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 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 (2007) - IDP index by Gómez & Licursi (2001, <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, <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-Kovács et al. (2018, <doi:10.1016/j.ecolind.2018.07.026>) - EDI index by Chamorro et al. (2024, <doi:10.1021/acsestwater.4c00126>) - DDI index by Álvarez-Blanco et al. (2013, <doi:10.1007/s10661-012-2607-z>) - PDISE index by Kahlert et al. (2023, <doi:10.1007/s10661-023-11378-4>).
| Version: | 0.1.5 |
| Depends: | R (≥ 2.10),stringdist,vegan,ggplot2,tidyr |
| Imports: | data.table,purrr,stringr,tibble |
| Suggests: | knitr,rmarkdown |
| Published: | 2024-12-20 |
| DOI: | 10.32614/CRAN.package.diathor |
| Author: | Maria Mercedes Nicolosi Gelis [aut], Maria Belen Sathicq [aut], Joaquin Cochero [cre] |
| Maintainer: | Joaquin Cochero <jcochero at ilpla.edu.ar> |
| License: | GPL-2 |GPL-3 [expanded from: GNU General Public License] |
| NeedsCompilation: | no |
| Materials: | README |
| CRAN checks: | diathor results |
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