Summarize Reflora collections

Here we present a practical guide to the reflora_summary() function of the refloraR package. This function provides summary statistics for plant specimen records available in the Reflora Virtual Herbarium hosted by the Rio de Janeiro Botanical Garden and published via the Integrated Publishing Toolkit (IPT).

Reflora aggregates collections from both Brazilian and international herbaria that hold Brazilian specimens. In this context, “digital repatriation” refers to making high-resolution images and associated specimen metadata openly accessible through a Brazilian public infrastructure (HVR/IPT), even when the physical specimens remain curated in the holding herbarium. The reflora_summary() output includes a repatriation status field to help users identify these digitally repatriated collections.

Function Overview

The reflora_summary() function retrieves summary information for one or more Reflora-associated herbarium collections. It allows users to filter collections and optionally save the summary as a CSV file. It also provides metadata such as the number of records, publication version and date, and a direct link to each herbarium’s IPT page.

Arguments

Argument Description
herbarium A character vector of herbarium acronyms (e.g., "RB", "K"). Use NULL to summarize all collections.
verbose Logical. If TRUE, messages describing summary progress will be shown.
save Logical. If TRUE, the summary will be saved as a CSV file.
records Character. Use "gbif" (the default) to request indexed occurrence counts from GBIF, or "none" to skip those requests and return NA in Records for a faster, metadata-only summary.
dir Directory path to save the file. Default is "reflora_summary".

Output columns

reflora_summary() returns one row per collection with the following fields:

  • collectionCode: Herbarium acronym (e.g., RB, K) identifying the collection.
  • rightsHolder: Institution responsible for the collection, as reported in the IPT metadata.
  • Repatriated: Logical. Indicates whether the collection is digitally repatriated (Brazilian specimens digitized from a foreign herbarium and served through Reflora) versus a non-repatriated collection.
  • contactPoint: Name of the contact person or curator associated with the collection.
  • hasEmail: Contact email address for the contactPoint, when available.
  • Version: The IPT resource release/version identifier for the currently published dataset (useful for reproducibility and citation).
  • Published.on: Date and hour when the current version was published/updated in the IPT.
  • Records: Number of specimen records currently indexed by GBIF for the collection. Populated when records = "gbif" (the default); returned as NA when records = "none".
  • Reflora_URL: Direct link to the collection’s page in the Reflora Virtual Herbarium.

Summarize All Reflora Collections

Use the function with default settings to get a summary of all collections, including the herbarium acronym, curator’s contact, record count, and a direct IPT link:

summary_df <- reflora_summary(
  verbose = TRUE,
  save = TRUE,
  dir = "reflora_summary"
)

Summarize Specific Collections

Specify one or more herbaria with the herbarium argument:

summary_some_df <- reflora_summary(
  herbarium = c("ALCB", "HUEFS", "K", "RB"),
  verbose = TRUE,
  save = TRUE,
  dir = "reflora_summary"
)

Save Summary to Custom Directory

You can customize the output directory for the summary file:

reflora_summary(
  herbarium = "RB",
  verbose = TRUE,
  save = TRUE,
  dir = "custom_summary"
)

Disable Verbose Output

Suppress progress messages with verbose = FALSE:

reflora_summary(
  verbose = FALSE
)

Skip GBIF Record Counts

By default, reflora_summary() queries GBIF for indexed occurrence counts to populate the Records column. Set records = "none" to skip these requests and get a faster, metadata-only summary (Records is returned as NA):

summary_fast_df <- reflora_summary(
  records = "none",
  save = FALSE
)

Additional Tips

  • The summary is designed as a discovery step: it helps you identify which collections are available, how many records they contain, and where they are published in the IPT.
  • Use Repatriated to distinguish digitally repatriated collections (Brazilian specimens imaged/served via Reflora from foreign herbaria) from other published collections.
  • Use Version and Published.on to document exactly which IPT release you used, improving reproducibility when you later download or parse records.
  • Use records = "none" when you only need collection metadata (contacts, versions, IPT links) and want to avoid the extra GBIF requests.
  • If save = TRUE, the summary is written to disk as a CSV file for offline inspection and reporting.

See Also