Calculate Ecological Information and Diatom Based Indices

Calculates ecological information and biotic indices for diatoms in a sample. It includes number/shape of chloroplasts diversity indices, size classes, ecological guilds, and multiple biotic indices. It outputs both a dataframe with all the results and plots of all the obtained data in a defined output folder. Sample data was taken from Nicolosi Gelis, Cochero & Gómez (2020, ). The package uses the 'Diat.Barcode' database to calculate morphological and ecological information by Rimet & Couchez (2012, ), and the combined classification of guilds and size classes established by B-Béres et al. (2017, ). Current diatom-based biotic indices include the DES index by Descy (1979, <>), the EPID index by Dell'Uomo (1996, ISBN: 3950009002), the IDAP index by Prygiel & Coste (1993, ), the ID-CH index by Hürlimann & Niederhauser (2007, <>), the IDP index by Gómez & Licursi (2001, ), the ILM index by Leclercq & Maquet (1987, <>), the IPS index by Coste (1982, <>), the LOBO index by Lobo, Callegaro, & Bender (2002, ISBN:9788585869908), the SLA by Sládeček (1986, ), the TDI index by Kelly, & Whitton (1995, ), the SPEAR(herbicide) index by Wood, Mitrovic, Lim, Warne, Dunlop, & Kefford (2019, ), the PBIDW index by Castro-Roa & Pinilla-Agudelo (2014), and the DISP index by Stenger-Kovácsa et al. (2018).


Reference manual

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0.0.9 by Joaquín Cochero, 14 days ago

Browse source code at

Authors: María Mercedes Nicolosi Gelis [aut] , María Belén Sathicq [aut] , Joaquín Cochero [cre]

Documentation:   PDF Manual  

GNU General Public License license

Imports data.table, purrr, stringr, tibble, algaeClassify

Depends on stringdist, vegan, ggplot2, tidyr

Suggests knitr, rmarkdown

See at CRAN