shinyppg

A Shiny app to view the Pteridophyte Phylogeny Group (PPG) taxonomic database.

The app can be accessed at: https://pteridogroup.shinyapps.io/shinyppg/

Installation

General usage

Install from GitHub:

# install.packages("remotes")
remotes::install_github("pteridogroup/shinyppg")

Development

Developers can install a local version from the project root:

# install.packages("devtools")
devtools::install()

Usage

Launch the app with:

library(shinyppg)
ppg_app()

The app provides a viewer interface to browse and explore PPG taxonomic data. You can filter by order, family, or genus to view specific taxonomic groups.

Deploying

The app is deployed on shinyapps.io.

A scheduled GitHub Actions workflow (.github/workflows/update-ppg-and-deploy.yml) runs once a day and handles both updating the PPG data and deploying the app automatically (see Development below for details). It can also be triggered manually from the Actions tab.

To deploy manually instead, use rsconnect::deployApp() (requires setting up an account on shinyapps.io and authenticating).

Development

Updating the PPG Version

Updating to a new PPG release version is automated: the daily GitHub Actions workflow checks the latest PPG release, and if it's newer than the version in data-raw/ppg_version.R, it updates the version, regenerates the data, commits the changes, and redeploys the app. No manual action is needed.

To update manually instead:

1. Edit data-raw/ppg_version.R and change the version string to the new version number (e.g., "0.0.0.9003")
2. Run Rscript data-raw/ppg_version.R to save the version data object
3. Run Rscript data-raw/ppg_full.R to download and process the new version
4. The app heading will automatically display the updated version