diff --git a/README.Rmd b/README.Rmd index 0233fc8a..f109948b 100644 --- a/README.Rmd +++ b/README.Rmd @@ -16,21 +16,20 @@ ggplot2::theme_set(ggplot2::theme_bw()) # Delphi Epidata R client - [![License: MIT][mit-image]][mit-url] [![Github Actions][github-actions-image]][github-actions-url] [![codecov](https://codecov.io/gh/dsweber2/epidatr/branch/dev/graph/badge.svg?token=jVHL9eHZNZ)](https://app.codecov.io/gh/dsweber2/epidatr) - - -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 for the USA at various geographical resolutions, both from official government sources such as the [Center for Disease Control (CDC)](https://www.cdc.gov/datastatistics/index.html) and [Google Trends](https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/google-symptoms.html) and private partners such as [Facebook](https://delphi.cmu.edu/blog/2020/08/26/covid-19-symptom-surveys-through-facebook/) and [Change Healthcare](https://www.changehealthcare.com/). It is built and maintained by the Carnegie Mellon University [Delphi research group](https://delphi.cmu.edu/). +The [Delphi Epidatr package](https://cmu-delphi.github.io/epidatr/) is an R front-end for the [Delphi Epidata API](https://cmu-delphi.github.io/delphi-epidata/), which 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)](https://www.cdc.gov/datastatistics/index.html) and [Google Trends](https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/google-symptoms.html) and private partners such as [Facebook](https://delphi.cmu.edu/blog/2020/08/26/covid-19-symptom-surveys-through-facebook/) and [Change Healthcare](https://www.changehealthcare.com/). It is built and maintained by the Carnegie Mellon University [Delphi research group](https://delphi.cmu.edu/). This package is designed to streamline the downloading and usage of data from the [Delphi Epidata API](https://cmu-delphi.github.io/delphi-epidata/). It provides a simple R interface to the API, including functions for downloading data, parsing the results, and converting the data into a tidy format. The API stores a historical record of all data, including corrections and updates, which is particularly useful for accurately backtesting forecasting models. We also provide packages for downstream data processing ([epiprocess](https://github.com/cmu-delphi/epiprocess)) and modeling ([epipredict](https://github.com/cmu-delphi/epipredict)). ## Usage +You can find detailed docs here: + ```{r} library(epidatr) # Obtain the smoothed covid-like illness (CLI) signal from the @@ -63,16 +62,23 @@ ggplot(epidata, aes(x = time_value, y = value)) + ## Installation -Install from GitHub: +You can install the stable version of this package from CRAN: + +```R +install.packages("epidatr") +pak::pkg_install("epidatr") +renv::install("epidatr") +``` + +Or if you want the development version, install from GitHub: ```R # Install the dev version using `pak` or `remotes` pak::pkg_install("cmu-delphi/epidatr") remotes::install_github("cmu-delphi/epidatr") +renv::install("cmu-delphi/epidatr") ``` -CRAN version coming soon. - ### API Keys The Delphi API requires a (free) API key for full functionality. To generate diff --git a/README.md b/README.md index f04b7be9..96a846f5 100644 --- a/README.md +++ b/README.md @@ -12,11 +12,13 @@ Actions](https://github.com/cmu-delphi/epidatr/workflows/ci/badge.svg)](https:// [![codecov](https://codecov.io/gh/dsweber2/epidatr/branch/dev/graph/badge.svg?token=jVHL9eHZNZ)](https://app.codecov.io/gh/dsweber2/epidatr) -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 for the USA at various -geographical resolutions, both from official government sources such as -the [Center for Disease Control +The [Delphi Epidatr package](https://cmu-delphi.github.io/epidatr/) is +an R front-end for the [Delphi Epidata +API](https://cmu-delphi.github.io/delphi-epidata/), which 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)](https://www.cdc.gov/datastatistics/index.html) and [Google Trends](https://cmu-delphi.github.io/delphi-epidata/api/covidcast-signals/google-symptoms.html) and private partners such as @@ -38,6 +40,8 @@ modeling ([epipredict](https://github.com/cmu-delphi/epipredict)). ## Usage +You can find detailed docs here: + ``` r library(epidatr) # Obtain the smoothed covid-like illness (CLI) signal from the @@ -87,16 +91,23 @@ ggplot(epidata, aes(x = time_value, y = value)) + ## Installation -Install from GitHub: +You can install the stable version of this package from CRAN: + +``` r +install.packages("epidatr") +pak::pkg_install("epidatr") +renv::install("epidatr") +``` + +Or if you want the development version, install from GitHub: ``` r # Install the dev version using `pak` or `remotes` pak::pkg_install("cmu-delphi/epidatr") remotes::install_github("cmu-delphi/epidatr") +renv::install("cmu-delphi/epidatr") ``` -CRAN version coming soon. - ### API Keys The Delphi API requires a (free) API key for full functionality. To diff --git a/man/figures/README-fb-cli-signal-1.png b/man/figures/README-fb-cli-signal-1.png index 5a76514d..21c040f1 100644 Binary files a/man/figures/README-fb-cli-signal-1.png and b/man/figures/README-fb-cli-signal-1.png differ diff --git a/man/get_api_key.Rd b/man/get_api_key.Rd index 18f7ae65..40774c66 100644 --- a/man/get_api_key.Rd +++ b/man/get_api_key.Rd @@ -52,7 +52,7 @@ Delphi Epidata API Registration Form. \url{https://api.delphi.cmu.edu/epidata/admin/registration_form} } \seealso{ -\code{\link[usethis:edit_r_environ]{usethis::edit_r_environ()}} to automatically edit the \code{.Renviron} -file; \code{\link[usethis:edit_r_profile]{usethis::edit_r_profile()}} to automatically edit the \code{.Rprofile} +\code{\link[usethis:edit]{usethis::edit_r_environ()}} to automatically edit the \code{.Renviron} +file; \code{\link[usethis:edit]{usethis::edit_r_profile()}} to automatically edit the \code{.Rprofile} file }