Package: diathor
Type: Package
Title: Calculate Ecological Information and Diatom Based Indices
Version: 0.0.5
Authors@R: c(
person("María Mercedes", "Nicolosi Gelis", email = "mercedesnicolosi@ilpla.edu.ar", role = "aut", comment = c(ORCID = "0000-0001-6324-7930")),
person("María Belén", "Sathicq", email = "mbelen@ilpla.edu.ar", role = "aut", comment = c(ORCID = "0000-0002-3534-8950")),
person("Joaquín", "Cochero", email = "jcochero@ilpla.edu.ar", role = "cre", comment = c(ORCID = "0000-0003-3957-6819")))
Maintainer: Joaquín Cochero <jcochero@ilpla.edu.ar>
Description:
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>).
License: GNU General Public License
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.1.1
Depends: R (>= 2.10), stringdist, vegan, ggplot2, tidyr
Imports: data.table, purrr, stringr, tibble
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2021-04-03 14:02:58 UTC; Juaco
Author: María Mercedes Nicolosi Gelis [aut]
(<https://orcid.org/0000-0001-6324-7930>),
María Belén Sathicq [aut] (<https://orcid.org/0000-0002-3534-8950>),
Joaquín Cochero [cre] (<https://orcid.org/0000-0003-3957-6819>)
Repository: CRAN
Date/Publication: 2021-04-03 14:20:02 UTC