diat_diversity

The resulting list obtained from the diat_loadData() function

resultLoad

The input for these functions is the resulting dataframe obtained from the diat_loadData() function, to calculate diversity data using the vegan package
Sample data in the examples is taken from:<ul>
<li>Nicolosi Gelis, Mar&lt;U+00ED&gt;a Mercedes; Cochero, Joaqu&lt;U+00ED&gt;n; Donadelli, Jorge; G&lt;U+00F3&gt;mez, Nora. 2020. "Exploring the use of nuclear alterations, motility and ecological guilds in epipelic diatoms as biomonitoring tools for water quality improvement in urban impacted lowland streams". Ecological Indicators, 110, 105951. https://doi.org/10.1016/j.ecolind.2019.105951</li>
</ul>Diversity index (Shannons H') is calculated using the vegan package, following:<ul>
<li>Shannon, C. E., and Weaver, W. (1949). &lt;U+2018&gt;The Mathematical Theory of Communication.&lt;U+2019&gt; (University of Illinios Press: Urbana, IL, USA.)</li>
</ul>

Ecology

bioindicator

biotic

diatom

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 & G<c3><b3>mez (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 H<c3><bc>rlimann & 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 G<c3><b3>mez & 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 Sl<c3><a1>de<c4><8d>ek (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>).

Joaqu<c3><ad>n Cochero

diathor

Calculate Ecological Information and Diatom Based Indices

Mar<c3><ad>a Mercedes Nicolosi Gelis

Mar<c3><ad>a Bel<c3><a9>n Sathicq

diat_diversity function

Calculate diversity parameters for diatoms using the vegan package — diat_diversity

Calculate diversity parameters for diatoms using the vegan package

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diat_diversity: Calculate diversity parameters for diatoms using the vegan package

Description

Usage

Arguments