExposedState/model.R
+Rscript examples/si-vital-dynamics/model.R
 ```
 
 ### Running All Examples
@@ -63,27 +63,18 @@ bash test.sh
 This runs each example's `model.R` and reports pass/fail with timing.
 
 
-## How to Use
-
-You may use and extend any of these examples in any way you want. We ask that if you publish a paper using EpiModel (with or without these gallery examples), you include a citation (see below).
-
-
 ## Contributing
 
 Contributions of new gallery examples are welcome! To contribute:
 
 1. Fork this repository on GitHub.
-2. Create a new subdirectory named `YYYY-MM-Description/` containing three files:
-   - `README.md` -- explanation of the model, authors, and details
+2. Create a new subdirectory under `examples/` containing:
    - `model.R` -- main script for network estimation and simulation
    - `module-fx.R` -- custom module functions plugged into `control.net()`
+   - `index.qmd` -- annotated Quarto document
 3. Include the standard unit test lines near the top of `model.R` (see existing examples).
 4. Verify your example passes: `bash test.sh`
-5. Submit a Pull Request. We will review, request changes if needed, and merge.
-
-### Requesting New Examples
-
-If you'd like to ask "how would you build a network model in EpiModel that does X?", file a [GitHub Issue](https://github.com/EpiModel/EpiModel-Gallery/issues) with a detailed description. We may generalize specific requests so the example is broadly useful.
+5. Submit a Pull Request.
 
 
 ## Citation