nmdsdata

The <code>nmdsdata</code> class is designed for storing results of non-metric multidimensional scaling (NMDS).

Tools for multivariate analyses of morphological data, wrapped in one package, to make the workflow convenient and fast. Statistical and graphical tools provide a comprehensive framework for checking and manipulating input data, statistical analyses, and visualization of results. Several methods are provided for the analysis of raw data, to make the dataset ready for downstream analyses. Integrated statistical methods include hierarchical classification, principal component analysis, principal coordinates analysis, non-metric multidimensional scaling, and multiple discriminant analyses: canonical, stepwise, and classificatory (linear, quadratic, and the non-parametric k nearest neighbours). The philosophy of the package is described in Šlenker et al. 2022.

Marek Slenker

MorphoTools2

Multivariate Morphometric Analysis

Marek Šlenker

Petr Koutecký

Karol Marhold

nmdsdata function

Class <code>nmdsdata</code>.<dl>
	<dt>objects</dt>
<dd><dl>
				<dt>ID</dt>
<dd>IDs of each row of <code>scores</code> object.</dd>				<dt>Population</dt>
<dd>population membership of each row of <code>scores</code> object.</dd>				<dt>Taxon</dt>
<dd>taxon membership of each row of <code>scores</code> object.</dd>				<dt>scores</dt>
<dd>ordination scores of cases (objects, OTUs).</dd>			
</dl></dd>	<dt>stress</dt>
<dd>stress value, e.i., goodness of fit.</dd>	<dt>groupMeans</dt>
<dd><code>data.frame</code> containing the means for the taxa.</dd>	<dt>distMethod</dt>
<dd>used distance measure.</dd>	<dt>rank</dt>
<dd>number of possitive eigenvalues.</dd>
	
</dl>

Format

Class nmdsdata — nmdsdata

Class <code>nmdsdata</code>.<dl>
	<dt>objects</dt>
<dd><dl>
				<dt>ID</dt>
<dd>IDs of each row of <code>scores</code> object.</dd>

				<dt>Population</dt>
<dd>population membership of each row of <code>scores</code> object.</dd>

				<dt>Taxon</dt>
<dd>taxon membership of each row of <code>scores</code> object.</dd>

				<dt>scores</dt>
<dd>ordination scores of cases (objects, OTUs).</dd>

			
</dl></dd>

	<dt>stress</dt>
<dd>stress value, e.i., goodness of fit.</dd>

	<dt>groupMeans</dt>
<dd><code>data.frame</code> containing the means for the taxa.</dd>

	<dt>distMethod</dt>
<dd>used distance measure.</dd>

	<dt>rank</dt>
<dd>number of possitive eigenvalues.</dd>


	
</dl>

nmdsdata: Class nmdsdata

Description

Arguments

Format