DiaThor: R package for computing diatom metrics and biotic indices

• Published in: bioRxiv
• Main Authors: Maria Mercedes Nicolosi Gelis, Sathicq, Maria Belen, Jupke, Jonathan, Cochero, Joaquin
• Format: Paper
• Language: English
• Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 03.04.2021
• Subjects: Chloroplasts; Environmental conditions; Guilds; Herbicides; Marine microorganisms; Morphology; Quality control; Species richness; Water quality
• DOI: 10.1101/2021.03.31.437895

Diatoms are widely used to detect changes in water quality due to their specific sensibility to a variety of environmental conditions. Among the different diatom-based tools to measure water quality, the biotic indices, ecological and morphological traits are the most commonly used. DiaThor, contains 19 functions that provide morphological data of the samples (number and shape of chloroplasts, total biovolume), ecological data (species richness, evenness, diversity, size classes, ecological guilds, ecological preferences) and biotic indices (Descy Index, EPID Index, Indice Diatomique Artois-Picardie, Swiss Diatom Index, Pampean Diatom Index, ILM index, Specific Pollution sensitivity Index, Lobo Index, Sladecek index, SPEAR(herbicides) index and the Trophic index). A web application (in Shiny) was also developed to provide access to the package for those users not familiar with the R environment. The structure of the package, how it functions and the structure of the input and output data are explained. To demonstrate the most common use of DiaThor, an example of the package performance is also provided. The DiaThor package aims to contribute to the water quality assessment based on diatom assemblages, while also providing researchers with an open platform to suggest new statistics and functionalities to be integrated into future builds. Competing Interest Statement The authors have declared no competing interest. Footnotes * https://cran.r-project.org/web/packages/diathor/index.html