README.md

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:
  2. Install devtools, if needed: install.packages("devtools")
  3. Install from Github: devtools::install_github('Smithsonian/GBIF-Dataset-Explorer')
  4. Download a DarwinCore zip from GBIF
  5. Setup a database, currently only for Postgres
  6. Copy the file inst/shinyApp/gde_settings.R.template to gde_settings.R in the working directory and edit the values
  7. 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.


Try the gde package in your browser

Any scripts or data that you put into this service are public.

gde documentation built on Nov. 23, 2021, 5:06 p.m.