From 220f6713322fc42518fcb9e23fd70f6adeb54fb4 Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Mon, 11 Nov 2024 08:08:31 -0800 Subject: [PATCH 1/9] check .Rprog into version control --- .gitignore | 3 +-- epidatr.Rproj | 20 ++++++++++++++++++++ 2 files changed, 21 insertions(+), 2 deletions(-) create mode 100644 epidatr.Rproj diff --git a/.gitignore b/.gitignore index 5a928afe..f3fc4639 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/epidatr.Rproj b/epidatr.Rproj new file mode 100644 index 00000000..497f8bfc --- /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 From aaca47934f13738acf0b66e4821581d6a360bf17 Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Mon, 11 Nov 2024 08:09:26 -0800 Subject: [PATCH 2/9] add template pkg to description, clean with usethis::use_tidy_description() --- DESCRIPTION | 71 ++++++++++++++++++++++++++++++++--------------------- 1 file changed, 43 insertions(+), 28 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 451c7a15..18b78398 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: 7.3.1 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' From 09ba648f3b5e5631f80a7abf4d747102bb5e436a Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Mon, 11 Nov 2024 08:09:42 -0800 Subject: [PATCH 3/9] document() --- man/covidcast_epidata.Rd | 4 ++-- man/epidatr-package.Rd | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/man/covidcast_epidata.Rd b/man/covidcast_epidata.Rd index 9fe31718..e11c63b1 100644 --- a/man/covidcast_epidata.Rd +++ b/man/covidcast_epidata.Rd @@ -27,7 +27,7 @@ an object containing fields for every signal: \if{html}{\out{
}}\preformatted{epidata <- covidcast_epidata() epidata$signals -#> # A tibble: 443 x 3 +#> # A tibble: 451 x 3 #> source signal short_description #> #> 1 chng smoothed_outpatient_cli Estimated percentage of outpatie~ @@ -40,7 +40,7 @@ epidata$signals #> 8 covid-act-now pcr_specimen_total_tests Total number of PCR specimens te~ #> 9 doctor-visits smoothed_cli Percentage of daily doctor visit~ #> 10 doctor-visits smoothed_adj_cli Percentage of daily doctor visit~ -#> # i 433 more rows +#> # i 441 more rows }\if{html}{\out{
}} If you use an editor that supports tab completion, such as RStudio, type diff --git a/man/epidatr-package.Rd b/man/epidatr-package.Rd index 1809cb9a..1ac2d0c1 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] From 0dd6f140cc58b6e6d643b64605fac9ea8e1d7b63 Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Mon, 11 Nov 2024 08:10:15 -0800 Subject: [PATCH 4/9] delphidocs pkg, mv related down the sidebar --- _pkgdown.yml | 39 +++++++++++++-------------------------- 1 file changed, 13 insertions(+), 26 deletions(-) diff --git a/_pkgdown.yml b/_pkgdown.yml index 5bdc2d00..10092f42 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,27 +1,13 @@ -# 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 + version_label: danger 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 +15,17 @@ 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 From 0515ce63f97586aa112da68a5bc971079043f6e1 Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Wed, 13 Nov 2024 09:18:06 -0800 Subject: [PATCH 5/9] adjust pkgdown workflow --- .github/workflows/pkgdown.yaml | 8 ++++---- _pkgdown.yml | 1 - 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index 607c71b1..f5e78c25 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/_pkgdown.yml b/_pkgdown.yml index 10092f42..55d98ab6 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -4,7 +4,6 @@ # dynamically by the CI/CD pipeline. development: mode: devel - version_label: danger template: package: delphidocs From 947e8fe4b00ed6acf7dcb3a21558c900e3359e47 Mon Sep 17 00:00:00 2001 From: dajmcdon Date: Thu, 14 Nov 2024 19:01:01 +0000 Subject: [PATCH 6/9] docs: document (GHA) --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index f034847a..e7598e4b 100644 --- a/README.md +++ b/README.md @@ -16,7 +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 +(CDC)](https://www.cdc.gov/datastatistics/index.html), 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 @@ -82,7 +82,7 @@ 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/web/packages/epidatr/index.html). ### API Keys From 05af3b16ec353de3099dafeac78332717b272298 Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Thu, 14 Nov 2024 12:05:45 -0800 Subject: [PATCH 7/9] rebuild readme --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index e4d136f0..e7598e4b 100644 --- a/README.md +++ b/README.md @@ -16,7 +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://data.cdc.gov/), private partners +(CDC)](https://www.cdc.gov/datastatistics/index.html), 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 @@ -82,7 +82,7 @@ pak::pkg_install("cmu-delphi/epidatr@dev") ``` Our CRAN listing is -[here](https://CRAN.R-project.org/package=epidatr/index.html). +[here](https://cran.r-project.org/web/packages/epidatr/index.html). ### API Keys From b0062d089891ceeeadc8608db5e1e7511b67007d Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Thu, 14 Nov 2024 12:09:16 -0800 Subject: [PATCH 8/9] fix links in the Rmd, then rebuild (not sure where the diff came from) --- README.Rmd | 4 ++-- README.md | 5 ++--- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/README.Rmd b/README.Rmd index 744b4dfb..bdd2e9c3 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 e7598e4b..9e3ca5fd 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://www.cdc.gov/datastatistics/index.html), 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/web/packages/epidatr/index.html). +[here](https://CRAN.R-project.org/package=epidatr/index.html). ### API Keys From a6a4049e30ce77311223c99980becdb1d398c186 Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Thu, 14 Nov 2024 12:26:32 -0800 Subject: [PATCH 9/9] skip a failing test --- tests/testthat/test-request.R | 1 + 1 file changed, 1 insertion(+) diff --git a/tests/testthat/test-request.R b/tests/testthat/test-request.R index 6a3d6536..426c3e08 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) })