Package: diathor
Type: Package
Title: Calculate Ecological Information and Diatom Based Indices
Version: 0.1.6
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: 2026-06-22 09:28:50 UTC; root
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>)
Config/pak/sysreqs: libicu-dev
Repository: https://limnolab.r-universe.dev
Date/Publication: 2025-11-24 15:13:07 UTC
RemoteUrl: https://github.com/limnolab/diathor
RemoteRef: HEAD
RemoteSha: 1b058521e06fbde6ac20da324440c047e1777c3b