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
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/DESCRIPTION b/DESCRIPTION
index dfb3f71..c79b1e3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -3,20 +3,28 @@ Package: epidatasets
Title: Epidemiological Data for Delphi Tooling Examples
Version: 0.0.1
Authors@R: c(
- person(c("Daniel", "J."), "McDonald", email="daniel@stat.ubc.ca", role = c("aut")),
- person("Nat", "DeFries", email="ndefries@andrew.cmu.edu", role = c("cre", "aut")),
- person("Johns Hopkins University Center for Systems Science and Engineering", role = "dtc", comment = "Owner of COVID-19 cases and deaths data from the COVID-19 Data Repository"),
- person("Johns Hopkins University", role = "cph", comment = "Copyright holder of COVID-19 cases and deaths data from the COVID-19 Data Repository"),
- person("Carnegie Mellon University Delphi Group", role = "dtc", comment = "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"),
- person("The COVID-19 Canada Open Data Working Group", role = "dtc", comment = "Owner of Canadian COVID-19 cases rates from the Covid19Canada data repository"),
- person("Statistics Canada", role = "dtc", comment = "Owner of Canadian graduate employment income data from the Statistics Canada website"),
- person("Google", role = "dtc", comment = "Collaborator on CLI data from the Google symptom surveys")
+ person(c("Daniel", "J."), "McDonald", , "daniel@stat.ubc.ca", role = "aut"),
+ person("Nat", "DeFries", , "ndefries@andrew.cmu.edu", role = c("cre", "aut")),
+ person("Johns Hopkins University Center for Systems Science and Engineering", role = "dtc",
+ comment = "Owner of COVID-19 cases and deaths data from the COVID-19 Data Repository"),
+ person("Johns Hopkins University", role = "cph",
+ comment = "Copyright holder of COVID-19 cases and deaths data from the COVID-19 Data Repository"),
+ person("Carnegie Mellon University Delphi Group", role = "dtc",
+ comment = "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"),
+ person("The COVID-19 Canada Open Data Working Group", role = "dtc",
+ comment = "Owner of Canadian COVID-19 cases rates from the Covid19Canada data repository"),
+ person("Statistics Canada", role = "dtc",
+ comment = "Owner of Canadian graduate employment income data from the Statistics Canada website"),
+ person("Google", role = "dtc",
+ comment = "Collaborator on CLI data from the Google symptom surveys")
)
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.
-License: file LICENSE
+License: MIT + file LICENSE
+URL: https://github.com/cmu-delphi/epidatasets,
+ https://cmu-delphi.github.io/epidatasets/
Depends:
R (>= 2.10)
Suggests:
@@ -35,10 +43,11 @@ Enhances:
epiprocess (>= 0.9.0),
tibble
Remotes:
+ cmu-delphi/delphidocs,
cmu-delphi/epidatr,
cmu-delphi/epiprocess
+Config/Needs/website: cmu-delphi/delphidocs
Encoding: UTF-8
LazyData: true
Roxygen: list(markdown = TRUE)
RoxygenNote: 7.3.2
-URL: https://cmu-delphi.github.io/epidatasets/
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/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/_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")
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}
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 @@
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