A toolkit for standardizing, integrating, and cleaning biodiversity data

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Handle biodiversity data from several different sources is not an easy task. Here, we present the Biodiversity Data Cleaning (bdc), an R package to address quality issues and improve the fitness-for-use of biodiversity datasets. bdc contains functions to harmonize and integrate data from different sources following common standards and protocols, and implements various tests and tools to flag, document, clean, and correct taxonomic, spatial, and temporal data.

Compared to other available R packages, the main strengths of the bdc package are that it brings together available tools – and a series of new ones – to assess the quality of different dimensions of biodiversity data into a single and flexible toolkit. The functions can be applied to a multitude of taxonomic groups, datasets (including regional or local repositories), countries, or worldwide.

Structure of bdc

The bdc toolkit is organized in thematic modules related to different biodiversity dimensions.

:warning: The modules illustrated, and functions within, were linked to form a proposed reproducible workflow (see vignettes). However, all functions can also be executed independently.

1. Merge databases

Standardization and integration of different datasets into a standard database.

2. Pre-filter

Flagging and removal of invalid or non-interpretable information, followed by data amendments (e.g., correct transposed coordinates and standardize country names).

3. Taxonomy

Cleaning, parsing, and harmonization of scientific names against multiple taxonomic references.

4. Space

Flagging of erroneous, suspicious, and low-precision geographic coordinates.

5. Time

Flagging and, whenever possible, correction of inconsistent collection date.

Other functions

Aim to facilitate the documentation, visualization, and interpretation of results of data quality tests the package contains functions for documenting the results of the data-cleaning tests, including functions for saving i) records needing further inspection, ii) figures, and iii) data-quality reports.


You can install bdc from CRAN


or the development version from GitHub using:


Load the package with:


Package website

See bdc package website ( for detailed explanation on each module.

Getting help

If you encounter a clear bug, please file an issue here. For questions or suggestion, please send us a email (


Ribeiro, BR; Velazco, SJE; Guidoni-Martins, K; Tessarolo, G; Jardim, Lucas; Bachman, SP; Loyola, R (2022). bdc: A toolkit for standardizing, integrating, and cleaning biodiversity data. Methods in Ecology and Evolution.