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

Documentation:

Reference manual:

diathor.pdf

Downloads:

Package source:	diathor_0.1.5.tar.gz
Windows binaries:	r-devel: diathor_0.1.5.zip, r-release: diathor_0.1.5.zip, r-oldrel: diathor_0.1.5.zip
macOS binaries:	r-release (arm64): diathor_0.1.5.tgz, r-oldrel (arm64): diathor_0.1.5.tgz, r-release (x86_64): diathor_0.1.5.tgz, r-oldrel (x86_64): diathor_0.1.5.tgz
Old sources:	diathor archive

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