diathor: 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, <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 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, <doi:10.1007/BF00028033>), 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, <doi:10.1023/A:1011415209445>), 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, <doi:10.1002/aheh.19860140519>), the TDI index by Kelly, & Whitton (1995, <doi:10.1007/BF00003802>), and the SPEAR(herbicide) index by Wood, Mitrovic, Lim, Warne, Dunlop, & Kefford (2019, <doi:10.1016/j.ecolind.2018.12.035>).

Version: 0.0.4
Depends: R (≥ 2.10), stringdist, vegan, ggplot2, tidyr
Imports: data.table, purrr, stringr, tibble
Suggests: knitr, rmarkdown
Published: 2021-02-24
Author: María Mercedes Nicolosi Gelis ORCID iD [aut], María Belén Sathicq ORCID iD [aut], Joaquín Cochero ORCID iD [cre]
Maintainer: Joaquín Cochero <jcochero at ilpla.edu.ar>
BugReports: https://github.com/limnolab/DiaThor/issues
License: GPL-2 | GPL-3 [expanded from: GNU General Public License]
NeedsCompilation: no
Materials: README NEWS
CRAN checks: diathor results


Reference manual: diathor.pdf
Package source: diathor_0.0.4.tar.gz
Windows binaries: r-devel: diathor_0.0.4.zip, r-release: diathor_0.0.1.zip, r-oldrel: diathor_0.0.1.zip
macOS binaries: r-release: diathor_0.0.4.tgz, r-oldrel: diathor_0.0.1.tgz
Old sources: diathor archive


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