Filter JABOT specimen records

This guide demonstrates how to use the jabot_records() function in the jabotR package to retrieve specimen occurrence records for specific taxa from the Rio de Janeiro Botanical Garden’s JABOT online managing herbarium collection system.

Function Overview

The jabot_records() function retrieves filtered plant specimen records from JABOT collections based on taxon, herbarium, location, and date criteria. It handles downloading, parsing, filtering, and optionally saving the occurrence data.

This tool is ideal for floristic, taxonomic, or biogeographic research, especially when working with large datasets for a particular plant group.

Arguments

Argument Description
herbarium Vector of herbarium codes (e.g., "RB", "SP"). Use NULL for all collections.
repatriated Logical. If FALSE, skips repatriated herbaria.
taxon One or multiple family, genus, or species names to filter by.
state Vector of Brazilian states (e.g., "BA", "SP").
recordYear A specific year (e.g., "2001") or range (e.g., c("1990", "2024")).
indets If FALSE, filters out records not identified to species level.
reorder Controls column order of the final result (e.g., by herbarium, taxon, year).
path Optional directory containing existing JABOT DwC-A files.
updates If TRUE, checks for updated versions of data in the IPT.
verbose If TRUE, shows progress messages.
save If TRUE, saves results as CSV and log files.
dir Folder where output will be saved.
filename Name of the resulting CSV and log files.

Basic Use Case

jabot_records(
  taxon = c("Fabaceae", "Ochnaceae"),
  verbose = TRUE,
  save = TRUE,
  dir = "jabot_records",
  filename = "fabaceae_ochnaceae_records"
)

Filter by Herbarium and Year Range

jabot_records(
  taxon = "Fabaceae",
  herbarium = c("R", "RB"),
  recordYear = c("1995", "2023"),
  verbose = TRUE,
  save = FALSE
)

Filter by State and Remove Indeterminate Records

jabot_records(
  taxon = "Malpighiaceae",
  state = c("BA", "PE"),
  indets = FALSE,
  save = TRUE,
  dir = "malpighiaceae_ba_pe"
)

Using a Pre-Downloaded Dataset

jabot_records(
  path = "jabot_download",
  taxon = "Myrtaceae",
  updates = FALSE,
  save = FALSE
)

Visualizing Specimens by Year

library(dplyr)
library(ggplot2)

records <- jabot_records(taxon = "Fabaceae", 
                          herbarium = "RB", 
                          recordYear = c("2000", "2025"), 
                          save = FALSE)

records %>%
  count(year) %>%
  ggplot(aes(x = year, y = n)) +
  geom_col(fill = "steelblue") +
  labs(title = "Fabaceae Records by Year (RB Herbarium)",
       x = "",
       y = "Number of Records")

Tips

  • Use recordYear = c("YYYY", "YYYY") to analyze records over a time span.
  • Use jabot_summary() beforehand to check herbarium availability.
  • Set save = TRUE for reproducible outputs and logs.

See Also