María Mercedes Nicolosi Gelis, Belén Sathicq, Joaquín Cochero

DiaThor calculates several diatom-based indices commonly used for water quality assesment, directly from your species’ data


The package calculates multiple biotic indices using diatoms from environmental samples. Diatom species are recognized by their acronym or by their species’ name using a heuristic search, and their ecological data is retrieved from multiple sources.

Morphological information about the species is retrieved from the ‘Diat.Barcode’ project:

Size class classification is obtained from:

Guild classification is obtained from:

Ecological preferences are obtained form:

Diversity index (Shannons H’) is calculated using the vegan package, following:

Species tolerance and their ecological information to calculate each biotic index is retrieved from their original sources:

Sample data included in the package is taken from:


You can install the released version of diathor from CRAN with:


And the development version from GitHub with:

# install.packages("devtools")

CRAN vs. GitHub package

The package available in the CRAN repository does not automatically update the internal diatom database from the ‘Diat.Barcode’ project. It uses the internal version of such database, which is currently v.9.0 published on 14-09-2020

The GitHub version of the package will update to the most recent database, if it is different to the current internal version.