diathor - Calculate Ecological Information and Diatom Based Indices
Calculate multiple biotic indices using diatoms from
environmental samples. Diatom species are recognized by their
species' name using a heuristic search, and their ecological
data is retrieved from multiple sources. 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,
<doi:10.1016/j.ecolind.2019.105951>). - The package uses the
'Diat.Barcode' database to calculate morphological and
ecological information by Rimet & Couchez (2012,
<doi:10.1051/kmae/2012018>),and the combined classification of
guilds and size classes established by B-Béres et al. (2017,
<doi:10.1016/j.ecolind.2017.07.007>). - Current diatom-based
biotic indices include the DES index by
\href{<https://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=PASCAL8060205402>}{Descy
(1979)} - EPID index by Dell'Uomo (1996, ISBN: 3950009002) -
IDAP index by Prygiel & Coste (1993, <doi:10.1007/BF00028033>)
- ID-CH index by Hürlimann & Niederhauser \href{,
<https://www.bafu.admin.ch/bafu/fr/home/themes/eaux/publications/publications-eaux/methodes-analyse-appreciation-cours-eau-diatomees.html>)}{(2007)}
- IDP index by Gómez & Licursi (2001,
<doi:10.1023/A:1011415209445>) - ILM index by Leclercq & Maquet
\href{<https://www.vliz.be/imisdocs/publications/286641.pdf>}{(1987)}
- IPS index by Coste
\href{<https://www.oieau.org/eaudoc/notice/ETUDE-DES-METHODES-BIOLOGIQUES-DAPPRECIATION-QUANTITATIVE-DE-LA-QUALITE-DES-EAUX>}{(1982)}
- LOBO index by Lobo, Callegaro, & Bender (2002,
ISBN:9788585869908) - SLA by Sládeček (1986,
<doi:10.1002/aheh.19860140519>) - TDI index by Kelly, & Whitton
(1995, <doi:10.1007/BF00003802>) - SPEAR(herbicide) index by
Wood, Mitrovic, Lim, Warne, Dunlop, & Kefford (2019,
<doi:10.1016/j.ecolind.2018.12.035>) - PBIDW index by
Castro-Roa & Pinilla-Agudelo (2014) - DISP index by
Stenger-Kovácsa et al. (2018)
