clustur

clustur-package

A tool that implements the clustering algorithms from 'mothur' (Schloss PD et al. (2009) tools:::Rd_expr_doi("10.1128/AEM.01541-09")). 'clustur' make use of the cluster() and make.shared() command from 'mothur'. Our cluster() function has five different algorithms implemented: 'OptiClust', 'furthest', 'nearest', 'average', and 'weighted'. 'OptiClust' is an optimized clustering method for Operational Taxonomic Units, and you can learn more here, (Westcott SL, Schloss PD (2017) tools:::Rd_expr_doi("10.1128/mspheredirect.00073-17")). The make.shared() command is always applied at the end of the clustering command. This functionality allows us to generate and create clustering and abundance data efficiently.

internal

A tool that implements the clustering algorithms from 'mothur' (Schloss PD et al. (2009) <doi:10.1128/AEM.01541-09>). 'clustur' make use of the cluster() and make.shared() command from 'mothur'. Our cluster() function has five different algorithms implemented: 'OptiClust', 'furthest', 'nearest', 'average', and 'weighted'. 'OptiClust' is an optimized clustering method for Operational Taxonomic Units, and you can learn more here, (Westcott SL, Schloss PD (2017) <doi:10.1128/mspheredirect.00073-17>). The make.shared() command is always applied at the end of the clustering command. This functionality allows us to generate and create clustering and abundance data efficiently.

Patrick Schloss

Clustering

Gregory Johnson

Sarah Westcott

clustur-package function

Maintainer: Patrick Schloss <a href="/link/pschloss%40umich.edu?package=clustur&version=0.1.2" data-mini-rdoc="clustur::pschloss@umich.edu">pschloss@umich.edu</a> (<a href="https://orcid.org/0000-0002-6935-4275">ORCID</a>) [copyright holder]
Authors:<ul>
<li>Gregory Johnson <a href="/link/grejoh%40umich.edu?package=clustur&version=0.1.2" data-mini-rdoc="clustur::grejoh@umich.edu">grejoh@umich.edu</a> (<a href="https://orcid.org/0009-0008-3890-0297">ORCID</a>)</li>
<li>Sarah Westcott <a href="/link/swestcot%40umich.edu?package=clustur&version=0.1.2" data-mini-rdoc="clustur::swestcot@umich.edu">swestcot@umich.edu</a></li>
</ul>

Author

clustur: Clustering — clustur-package

Maintainer: Patrick Schloss <a href='mailto:pschloss@umich.edu'>pschloss@umich.edu</a> (<a href='https://orcid.org/0000-0002-6935-4275'>ORCID</a>) [copyright holder]
Authors:<ul>
<li>Gregory Johnson <a href='mailto:grejoh@umich.edu'>grejoh@umich.edu</a> (<a href='https://orcid.org/0009-0008-3890-0297'>ORCID</a>)</li>
<li>Sarah Westcott <a href='mailto:swestcot@umich.edu'>swestcot@umich.edu</a></li>
</ul>

clustur-package: clustur: Clustering

Description

Arguments

Author

See Also