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.
dir Directory path to save the file. Default is "reflora_summary".

Output columns

reflora_summary() returns one row per collection and includes, among others, the following fields:

  • collection_code / herbarium: Herbarium acronym (e.g., RB, K) identifying the collection.
  • records: Number of specimen records currently published for the collection in the REFLORA IPT.
  • version: The IPT resource release/version identifier for the currently published dataset (useful for reproducibility and citation).
  • publication_date: Date when the current version was published/updated in the IPT.
  • ipt_link: Direct link to the collection’s IPT resource page.
  • repatriation_status: Indicates whether the collection is digitally repatriated (Brazilian specimens digitized from a foreign herbarium and served through REFLORA) versus a non-repatriated collection.
  • contact / curator: Contact information provided in the IPT metadata for the collection.

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
)

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 repatriation_status to distinguish digitally repatriated collections (Brazilian specimens imaged/served via REFLORA from foreign herbaria) from other published collections.
  • Use version and publication_date to document exactly which IPT release you used, improving reproducibility when you later download or parse records.
  • If save = TRUE, the summary is written to disk as a CSV file for offline inspection and reporting.

See Also