Use delphidocs

.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

.gitignore

@@ -16,7 +16,6 @@ env
 /doc/
 /Meta/
 .secrets
-epidatr.Rproj
 renv.lock
 renv/
-.Rprofile
+.Rprofile

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

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. <https://github.com/cmu-delphi/delphi-epidata>.
-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.
+    <https://github.com/cmu-delphi/delphi-epidata>.
 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'

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
 #' )
 #' }

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
 

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

_pkgdown.yml

@@ -1,44 +1,30 @@
-# 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/
 
 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

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

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)
 })

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