diathor-package: diathor: Calculate Ecological Information and Diatom Based...

In jcochero/DiaThor: Calculate Ecological Information and Diatom Based Indices

diathor: Calculate Ecological Information and Diatom Based Indices

Description

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, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.ecolind.2019.105951")}). - The package uses the 'Diat.Barcode' database to calculate morphological and ecological information by Rimet & Couchez (2012, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1051/kmae/2012018")}),and the combined classification of guilds and size classes established by B-Béres et al. (2017, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.ecolind.2017.07.007")}). - Current diatom-based biotic indices include the DES index by Descy (1979) - EPID index by Dell'Uomo (1996, ISBN: 3950009002) - IDAP index by Prygiel & Coste (1993, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1007/BF00028033")}) - ID-CH index by Hürlimann & Niederhauser (2007) - IDP index by Gómez & Licursi (2001, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1023/A:1011415209445")}) - ILM index by Leclercq & Maquet (1987) - IPS index by Coste (1982) - LOBO index by Lobo, Callegaro, & Bender (2002, ISBN:9788585869908) - SLA by Sládeček (1986, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1002/aheh.19860140519")}) - TDI index by Kelly, & Whitton (1995, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1007/BF00003802")}) - SPEAR(herbicide) index by Wood, Mitrovic, Lim, Warne, Dunlop, & Kefford (2019, \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.ecolind.2018.12.035")}) - PBIDW index by Castro-Roa & Pinilla-Agudelo (2014) - DISP index by Stenger-Kovácsa et al. (2018)

Author(s)

Maintainer: Joaquin Cochero [e-mail] (ORCID)

Authors:

• Maria Mercedes Nicolosi Gelis [e-mail] (ORCID)

• Maria Belen Sathicq [e-mail] (ORCID)

jcochero/DiaThor documentation built on Aug. 17, 2024, 6:23 p.m.