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 calculates the DES index by Descy (1979, < http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=PASCAL8060205402>), the EPID index by Dell'Uomo (1996, ISBN: 3950009002), the IDAP index by Prygiel & Coste (1993, ), the ID-CH index by Hürlimann & Niederhauser (2007, < https://www.bafu.admin.ch/bafu/fr/home/themes/eaux/publications/publications-eaux/methodes-analyse-appreciation-cours-eau-diatomees.html>), the IDP index by Gómez & Licursi (2001, ), the ILM index by Leclercq & Maquet (1987, < http://www.vliz.be/imisdocs/publications/286641.pdf>), the IPS index by Coste (1982, < https://www.oieau.org/eaudoc/notice/ETUDE-DES-METHODES-BIOLOGIQUES-DAPPRECIATION-QUANTITATIVE-DE-LA-QUALITE-DES-EAUX>), the LOBO index by Lobo, Callegaro, & Bender (2002, ISBN:9788585869908), the SLA by Sládeček (1986, ), the TDI index by Kelly, & Whitton (1995, ), and the SPEAR(herbicide) index by Wood, Mitrovic, Lim, Warne, Dunlop, & Kefford (2019, ).


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install.packages("diathor")

0.0.1 by Joaquín Cochero, 2 months ago


Report a bug at https://github.com/jcochero/DiaThor/issues


Browse source code at https://github.com/cran/diathor


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


Documentation:   PDF Manual  


GNU General Public License license


Depends on stringdist, vegan, ggplot2, tidyr

Suggests knitr, rmarkdown


See at CRAN