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/.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/CRAN-SUBMISSION b/CRAN-SUBMISSION index 51a56aa1..e9ed91c2 100644 --- a/CRAN-SUBMISSION +++ b/CRAN-SUBMISSION @@ -1,3 +1,3 @@ -Version: 1.1.1 -Date: 2024-03-02 01:36:14 UTC -SHA: 75ae42aed7a035d184af69129e049c31e76e5f3b +Version: 1.2.0 +Date: 2024-06-20 18:52:31 UTC +SHA: 9a79a8bcb534ccd915a1189294cd6131053bc666 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' diff --git a/R/endpoints.R b/R/endpoints.R index d920b77c..1f789d18 100644 --- a/R/endpoints.R +++ b/R/endpoints.R @@ -163,8 +163,8 @@ pub_covid_hosp_facility_lookup <- function( #' ) #' #' pub_covid_hosp_facility( -#' hospital_pks = "100075", -#' collection_weeks = epirange(202001, 202005) +#' hospital_pks = "050063", +#' collection_weeks = epirange(20240101, 20240301) #' ) #' } #' @param hospital_pks character. Facility identifiers. @@ -1848,7 +1848,7 @@ pub_nidss_flu <- function( #' \dontrun{ #' pvt_norostat( #' auth = Sys.getenv("SECRET_API_AUTH_NOROSTAT"), -#' locations = "1", +#' locations = "Minnesota, Ohio, Oregon, Tennessee, and Wisconsin", #' epiweeks = 201233 #' ) #' } 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 e4d136f0..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://data.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 diff --git a/_pkgdown.yml b/_pkgdown.yml index 5bdc2d00..55d98ab6 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 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 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] diff --git a/man/pub_covid_hosp_facility.Rd b/man/pub_covid_hosp_facility.Rd index 59f4ff9b..c71f21c0 100644 --- a/man/pub_covid_hosp_facility.Rd +++ b/man/pub_covid_hosp_facility.Rd @@ -48,8 +48,8 @@ pub_covid_hosp_facility( ) pub_covid_hosp_facility( - hospital_pks = "100075", - collection_weeks = epirange(202001, 202005) + hospital_pks = "050063", + collection_weeks = epirange(20240101, 20240301) ) } } diff --git a/man/pvt_norostat.Rd b/man/pvt_norostat.Rd index 24ffd778..180182e1 100644 --- a/man/pvt_norostat.Rd +++ b/man/pvt_norostat.Rd @@ -30,7 +30,7 @@ the Delphi’s epidemiological data. \dontrun{ pvt_norostat( auth = Sys.getenv("SECRET_API_AUTH_NOROSTAT"), - locations = "1", + locations = "Minnesota, Ohio, Oregon, Tennessee, and Wisconsin", epiweeks = 201233 ) } 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) }) diff --git a/vignettes/epidatr.Rmd b/vignettes/epidatr.Rmd index d96a2fdf..4d336733 100644 --- a/vignettes/epidatr.Rmd +++ b/vignettes/epidatr.Rmd @@ -117,7 +117,9 @@ pub_covidcast( ) ``` -We can fetch a subset of states by listing out the desired locations: +Alternatively, we can fetch the full time series for a subset of states by +listing out the desired locations in the `geo_value` argument and using `*` +in the `time_values` argument: ```{r, eval = FALSE} # Obtain the most up-to-date version of the smoothed covid-like illness (CLI) @@ -128,24 +130,8 @@ pub_covidcast( geo_type = "state", time_type = "day", geo_values = c("pa", "ca", "fl"), - time_values = epirange(20210105, 20210410) -) -``` - -We can also request data for a single location at a time, via the `geo_values` argument. - -```{r} -# Obtain the most up-to-date version of the smoothed covid-like illness (CLI) -# signal from the COVID-19 Trends and Impact survey for Pennsylvania -epidata <- pub_covidcast( - source = "fb-survey", - signals = "smoothed_cli", - geo_type = "state", - time_type = "day", - geo_values = "pa", - time_values = epirange(20210105, 20210410) + time_values = "*" ) -knitr::kable(head(epidata)) ``` ## Getting versioned data