Summarize REFLORA collections

Here we present a complete 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).

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".

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 includes fields such as collection code, record count, repatriation status, contact information, and a link to the IPT entry.
  • Use this summary to filter or preview collections before downloading or parsing records.
  • If save = TRUE, the function will automatically store the results in CSV format.

See Also