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CyGeiCyGei
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Re-run flusight with backend scripts - (in the future just keep the vignette)
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‎.github/workflows/R-CMD-check.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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name: R-CMD-check.yaml
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permissions: read-all
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jobs:
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R-CMD-check:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.r }})
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strategy:
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fail-fast: false
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matrix:
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config:
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- {os: macos-latest, r: "release"}
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- {os: windows-latest, r: "release"}
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- {os: ubuntu-latest, r: "devel", http-user-agent: "release"}
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- {os: ubuntu-latest, r: "release"}
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- {os: ubuntu-latest, r: "oldrel-1"}
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_KEEP_PKG_SOURCE: yes
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steps:
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- uses: actions/checkout@v6
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- uses: r-lib/actions/setup-pandoc@v2
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- uses: r-lib/actions/setup-r@v2
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with:
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r-version: ${{ matrix.config.r }}
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http-user-agent: ${{ matrix.config.http-user-agent }}
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use-public-rspm: true
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extra-repositories: https://mrc-ide.r-universe.dev
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::rcmdcheck
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needs: check
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- uses: r-lib/actions/check-r-package@v2
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with:
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upload-snapshots: true
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build_args: 'c("--no-manual", "--compact-vignettes=gs+qpdf")'

‎.github/workflows/test-coverage.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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push:
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branches: [main, master]
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pull_request:
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name: test-coverage.yaml
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permissions: read-all
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jobs:
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test-coverage:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- uses: actions/checkout@v6
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- uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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extra-repositories: https://mrc-ide.r-universe.dev
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- uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::covr, any::xml2
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needs: coverage
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- name: Test coverage
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run: |
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cov <- covr::package_coverage(
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quiet = FALSE,
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clean = FALSE,
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install_path = file.path(
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normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"),
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"package"
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)
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)
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print(cov)
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covr::to_cobertura(cov)
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shell: Rscript {0}
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- uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7
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with:
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# Fail on upload errors outside PRs, or when a PR has a Codecov token.
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fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
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files: ./cobertura.xml
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plugins: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Show testthat output
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if: always()
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run: |
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find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload test results
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if: failure()
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uses: actions/upload-artifact@v7
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with:
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name: coverage-test-failures
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path: ${{ runner.temp }}/package

‎.gitignore‎

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.Ruserdata
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**/*.quarto_ipynb
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# Resumable FluSight backtest cache
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data-raw/flusight-cache/

‎R/FluSight-data.R‎

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#' Scores from the 2025--26 FluSight backtest
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#'
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#' Score summaries comparing `incast` with selected FluSight models. They let
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#' the FluSight vignette run without refitting models or downloading Hub data.
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#' Score summaries comparing `incast` with official FluSight team submissions.
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#' They let the vignette run without refitting models or downloading Hub data.
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#'
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#' `flusight_scores` contains scores pooled across locations.
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#' `flusight_scores_by_location` contains scores stratified by location.
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#' \item{wis_scaled_relative_skill}{Relative WIS scaled to the
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#' `FluSight-ensemble`; values below one are better.}
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#' \item{count}{Number of forecast tasks scored.}
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#' \item{model_group}{One of `"FluSight ensemble"`, `"FluSight model"`,
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#' or `"incast model"`.}
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#' \item{model_group}{One of `"FluSight ensemble"`, `"FluSight baseline"`,
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#' `"FluSight model"`, or `"incast model"`.}
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#' \item{display}{Whether the vignette's concise comparison displays the
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#' model. All models remain available for custom filtering.}
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#' }
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#'
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#' @source Forecasts and target data from the
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#' \item{wis_scaled_relative_skill}{Relative WIS scaled to the
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#' `FluSight-ensemble`; values below one are better.}
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#' \item{count}{Number of forecast tasks scored.}
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#' \item{model_group}{One of `"FluSight ensemble"`, `"FluSight model"`,
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#' or `"incast model"`.}
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#' \item{model_group}{One of `"FluSight ensemble"`, `"FluSight baseline"`,
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#' `"FluSight model"`, or `"incast model"`.}
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#' \item{state}{Two-letter state abbreviation.}
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#' \item{display}{Whether the vignette's concise comparison displays the
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#' model. All models remain available for custom filtering.}
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#' }
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#' @source Forecasts and target data from the
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#' \href{https://github.com/cdcepi/FluSight-forecast-hub/tree/v1.2.0}{

‎README.Rmd‎

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# incast <a href="https://accidda.github.io/incast/"><img src="man/figures/logo.png" align="right" height="139" alt="incast website" /></a>
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<!-- badges: start -->
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[![R-CMD-check](https://github.com/ACCIDDA/incast/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ACCIDDA/incast/actions/workflows/R-CMD-check.yaml)
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[![Codecov test coverage](https://codecov.io/gh/ACCIDDA/incast/graph/badge.svg)](https://app.codecov.io/gh/ACCIDDA/incast)
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<!-- badges: end -->
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`incast` is an R package for infectious disease nowcasting and forecasting. It was developed through **[Insight Net](https://www.cdc.gov/insight-net)**, a **[CDC Center for Forecasting and Outbreak Analytics](https://www.cdc.gov/forecast-outbreak-analytics/index.html)** initiative.

‎README.md‎

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# incast <a href="https://accidda.github.io/incast/"><img src="man/figures/logo.png" align="right" height="139" alt="incast website" /></a>
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<!-- badges: start -->
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[![R-CMD-check](https://github.com/ACCIDDA/incast/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/ACCIDDA/incast/actions/workflows/R-CMD-check.yaml)
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[![Codecov test coverage](https://codecov.io/gh/ACCIDDA/incast/graph/badge.svg)](https://app.codecov.io/gh/ACCIDDA/incast)
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<!-- badges: end -->
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`incast` is an R package for infectious disease nowcasting and

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