Download JABOT specimen records

Here we present a complete guide to the jabot_download() function of the jabotR package. This function allows users to retrieve plant specimen records in Darwin Core Format from the Rio de Janeiro Botanical Garden’s JABOT online managing herbarium collection system.

Function Overview

The jabot_download() function downloads specimen data for all or specific JABOT-associated herbarium collections. It offers flexibility through several arguments.

Arguments

Argument Description
herbarium A character vector of herbarium acronyms (e.g., "RB", "K"). Use NULL to download all collections.
repatriated Logical. If FALSE, repatriated herbaria will be skipped. Use jabot_summary() to identify them.
verbose Logical. If TRUE, messages describing download progress will be shown.
dir Directory path to save the files. Default is "jabot_download".

Download All JABOT Specimen Records

Use the function with default settings to download all JABOT data.

jabot_download(
  verbose = TRUE, 
  dir = "jabot_download"
)

Download Specimens from Selected Collections

Specify collection codes with the herbarium argument:

jabot_download(
  herbarium = c("AFR", "R", "RB"),
  verbose = TRUE,
  dir = "jabot_download"
)

Skipping Repatriated Collections

To exclude collections marked as repatriated:

jabot_download(
  repatriated = FALSE,
  verbose = TRUE,
  dir = "jabot_download"
)

Example: Custom Directory Without Verbose Messages

jabot_download(
  herbarium = "RB",
  verbose = FALSE,
  dir = "custom_directory"
)

Additional Tips

  • Use jabot_summary() to inspect which collections are available and whether they are repatriated.
  • Ensure internet access is available when running jabot_download().
  • Review the contents of the downloaded folder to verify occurrence.txt and metadata presence.

See Also