Quasi-fork of all contents from wwinference package (#3)

.Rbuildignore

@@ -0,0 +1,6 @@
+^_pkgdown\.yml$
+^docs$
+^pkgdown$
+^\.github$
+^.*\.Rproj$
+^\.Rproj\.user$

.github/.gitignore

@@ -0,0 +1 @@
+*.html

.github/CODEOWNERS

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+*@kaitejohnson @dylanhmorris

.github/CONTRIBUTING.md

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+# Contributing to `wwinference`
+
+This outlines how to propose a change to `wwinference`.
+
+## Fixing typos
+
+You can fix typos, spelling mistakes, or grammatical errors in the documentation directly using the GitHub web interface, as long as the changes are made in the _source_ file.
+This generally means you'll need to edit [roxygen2 comments](https://roxygen2.r-lib.org/articles/roxygen2.html) in an `.R`, not a `.Rd` file.
+You can find the `.R` file that generates the `.Rd` by reading the comment in the first line.
+
+## Bigger changes
+
+If you want to make a bigger change, it's a good idea to first file an issue and make sure someone from the team agrees that it’s needed.
+If you’ve found a bug, please file an issue that illustrates the bug with a minimal
+[reprex](https://www.tidyverse.org/help/#reprex) (this will also help you write a unit test, if needed).
+See our guide on [how to create a great issue](https://code-review.tidyverse.org/issues/) for more advice.
+
+### Pull request process
+
+*   Fork the package and clone onto your computer. If you haven't done this before, we recommend using `usethis::create_from_github("CDCgov/ww-inference-model", fork = TRUE)`.
+
+*   Install all development dependencies with `devtools::install_dev_deps()`, and then make sure the package passes R CMD check by running `devtools::check()`.
+    If R CMD check doesn't pass cleanly, it's a good idea to ask for help before continuing.
+*   Create a Git branch for your pull request (PR). We recommend using `usethis::pr_init("brief-description-of-change")`.
+
+*   Make your changes, commit to git, and then create a PR by running `usethis::pr_push()`, and following the prompts in your browser.
+    The title of your PR should briefly describe the change.
+    The body of your PR should contain `Fixes #issue-number`.
+
+*  For user-facing changes, add a bullet to the top of `NEWS.md` (i.e. just below the first header). Follow the style described in <https://style.tidyverse.org/news.html>.
+
+### Code style
+
+*   New code should follow the tidyverse [style guide](https://style.tidyverse.org).
+    You can use the [styler](https://CRAN.R-project.org/package=styler) package to apply these styles, but please don't restyle code that has nothing to do with your PR.
+
+*  We use [roxygen2](https://cran.r-project.org/package=roxygen2), with [Markdown syntax](https://cran.r-project.org/web/packages/roxygen2/vignettes/rd-formatting.html), for documentation.
+
+*  We use [testthat](https://cran.r-project.org/package=testthat) for unit tests.
+   Contributions with test cases included are easier to accept.
+
+## Code of Conduct
+
+Please note that the RtGam project is released with a
+[Contributor Code of Conduct](CODE_OF_CONDUCT.md). By contributing to this
+project you agree to abide by its terms.

.github/ISSUE_TEMPLATE/bug_report.md

@@ -8,10 +8,7 @@ assignees: ''
 ---
 
 **Describe the bug**
-A clear and concise description of what feature is not working.
-
-**Impact**
-Please describe the impact this bug is causing to your program or organization.
+A clear and concise description of what the bug is.
 
 **To Reproduce**
 Steps to reproduce the behavior:
@@ -26,9 +23,6 @@ A clear and concise description of what you expected to happen.
 **Screenshots**
 If applicable, add screenshots to help explain your problem.
 
-**Logs**
-If applicable, please attach logs to help describe your problem.
-
 **Desktop (please complete the following information):**
  - OS: [e.g. iOS]
  - Browser [e.g. chrome, safari]

.github/ISSUE_TEMPLATE/scientific-improvement.md

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+---
+name: Scientific improvement
+about: Suggest a way to improve an existing tool or pipeline
+title: ''
+labels: ''
+assignees: ''
+
+---
+
+## Describe the improvement that needs to be made
+(e.g. update a parameter estimate, tweak the prior, modify the model)
+
+## Provide links to references to methods or data sources
+
+## Describe the changes expected to the model's outputs
+
+## Suggest new tests that will need to be implemented

.github/SUPPORT.md

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+# Getting help with wwinference
+
+Thanks for using wwinference!
+Before filing an issue, there are a few places to explore and pieces to put together to make the process as smooth as possible.
+
+## Make a reprex
+
+Start by making a minimal **repr**oducible **ex**ample using the  [reprex](https://reprex.tidyverse.org/) package.
+If you haven't heard of or used reprex before, you're in for a treat!
+Seriously, reprex will make all of your R-question-asking endeavors easier (which is a pretty insane ROI for the five to ten minutes it'll take you to learn what it's all about).
+For additional reprex pointers, check out the [Get help!](https://www.tidyverse.org/help/) section of the tidyverse site.
+
+## Where to ask?
+
+[File an issue](https://github.com/CDCgov/ww-inference-model/issues/new)!
+
+Before opening a new issue, be sure to [search issues and pull requests](https://github.com/CDCgov/ww-inference-model/issues) to make sure the bug hasn't been reported and/or already fixed in the development version.
+By default, the search will be pre-populated with `is:issue is:open`.
+You can [edit the qualifiers](https://help.github.com/articles/searching-issues-and-pull-requests/)  (e.g. `is:pr`, `is:closed`) as needed.
+For example, you'd simply remove `is:open` to search _all_ issues in the repo, open or closed.

.github/workflows/pkgdown.yaml

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+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, prod]
+  pull_request:
+    branches: [main, prod]
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+      id-token: write
+      pages: write
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: r-lib/actions/setup-pandoc@v2
+        with:
+          pandoc-version: "2.19.2"
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: "release"
+          use-public-rspm: true
+          install-r: false
+          extra-repositories: "https://mc-stan.org/r-packages/"
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          pak-version: rc
+          extra-packages: any::pkgdown local::.
+          needs: website
+
+      - name: "Install cmdstan via cmdstanr"
+        uses: epinowcast/actions/install-cmdstan@v1
+        with:
+          cmdstan-version: "latest"
+
+      - name: Build site
+        run: "pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)"
+        shell: Rscript {0}
+
+      - name: Upload artifact for GH pages deployment
+        uses: actions/upload-pages-artifact@v2
+        with:
+          path: "docs/"
+
+  deploy:
+    # check builds on PRs but only deploy when main changes
+    if: ${{ github.event_name != 'pull_request' }}
+    needs: build
+    runs-on: ubuntu-latest
+    permissions:
+      pages: write
+      id-token: write
+
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    steps:
+      - name: Deploy to GitHub pages
+        uses: actions/[email protected]

.github/workflows/pre-commit.yaml

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+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: "3.12"
+    - uses: actions/cache@v4
+      with:
+        path: |
+          ~/.cache/R/renv
+        key: r-precommit-cache|${{ env.pythonLocation }}|${{ hashFiles('.pre-commit-config.yaml') }}
+    - uses: pre-commit/[email protected]

.github/workflows/r-cmd-check.yaml

@@ -0,0 +1,28 @@
+name: R CMD check project packages
+
+on:
+  pull_request:
+  push:
+    branches: [main, prod]
+
+jobs:
+  check-package:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/checkout@v4
+    - uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: "release"
+        use-public-rspm: true
+        extra-repositories: "https://mc-stan.org/r-packages/"
+    - name: "Set up dependencies for wwinference"
+      uses: r-lib/actions/setup-r-dependencies@v2
+      with:
+        needs: check
+    - name: "Install cmdstan via cmdstanr"
+      uses: epinowcast/actions/install-cmdstan@v1
+      with:
+        cmdstan-version: "latest"
+    - name: "Check wwinference package"
+      uses: r-lib/actions/check-r-package@v2