From 1c012fb45babe9d6eada5102f3742cae0c385325 Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Mon, 11 Nov 2024 13:52:00 -0800 Subject: [PATCH 1/5] rebuild readme --- README.Rmd | 4 +- README.md | 4 +- man/figures/README-unnamed-chunk-5-1.svg | 56 ++++++++++++------------ 3 files changed, 32 insertions(+), 32 deletions(-) diff --git a/README.Rmd b/README.Rmd index be8e31e..fa9982c 100644 --- a/README.Rmd +++ b/README.Rmd @@ -29,8 +29,8 @@ examples here for easy offline use. You can install the development version of `{epidatasets}` like so: ``` r -# install.packages("remotes") -remotes::install_github("cmu-delphi/epidatasets") +# install.packages("pak") +pak::pkg_install("cmu-delphi/epidatasets") ``` diff --git a/README.md b/README.md index 3895a84..6273e51 100644 --- a/README.md +++ b/README.md @@ -17,8 +17,8 @@ Delphi Epidata API, and deposit some examples here for easy offline use. You can install the development version of `{epidatasets}` like so: ``` r -# install.packages("remotes") -remotes::install_github("cmu-delphi/epidatasets") +# install.packages("pak") +pak::pkg_install("cmu-delphi/epidatasets") ``` ## Contents diff --git a/man/figures/README-unnamed-chunk-5-1.svg b/man/figures/README-unnamed-chunk-5-1.svg index 3f429b0..0ec156c 100644 --- a/man/figures/README-unnamed-chunk-5-1.svg +++ b/man/figures/README-unnamed-chunk-5-1.svg @@ -111,7 +111,7 @@ - + @@ -186,7 +186,7 @@ - + @@ -256,7 +256,7 @@ - + @@ -331,7 +331,7 @@ - + @@ -560,40 +560,40 @@ - - - - - - - - - - - - - + + + + + + + + + + + + + - - + + - + - - + + - - + + - - + + - - + + From cbb0152b6b42bfd2ff34938d0bb482c708bac1be Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Mon, 11 Nov 2024 14:01:06 -0800 Subject: [PATCH 2/5] add config --- DESCRIPTION | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 0fdef78..ec1fb0b 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -9,6 +9,7 @@ Description: This package contains data sets used to compile vignettes and to the Delphi Epidata API, and deposit some examples here for easy offline use. License: MIT + file LICENSE +URL: https://cmu-delphi.github.io/epidatasets/ Depends: R (>= 2.10) Suggests: @@ -22,10 +23,11 @@ Suggests: purrr, readr Remotes: + cmu-delphi/delphidocs, cmu-delphi/epidatr, cmu-delphi/epipredict, cmu-delphi/epiprocess +Config/Needs/website: cmu-delphi/delphidocs Encoding: UTF-8 LazyData: true RoxygenNote: 7.2.3 -URL: https://cmu-delphi.github.io/epidatasets/ From 46df0bdf7b67298de3e6ffa659c9f80e15a0e891 Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Mon, 11 Nov 2024 14:12:09 -0800 Subject: [PATCH 3/5] add package documentation --- R/epidatasets-package.R | 6 ++++++ man/epidatasets-package.Rd | 38 ++++++++++++++++++++++++++++++++++++++ 2 files changed, 44 insertions(+) create mode 100644 R/epidatasets-package.R create mode 100644 man/epidatasets-package.Rd diff --git a/R/epidatasets-package.R b/R/epidatasets-package.R new file mode 100644 index 0000000..a65cf64 --- /dev/null +++ b/R/epidatasets-package.R @@ -0,0 +1,6 @@ +#' @keywords internal +"_PACKAGE" + +## usethis namespace: start +## usethis namespace: end +NULL diff --git a/man/epidatasets-package.Rd b/man/epidatasets-package.Rd new file mode 100644 index 0000000..d581a19 --- /dev/null +++ b/man/epidatasets-package.Rd @@ -0,0 +1,38 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/epidatasets-package.R +\docType{package} +\name{epidatasets-package} +\alias{epidatasets} +\alias{epidatasets-package} +\title{epidatasets: Epidemiological Data for Delphi Tooling Examples} +\description{ +This package contains data sets used to compile vignettes and other documentation in Delphi R Packages. The goal is to avoid calls to the Delphi Epidata API, and to deposit some examples here for easy offline use. +} +\seealso{ +Useful links: +\itemize{ + \item \url{https://github.com/cmu-delphi/epidatasets} + \item \url{https://cmu-delphi.github.io/epidatasets/} +} + +} +\author{ +\strong{Maintainer}: Nat DeFries \email{ndefries@andrew.cmu.edu} + +Authors: +\itemize{ + \item Daniel J. McDonald \email{daniel@stat.ubc.ca} +} + +Other contributors: +\itemize{ + \item Johns Hopkins University Center for Systems Science and Engineering (Owner of COVID-19 cases and deaths data from the COVID-19 Data Repository) [data contributor] + \item Johns Hopkins University (Copyright holder of COVID-19 cases and deaths data from the COVID-19 Data Repository) [copyright holder] + \item Carnegie Mellon University Delphi Group (Owner of masking, social-distancing, and CLI data from the COVID-19 Trends and Impacts Survey. Owner of claims-based CLI data from the Delphi Epidata API) [data contributor] + \item The COVID-19 Canada Open Data Working Group (Owner of Canadian COVID-19 cases rates from the Covid19Canada data repository) [data contributor] + \item Statistics Canada (Owner of Canadian graduate employment income data from the Statistics Canada website) [data contributor] + \item Google (Collaborator on CLI data from the Google symptom surveys) [data contributor] +} + +} +\keyword{internal} From 65518c9673f7d249130edab7eddfbc87afffabba Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Mon, 11 Nov 2024 14:13:42 -0800 Subject: [PATCH 4/5] move to delphidocs --- .gitignore | 2 +- _pkgdown.yml | 42 ++++++++++++++++++++++-------------------- 2 files changed, 23 insertions(+), 21 deletions(-) diff --git a/.gitignore b/.gitignore index 7c06555..50dbdb4 100644 --- a/.gitignore +++ b/.gitignore @@ -2,5 +2,5 @@ .Rhistory .RData .Ruserdata -.DS_Store +*.DS_Store docs diff --git a/_pkgdown.yml b/_pkgdown.yml index 3963f4a..a7ae2f7 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -1,24 +1,26 @@ url: https://cmu-delphi.github.io/epidatasets/ + template: - bootstrap: 5 - bootswatch: cosmo - bslib: - font_scale: 1.0 - primary: '#C41230' - link-color: '#C41230' - navbar-bg: '#C41230' - navbar-fg: '#f8f8f8' -navbar: - bg: '#C41230' - fg: '#f8f8f8' + package: delphidocs + +repo: + url: + home: https://github.com/cmu-delphi/epidatasets/ + source: https://github.com/cmu-delphi/epidatasets/ + issue: https://github.com/cmu-delphi/epidatasets/issues + home: - links: - - 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 covidcast R package - href: https://cmu-delphi.github.io/covidcast/covidcastR/ - - text: The epidatr R package - href: https://github.com/cmu-delphi/epidatr/ + sidebar: + structure: [links, license, community, citation, authors, dev, related] + components: + related: + title: Delphi packages and resources + text: | + * [The epidatr package](https://github.com/cmu-delphi/epidatr/) + * [The epiprocess package](https://cmu-delphi.github.io/epiprocess/) + * [The epipredict package](https://cmu-delphi.github.io/epipredict) + * [Introduction to Delphi's Tooling Work](https://cmu-delphi.github.io/delphi-tooling-book/) +reference: +- title: Included data +- contents: has_keyword("datasets") From e7bea15a9f46eb6aa49b57ae4115fd4fb4d6278c Mon Sep 17 00:00:00 2001 From: "Daniel J. McDonald" Date: Wed, 13 Nov 2024 09:21:00 -0800 Subject: [PATCH 5/5] bump workflow versions --- .github/workflows/R-CMD-check.yaml | 2 +- .github/workflows/pkgdown.yaml | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml index f4b17a4..c4b778d 100644 --- a/.github/workflows/R-CMD-check.yaml +++ b/.github/workflows/R-CMD-check.yaml @@ -15,7 +15,7 @@ jobs: GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} R_KEEP_PKG_SOURCE: yes steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-r@v2 with: diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml index ed7650c..a7276e8 100644 --- a/.github/workflows/pkgdown.yaml +++ b/.github/workflows/pkgdown.yaml @@ -22,7 +22,7 @@ jobs: permissions: contents: write steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - uses: r-lib/actions/setup-pandoc@v2 @@ -41,7 +41,7 @@ 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