refloraR

Codecov test coverage Test Coverage CRAN Downloads R-CMD-check License: MIT

refloraR is an R package for accessing and analyzing plant specimen data from the REFLORA Virtual Herbarium, hosted by the Rio de Janeiro Botanical Garden. It provides tools for downloading, summarizing, and filtering herbarium records in Darwin Core Archive (DwC-A) format via the REFLORA IPT.

Installation

You can install the development version of refloraR from GitHub with:

# install.packages("devtools")
devtools::install_github("DBOSlab/refloraR")
library(refloraR)

Usage

A general description of the available main functions (reflora_download and reflora_summary) that extract original REFLORA collections are provided below.

1. reflora_summary: Summarizing REFLORA collections

The following code can be used to extract a summary of all REFLORA-associated collections, including herbarium acronym, curator’s email contact, number of records and a direct link to the original REFLORA Integrated Publishing Toolkit (IPT).

library(refloraR)

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

By specifying a vector of herbarium acronyms, the user can extract a summary for just the specific herbarium collection.

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

2. reflora_download: Downloading REFLORA specimen records

The following code can be used to download original specimen records in DwC-A format and associated metada for all REFLORA collections.

library(refloraR)

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

By specifying a vector of herbarium acronyms, the user can download specimens records for just the specific herbarium collection.

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

Documentation

Full function documentation and articles are available at the refloraR website.

Citation

Cardoso, D. & Calderón, C. 2025. refloraR: An R Package for Exploring Plant Specimen Collections from REFLORA Virtual Herbarium. https://github.com/dboslab/refloraR