trans_rare

The <code>trans_rare()</code> is an extension of the <code>rrarefy</code>
function of the vegan package for <code>easynem-class</code> data, which is
used to randomly rarefied OTU or ASV tables of nematodes for amplicon sequencing
data. The default is to rare according to the minimum abundance of nematode
in each treatment.

Provides a built-in Nemaplex database for nematodes,
which can be used to search for various nematodes.
Also supports various nematode community and functional
analyses such as nematode diversity, maturity index, metabolic footprint,
and functional guild. The methods are based on
<https://shiny.wur.nl/ninja/>, Bongers, T. (1990)
<doi:10.1007/BF00324627>, Ferris, H. (2010)
<doi:10.1016/j.ejsobi.2010.01.003>, Wan, B. et al. (2022)
<doi:10.1016/j.soilbio.2022.108695>, and Van Den Hoogen, J. et al.
(2019) <doi:10.1038/s41586-019-1418-6>.

Wang Kunguang

easynem

Nematode Community Analysis

trans_rare function

<dl><dt>data</dt>
<dd>An <code>easynem-class</code> data.</dd>
<dt>sample</dt>
<dd>Subsample size for rarefying community. The default <code>sample = 0</code>,
the minimum abundance is used for rarefied OTU or ASV tables of nematodes.</dd>
<dt>...</dt>
<dd>Other parameters of the <code>rrarefy</code> function of
the vegan package.</dd></dl>

Arguments

Randomly rarefied OTU or ASV tables of nematodes for amplicon sequencing data — trans_rare

<dl>

<dt>data</dt>
<dd>An <code>easynem-class</code> data.</dd>


<dt>sample</dt>
<dd>Subsample size for rarefying community. The default <code>sample = 0</code>,
the minimum abundance is used for rarefied OTU or ASV tables of nematodes.</dd>


<dt>...</dt>
<dd>Other parameters of the <code>rrarefy</code> function of
the vegan package.</dd>

</dl>

trans_rare: Randomly rarefied OTU or ASV tables of nematodes for amplicon sequencing data

Description

Usage

Value

Arguments

Details

See Also

Examples