Download REFLORA specimen records

Here we present a complete guide to the reflora_download() function of the refloraR package. This function allows users to retrieve plant specimen records in Darwin Core Format from the REFLORA Virtual Herbarium hosted by the Rio de Janeiro Botanical Garden.

Function Overview

The reflora_download() function downloads specimen data for all or specific REFLORA-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 reflora_summary() to identify them.
verbose	Logical. If TRUE, messages describing download progress will be shown.
dir	Directory path to save the files. Default is "reflora_download".

Download All REFLORA Specimen Records

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

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

Download Specimens from Selected Collections

Specify collection codes with the herbarium argument:

reflora_download(
  herbarium = c("ALCB", "HUEFS", "RB", "US", "K"),
  verbose = TRUE,
  dir = "reflora_download"
)

Skipping Repatriated Collections

To exclude collections marked as repatriated:

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

Example: Custom Directory Without Verbose Messages

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

Additional Tips

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

See Also

• reflora_summary(): Get a summary of REFLORA collections