diathor: Calculate Ecological Information and Diatom Based Indices
Calculate multiple biotic indices using diatoms from environmental samples. Diatom species are identified by their species names through a heuristic search, and ecological data is retrieved from multiple sources. The package includes the calculation of chloroplast diversity indices, size classes, ecological guilds, and various biotic indices. It outputs both a dataframe with all the results and plots of the obtained data in a specified output folder. Sample data is sourced from Nicolosi Gelis, Cochero, & Gómez (2020, <doi:10.1016/j.ecolind.2019.105951>).
The package utilizes the 'Diat.Barcode' database for morphological and ecological information by Rimet & Couchez (2012, <doi:10.1051/kmae/2012018>), along with the combined classification of guilds and size classes from B-Beres et al. (2017, <doi:10.1016/j.ecolind.2017.07.007>). Currently supported diatom-based biotic indices include DES index (Descy, 1979); EPID index (Dell'Uomo, 1996); IDAP index (Prygiel & Coste, 1993); ID-CH index (Hürlimann & Niederhauser, 2007); IDP index (Gómez & Licursi, 2001); ILM index (Leclercq & Maquet, 1987); IPS index (Coste, 1982); LOBO index (Lobo, Callegaro, & Bender, 2002); SLA index (Sladecek, 1986); TDI index (Kelly & Whitton, 1995); SPEAR(herbicide) index (Wood et al., 2019); PBIDW index (Castro-Roa & Pinilla-Agudelo, 2014); DISP index (Stenger-Kovácsa et al., 2018).
Version: |
0.1.4 |
Depends: |
R (≥ 2.10), stringdist, vegan, ggplot2, tidyr |
Imports: |
data.table, purrr, stringr, tibble |
Suggests: |
knitr, rmarkdown |
Published: |
2024-09-20 |
DOI: |
10.32614/CRAN.package.diathor |
Author: |
Maria Mercedes Nicolosi Gelis
[aut],
Maria Belen 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 |
CRAN checks: |
diathor results |
Documentation:
Downloads:
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