Package: diathor
Type: Package
Title: Calculate Ecological Information and Diatom Based Indices
Version: 0.1.5
Authors@R: c(
    person("Maria Mercedes", "Nicolosi Gelis", email = "mercedesnicolosi@ilpla.edu.ar", role = "aut", comment = c(ORCID = "0000-0001-6324-7930")),
    person("Maria Belen", "Sathicq", email = "mbelen@ilpla.edu.ar", role = "aut", comment = c(ORCID = "0000-0002-3534-8950")),
    person("Joaquin", "Cochero", email = "jcochero@ilpla.edu.ar", role = "cre", comment = c(ORCID = "0000-0003-3957-6819")))
Maintainer: Joaquin Cochero <jcochero@ilpla.edu.ar>
Description: 
    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>).
License: GNU General Public License
Encoding: UTF-8
LazyData: true
RoxygenNote: 7.3.2
Depends: R (>= 2.10), stringdist, vegan, ggplot2, tidyr
Imports: data.table, purrr, stringr, tibble
Suggests: knitr, rmarkdown,
NeedsCompilation: no
Packaged: 2024-12-20 12:02:00 UTC; Juaco
Author: Maria Mercedes Nicolosi Gelis [aut]
    (<https://orcid.org/0000-0001-6324-7930>),
  Maria Belen Sathicq [aut] (<https://orcid.org/0000-0002-3534-8950>),
  Joaquin Cochero [cre] (<https://orcid.org/0000-0003-3957-6819>)
Repository: CRAN
Date/Publication: 2024-12-20 12:30:01 UTC
Built: R 4.4.3; ; 2025-12-08 04:43:29 UTC; windows
