Compare Herbarium Sources

Overview

When working with plant specimen data from multiple biodiversity repositories (e.g., GBIF, JABOT, speciesLink), users often encounter overlapping records across sources. barRoso offers the barroso_cat() function to merge, harmonize, and optionally deduplicate these datasets based on collection codes.

This article demonstrates how to:

• Merge multiple data sources into a unified data frame
• Identify and remove overlapping records
• Prioritize a preferred source when conflicts occur

Function: barroso_cat()

combined_df <- barroso_cat(
  list_sources = list(
    GBIF = gbif_data,
    speciesLink = splink_data,
    JABOT = jabot_data
  ),
  keep_source = "GBIF"
)

Arguments

• list_sources: A named list of data frames. Each represents a biodiversity source.
• keep_source: Optionally specify a preferred source (e.g., “GBIF”). When overlaps are detected via collectionCode, records from the preferred source are retained.

If no source is specified, the function merges all sources, retaining potential duplicates for further reconciliation.

Example

library(barRoso)

# Load three herbarium datasets
jabot <- read.csv("jabot.csv")
gbif <- read.csv("gbif.csv")
splink <- read.csv("splink.csv")

# Merge, giving preference to GBIF for overlapping herbaria
combined_df <- barroso_cat(
  list_sources = list(
    GBIF = gbif,
    speciesLink = splink,
    JABOT = jabot
  ),
  keep_source = "GBIF"
)

How It Works

• collectionCode is used to detect overlapping herbaria
• Only one record is retained when keep_source is defined
• All datasets are aligned to a common column structure
• Missing fields are filled with NA for consistency

This harmonization step is especially useful before running downstream standardization (barroso_std()) or duplicate detection (barroso_flag_duplicates()).

Tips

• Ensure each dataset includes a collectionCode column
• Use keep_source = NULL if you want to preserve all records
• Use barroso_std() after combining to clean remaining fields