diat_getDiatBarcode

<p>The package downloads and installs a wrapper for the 'Diat.Barcode' project. Besides citing the DiaThor package, the Diat.Barcode project should also be cited, as follows:</p><ul>
<li><p>Rimet F., Gusev E., Kahlert M., Kelly M., Kulikovskiy M., Maltsev Y., Mann D., Pfannkuchen M., Trobajo R., Vasselon V., Zimmermann J., Bouchez A., 2019. Diat.barcode, an open-access curated barcode library for diatoms. Scientific Reports. https://www.nature.com/articles/s41598-019-51500-6</p></li>
</ul>


Ecology

bioindicator

biotic

diatom

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>).

Joaqu<c3><ad>n Cochero

diathor

Calculate Ecological Information and Diatom Based Indices

Maria Mercedes Nicolosi Gelis

Maria Belen Sathicq

Joaquin Cochero

diat_getDiatBarcode function

Loads the 'Diat.Barcode' database into DiaThor in the correct format — diat_getDiatBarcode

Loads the 'Diat.Barcode' database into DiaThor in the correct format

diat_getDiatBarcode: Loads the 'Diat.Barcode' database into DiaThor in the correct format

Description

Usage

Arguments