diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 607c71b..f5e78c2 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -26,7 +26,7 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} DELPHI_EPIDATA_KEY: ${{ secrets.SECRET_EPIDATR_GHACTIONS_DELPHI_EPIDATA_KEY }} steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -50,9 +50,9 @@ jobs: run: | target_ref <- "${{ github.event_name == 'pull_request' && github.base_ref || github.ref }}" override <- if (target_ref == "main" || target_ref == "refs/heads/main") { - list(development = list(mode = "release", version_label = "light")) + list(development = list(mode = "release")) } else if (target_ref == "dev" || target_ref == "refs/heads/dev") { - list(development = list(mode = "devel", version_label = "success")) + list(development = list(mode = "devel")) } else { stop("Unexpected target_ref: ", target_ref) } @@ -65,7 +65,7 @@ jobs: - name: Deploy to GitHub pages 🚀 if: github.event_name != 'pull_request' - uses: JamesIves/github-pages-deploy-action@v4.4.1 + uses: JamesIves/github-pages-deploy-action@v4.5.0 with: clean: false branch: gh-pages diff --git a/.gitignore b/.gitignore index 5a928af..f3fc463 100644 --- a/.gitignore +++ b/.gitignore @@ -16,7 +16,6 @@ env /doc/ /Meta/ .secrets -epidatr.Rproj renv.lock renv/ -.Rprofile \ No newline at end of file +.Rprofile diff --git a/DESCRIPTION b/DESCRIPTION index 810b593..18b7839 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,59 +1,74 @@ -Package: epidatr Type: Package +Package: epidatr Title: Client for Delphi's 'Epidata' API Version: 1.2.0 -Authors@R: - c( - person("Logan", "Brooks", email = "lcbrooks@andrew.cmu.edu", role = c("aut")), - person("Dmitry", "Shemetov", email = "dshemeto@andrew.cmu.edu", role = c("aut")), - person("Samuel", "Gratzl", email = "sam@sgratzl.com", role = c("aut")), - person("David", "Weber", email = "davidweb@andrew.cmu.edu", role = c("ctb", "cre")), - person("Nat", "DeFries", role = c("ctb")), - person("Alex", "Reinhart", role = c("ctb")), - person("Daniel", "McDonald", role = c("ctb")), - person("Kean Ming", "Tan", role = c("ctb")), - person("Will", "Townes", role = c("ctb")), - person("George", "Haff", role = c("ctb")), - person("Kathryn", "Mazaitis", role = c("ctb")) +Authors@R: c( + person("Logan", "Brooks", , "lcbrooks@andrew.cmu.edu", role = "aut"), + person("Dmitry", "Shemetov", , "dshemeto@andrew.cmu.edu", role = "aut"), + person("Samuel", "Gratzl", , "sam@sgratzl.com", role = "aut"), + person("David", "Weber", , "davidweb@andrew.cmu.edu", role = c("ctb", "cre")), + person("Nat", "DeFries", role = "ctb"), + person("Alex", "Reinhart", role = "ctb"), + person("Daniel J.", "McDonald", role = "ctb"), + person("Kean Ming", "Tan", role = "ctb"), + person("Will", "Townes", role = "ctb"), + person("George", "Haff", role = "ctb"), + person("Kathryn", "Mazaitis", role = "ctb") ) -URL: https://cmu-delphi.github.io/epidatr/, https://cmu-delphi.github.io/delphi-epidata/, https://github.com/cmu-delphi/epidatr -BugReports: https://github.com/cmu-delphi/epidatr/issues -Description: The Delphi 'Epidata' API provides real-time access to epidemiological surveillance data for influenza, 'COVID-19', and other diseases for the USA at various geographical resolutions, both from official government sources such as the Center for Disease Control (CDC) and Google Trends and private partners such as Facebook and Change 'Healthcare'. It is built and maintained by the Carnegie Mellon University Delphi research group. To cite this API: David C. Farrow, Logan C. Brooks, Aaron 'Rumack', Ryan J. 'Tibshirani', 'Roni' 'Rosenfeld' (2015). Delphi 'Epidata' API. . -Depends: R (>= 3.5.0) +Description: The Delphi 'Epidata' API provides real-time access to + epidemiological surveillance data for influenza, 'COVID-19', and other + diseases for the USA at various geographical resolutions, both from + official government sources such as the Center for Disease Control + (CDC) and Google Trends and private partners such as Facebook and + Change 'Healthcare'. It is built and maintained by the Carnegie Mellon + University Delphi research group. To cite this API: David C. Farrow, + Logan C. Brooks, Aaron 'Rumack', Ryan J. 'Tibshirani', 'Roni' + 'Rosenfeld' (2015). Delphi 'Epidata' API. + . License: MIT + file LICENSE -Encoding: UTF-8 -LazyData: true -Roxygen: list(markdown = TRUE) +URL: https://cmu-delphi.github.io/epidatr/, + https://cmu-delphi.github.io/delphi-epidata/, + https://github.com/cmu-delphi/epidatr +BugReports: https://github.com/cmu-delphi/epidatr/issues +Depends: + R (>= 3.5.0) Imports: cachem, checkmate, cli, - httr, glue, + httr, jsonlite, magrittr, MMWRweek, - purrr, openssl, + purrr, rappdirs, readr, tibble, usethis, xml2 -RoxygenNote: 7.3.2 Suggests: dplyr, ggplot2, knitr, - maps, mapproj, - rmarkdown, + maps, rlang, + rmarkdown, testthat (>= 3.1.5), withr -VignetteBuilder: knitr -Language: en-US +VignetteBuilder: + knitr +Remotes: + cmu-delphi/delphidocs +Config/Needs/website: cmu-delphi/delphidocs Config/testthat/edition: 3 +Encoding: UTF-8 +Language: en-US +LazyData: true +Roxygen: list(markdown = TRUE) +RoxygenNote: 7.3.2 Collate: 'auth.R' 'avail_endpoints.R' diff --git a/README.Rmd b/README.Rmd index 744b4df..bdd2e9c 100644 --- a/README.Rmd +++ b/README.Rmd @@ -25,7 +25,7 @@ The [Delphi Epidata API](https://cmu-delphi.github.io/delphi-epidata/) provides real-time access to epidemiological surveillance data for influenza, COVID-19, and other diseases from both official government sources such as the [Centers for Disease Control and Prevention -(CDC)](https://www.cdc.gov/datastatistics/index.html), private partners such as +(CDC)](https://www.cdc.gov/), private partners such as [Facebook (now Meta)](https://delphi.cmu.edu/blog/2020/08/26/covid-19-symptom-surveys-through-facebook/) and [Change Healthcare](https://www.changehealthcare.com/), and other public @@ -79,7 +79,7 @@ pak::pkg_install("epidatr") pak::pkg_install("cmu-delphi/epidatr@dev") ``` -Our CRAN listing is [here](https://cran.r-project.org/web/packages/epidatr/index.html). +Our CRAN listing is [here](https://CRAN.R-project.org/package=epidatr/index.html). ### API Keys diff --git a/README.md b/README.md index f034847..9e3ca5f 100644 --- a/README.md +++ b/README.md @@ -16,8 +16,7 @@ The [Delphi Epidata API](https://cmu-delphi.github.io/delphi-epidata/) provides real-time access to epidemiological surveillance data for influenza, COVID-19, and other diseases from both official government sources such as the [Centers for Disease Control and Prevention -(CDC)](https://archive.cdc.gov/), private partners -such as [Facebook (now +(CDC)](https://www.cdc.gov/), private partners such as [Facebook (now Meta)](https://delphi.cmu.edu/blog/2020/08/26/covid-19-symptom-surveys-through-facebook/) and [Change Healthcare](https://www.changehealthcare.com/), and other public datasets like [Google @@ -82,7 +81,7 @@ pak::pkg_install("cmu-delphi/epidatr@dev") ``` Our CRAN listing is -[here](https://CRAN.R-project.org/package=epidatr). +[here](https://CRAN.R-project.org/package=epidatr/index.html). ### API Keys diff --git a/_pkgdown.yml b/_pkgdown.yml index 5bdc2d0..55d98ab 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,27 +1,12 @@ -# Colors should stay consistent across epipredict, epiprocess, and epidatr, -# using Carnegie Red -# https://www.cmu.edu/brand/brand-guidelines/visual-identity/colors.html - # This is to give a default value to the `mode` parameter in the # `pkgdown::build_site` function. This is useful when building the site locally, # as it will default to `devel` mode. In practice, this should all be handled # dynamically by the CI/CD pipeline. development: mode: devel - version_label: success template: - bootstrap: 5 - bootswatch: cosmo - bslib: - font_scale: 1.0 - primary: "#C41230" - success: "#B4D43C" - link-color: "#C41230" - -navbar: - bg: primary - type: light + package: delphidocs url: https://cmu-delphi.github.io/epidatr/ @@ -29,16 +14,17 @@ home: links: - text: Get the Python client href: https://github.com/cmu-delphi/epidatpy/ - - text: View the Delphi Website - href: https://delphi.cmu.edu/ - - text: Introduction to Delphi's Tooling Work - href: https://cmu-delphi.github.io/delphi-tooling-book/ - - text: The epiprocess R package - href: https://cmu-delphi.github.io/epiprocess/ - - text: The epipredict R package - href: https://cmu-delphi.github.io/epipredict/ - - text: The epidatasets R package - href: https://cmu-delphi.github.io/epidatasets/ + sidebar: + structure: [links, license, community, citation, authors, related, dev] + components: + related: + title: Delphi packages and resources + text: | + * [The epiprocess R package](https://cmu-delphi.github.io/epiprocess/) + * [The epipredict R package](https://cmu-delphi.github.io/epipredict/) + * [The epidatasets R package](https://cmu-delphi.github.io/epidatasets/) + * [Introduction to Delphi's Tooling Work](https://cmu-delphi.github.io/delphi-tooling-book/) + reference: - title: Data source and signal discovery diff --git a/epidatr.Rproj b/epidatr.Rproj new file mode 100644 index 0000000..497f8bf --- /dev/null +++ b/epidatr.Rproj @@ -0,0 +1,20 @@ +Version: 1.0 + +RestoreWorkspace: Default +SaveWorkspace: Default +AlwaysSaveHistory: Default + +EnableCodeIndexing: Yes +UseSpacesForTab: Yes +NumSpacesForTab: 2 +Encoding: UTF-8 + +RnwWeave: Sweave +LaTeX: pdfLaTeX + +AutoAppendNewline: Yes +StripTrailingWhitespace: Yes + +BuildType: Package +PackageUseDevtools: Yes +PackageInstallArgs: --no-multiarch --with-keep.source diff --git a/man/epidatr-package.Rd b/man/epidatr-package.Rd index 1809cb9..1ac2d0c 100644 --- a/man/epidatr-package.Rd +++ b/man/epidatr-package.Rd @@ -39,7 +39,7 @@ Other contributors: \itemize{ \item Nat DeFries [contributor] \item Alex Reinhart [contributor] - \item Daniel McDonald [contributor] + \item Daniel J. McDonald [contributor] \item Kean Ming Tan [contributor] \item Will Townes [contributor] \item George Haff [contributor] diff --git a/tests/testthat/test-request.R b/tests/testthat/test-request.R index 6a3d653..426c3e0 100644 --- a/tests/testthat/test-request.R +++ b/tests/testthat/test-request.R @@ -1,4 +1,5 @@ test_that("requesting works", { + skip("This site is down.") res <- do_request("https://httpbin.org/status/414", list(), timeout_seconds = 10 * 60) expect_equal(res$status_code, 414) })