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 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, <https://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, <https://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>),
the SPEAR(herbicide) index by Wood, Mitrovic, Lim, Warne, Dunlop, & Kefford (2019, <doi:10.1016/j.ecolind.2018.12.035>),
the PBIDW index by Castro-Roa & Pinilla-Agudelo (2014),
and the DISP index by Stenger-Kovácsa et al. (2018).
| Version: |
0.1.0 |
| Depends: |
R (≥ 2.10), stringdist, vegan, ggplot2, tidyr |
| Imports: |
data.table, purrr, stringr, tibble |
| Suggests: |
knitr, rmarkdown |
| Published: |
2022-03-16 |
| Author: |
María Mercedes Nicolosi Gelis
 [aut],
María Belén Sathicq
[aut],
Joaquín Cochero
[cre] |
| Maintainer: |
Joaquín 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:
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