GBIF-Dataset-Explorer (gde)

R Package to explore datasets from the biodivesity aggregator GBIF.

Once a DwC dataset is loaded, you can explore the issues and data values using a Shiny UI.

Currently works on Max/Linux.

Load data from a DwC download

1. Install the package:
   • Install devtools, if needed: install.packages("devtools")
   • Install from Github: devtools::install_github('Smithsonian/GBIF-Dataset-Explorer')
2. Download a DarwinCore zip from GBIF
3. Setup a database, currently only for Postgres
4. Copy the file inst/shinyApp/gde_settings.R.template to gde_settings.R in the working directory and edit the values
5. Run the function gde::load_gbif_dwc(zipfile = "000000.zip", tmpdir = "/tmp/"), editing the values as needed

Run the app locally

After loading the data to the database:

1. Copy the file inst/shinyApp/gde_settings.R.template to gde_settings.R in the working directory and edit the values.
2. Run using: gde::launchApp()

Serve the shiny app on a server

1. Install the package in the server: devtools::install_github(‘Smithsonian/GBIF-Dataset-Explorer’)
2. Copy the files in inst/shinyApp to the server.
3. Rename the file gde_settings.R.template to gde_settings.R and edit the values.