Diatom index calculation (IBD): R scripts

The IBD (Biological Diatom Index) is a quality index based on diatom species to assess pollution level (nutrients/organic matter). It has been developped for microscopy (Coste et al. 2009). We developped a gateway in R to make diatom metabarcoding floristic list similar to microscope floristic lists. It takes into account the genome copies of rbcL using a correction factor (Vasselon et al. 2018), use the 4 letters-code of Omindia (Lecointe et al., 1993) and deliver a file format adapted to SEEE plateform (https://seee.eaufrance.fr/) where IBD can be calculated. These information are retrieved from diat.barcode v15 and latter versions.

R script available at INRAE Gitlab:

https://forge.inrae.fr/laurine.viollaz/aquaref_b1.15/-/tree/7a8d5f9a226b6071a928423496ec7b3a0823db9d/

References

Coste, M.; Boutry, S.; Tison-Rosebery, J.; Delmas, F. Improvements of the Biological Diatom Index (BDI): Description and Efficiency of the New Version (BDI-2006). Ecol. Indic. 2009, 9 (4), 621–650. https://doi.org/10.1016/j.ecolind.2008.06.003.

Lecointe, C.; Coste, M.; Prygiel, J. “Omnidia”: Software for Taxonomy, Calculation of Diatom Indices and Inventories Management. Hydrobiologia 1993, 269–270, 509–513. https://doi.org/10.1007/BF00028048.

Vasselon, V.; Bouchez, A.; Rimet, F.; Jacquet, S.; Trobajo, R.; Corniquel, M.; Tapolczai, K.; Domaizon, I. Avoiding Quantification Bias in Metabarcoding: Application of a Cell Biovolume Correction Factor in Diatom Molecular Biomonitoring. Methods in Ecology and Evolution 2018, 9 (4), 1060–1069. https://doi.org/10.1111/2041-210X.12960.

Viollaz, L., Beauvais, M., Alric, B., & Rimet, F. (2026). R-pipeline for the Diatom Biological Index estimation from DNA data: "Establishing links between DBI values calculated using the conventional method and those calculated using the metabarcoding approach". Zenodo. https://doi.org/10.5281/zenodo.19480997