enve.recplot2.compareIdentities

Compare the distribution of identities between two
<code>enve.RecPlot2</code> objects.

A collection of functions for microbial ecology and other
applications of genomics and metagenomics. Companion package for the
Enveomics Collection (Rodriguez-R, L.M. and Konstantinidis, K.T., 2016
<DOI:10.7287/peerj.preprints.1900v1>).

Luis M RodriguezR

enveomics.R

Various Utilities for Microbial Genomics and Metagenomics

Luis M. Rodriguez-R

enve.recplot2.compareIdentities function

<dl><dt>x</dt>
<dd>First <code>enve.RecPlot2</code> object.</dd>
<dt>y</dt>
<dd>Second <code>enve.RecPlot2</code> object.</dd>
<dt>method</dt>
<dd>Distance method to use. This should be (an unambiguous abbreviation of)
one of:<ul>
<li>"hellinger"
 (Hellinger, 1090, doi:10.1515/crll.1909.136.210),</li>
<li>"bhattacharyya"
 (Bhattacharyya, 1943, Bull. Calcutta Math. Soc. 35),</li>
<li>"kl" or "kullback-leibler"
 (Kullback &amp; Leibler, 1951, doi:10.1214/aoms/1177729694), or</li>
<li>"euclidean"</li>
</ul></dd>
<dt>smooth.par</dt>
<dd>Smoothing parameter for cubic spline smoothing. Use 0 for no smoothing.
Use <code>NULL</code> to automatically determine this value using leave-one-out
cross-validation (see <code>smooth.spline</code> parameter <code>spar</code>).</dd>
<dt>pseudocounts</dt>
<dd>Smoothing parameter for Laplace smoothing. Use 0 for no smoothing, or
1 for add-one smoothing.</dd>
<dt>max.deviation</dt>
<dd>Maximum mean deviation between identity breaks tolerated (as percent
identity). Difference in number of <code>id.breaks</code> is never tolerated.</dd></dl>

Arguments

Author

Enveomics: Recruitment Plot (2) Compare Identities — enve.recplot2.compareIdentities

<dl>

<dt>x</dt>
<dd>First <code>enve.RecPlot2</code> object.</dd>


<dt>y</dt>
<dd>Second <code>enve.RecPlot2</code> object.</dd>


<dt>method</dt>
<dd>Distance method to use. This should be (an unambiguous abbreviation of)
one of:<ul>
<li>"hellinger"
 (Hellinger, 1090, doi:10.1515/crll.1909.136.210),</li>
<li>"bhattacharyya"
 (Bhattacharyya, 1943, Bull. Calcutta Math. Soc. 35),</li>
<li>"kl" or "kullback-leibler"
 (Kullback &amp; Leibler, 1951, doi:10.1214/aoms/1177729694), or</li>
<li>"euclidean"</li>
</ul></dd>


<dt>smooth.par</dt>
<dd>Smoothing parameter for cubic spline smoothing. Use 0 for no smoothing.
Use <code>NULL</code> to automatically determine this value using leave-one-out
cross-validation (see <code>smooth.spline</code> parameter <code>spar</code>).</dd>


<dt>pseudocounts</dt>
<dd>Smoothing parameter for Laplace smoothing. Use 0 for no smoothing, or
1 for add-one smoothing.</dd>


<dt>max.deviation</dt>
<dd>Maximum mean deviation between identity breaks tolerated (as percent
identity). Difference in number of <code>id.breaks</code> is never tolerated.</dd>

</dl>

enve.recplot2.compareIdentities: Enveomics: Recruitment Plot (2) Compare Identities

Description

Usage

Value

Arguments

Author