DiversityIndex-class

.DiversityIndex

An S4 class to represent a diversity measure.

internal

An easy way to examine archaeological count data. This
package provides several tests and measures of diversity:
heterogeneity and evenness (Brillouin, Shannon, Simpson, etc.),
richness and rarefaction (Chao1, Chao2, ACE, ICE, etc.), turnover and
similarity (Brainerd-Robinson, etc.). It allows to easily visualize
count data and statistical thresholds: rank vs abundance plots,
heatmaps, Ford (1962) and Bertin (1977) diagrams, etc.

Nicolas Frerebeau

tabula

Analysis and Visualization of Archaeological Count Data

Matthew Peeples

Ben Marwick

Jean-Baptiste Fourvel

Brice Lebrun

Université Bordeaux Montaigne 

CNRS 

DiversityIndex-class function

<dl>
<dt><code>.Data</code></dt>
<dd>A <code><a href="/link/numeric?package=tabula&version=3.3.0" data-mini-rdoc="tabula::numeric">numeric</a></code> vector of diversity measures.</dd></dl>
<dt><code>labels</code></dt>
<dd>A <code><a href="/link/character?package=tabula&version=3.3.0" data-mini-rdoc="tabula::character">character</a></code> vector giving the sample names.</dd>
<dt><code>size</code></dt>
<dd>An <code><a href="/link/integer?package=tabula&version=3.3.0" data-mini-rdoc="tabula::integer">integer</a></code> vector giving the sample sizes.</dd>
<dt><code>data</code></dt>
<dd>A <code><a href="/link/numeric?package=tabula&version=3.3.0" data-mini-rdoc="tabula::numeric">numeric</a></code> matrix of count data.</dd>
<dt><code>method</code></dt>
<dd>A <code><a href="/link/character?package=tabula&version=3.3.0" data-mini-rdoc="tabula::character">character</a></code> string specifying the method used.</dd>
<dt><code>simulation</code></dt>
<dd>A four columns <code><a href="/link/numeric?package=tabula&version=3.3.0" data-mini-rdoc="tabula::numeric">numeric</a></code> matrix giving the diversity
measures for the simulated assemblage (sample <code>size</code>, <code>mean</code> estimate,
<code>lower</code> and <code>upper</code> boundaries of the confidence interval).</dd>
<dt><code>seed</code></dt>
<dd>A <code><a href="/link/numeric?package=tabula&version=3.3.0" data-mini-rdoc="tabula::numeric">numeric</a></code> vector giving the value of <a href="/link/.Random.seed?package=tabula&version=3.3.0" data-mini-rdoc="tabula::.Random.seed">.Random.seed</a> before the
simulation was started; otherwise it is the user specified value with a
<code>kind</code> attribute with value <code>as.list(</code><code><a href="/link/RNGkind()?package=tabula&version=3.3.0" data-mini-rdoc="tabula::RNGkind()">RNGkind()</a></code><code>)</code>.</dd>

Slots

In the code snippets below, <code>x</code> is an <code>DiversityIndex</code> object.<dl>
<dt><code>as.data.frame(x)</code></dt>
<dd>Coerces to a <code><a href="/link/data.frame?package=tabula&version=3.3.0" data-mini-rdoc="tabula::data.frame">data.frame</a></code>.</dd>
</dl>

Coerce

Author

Diversity Index — DiversityIndex-class

<dl>
<dt><code>.Data</code></dt>
<dd>A <code><a href='https://rdrr.io/r/base/numeric.html'>numeric</a></code> vector of diversity measures.</dd>


<dt><code>labels</code></dt>
<dd>A <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> vector giving the sample names.</dd>


<dt><code>size</code></dt>
<dd>An <code><a href='https://rdrr.io/r/base/integer.html'>integer</a></code> vector giving the sample sizes.</dd>


<dt><code>data</code></dt>
<dd>A <code><a href='https://rdrr.io/r/base/numeric.html'>numeric</a></code> matrix of count data.</dd>


<dt><code>method</code></dt>
<dd>A <code><a href='https://rdrr.io/r/base/character.html'>character</a></code> string specifying the method used.</dd>


<dt><code>simulation</code></dt>
<dd>A four columns <code><a href='https://rdrr.io/r/base/numeric.html'>numeric</a></code> matrix giving the diversity
measures for the simulated assemblage (sample <code>size</code>, <code>mean</code> estimate,
<code>lower</code> and <code>upper</code> boundaries of the confidence interval).</dd>


<dt><code>seed</code></dt>
<dd>A <code><a href='https://rdrr.io/r/base/numeric.html'>numeric</a></code> vector giving the value of <a href='https://rdrr.io/r/base/Random.html'>.Random.seed</a> before the
simulation was started; otherwise it is the user specified value with a
<code>kind</code> attribute with value <code>as.list(</code><code><a href='https://rdrr.io/r/base/Random.html'>RNGkind()</a></code><code>)</code>.</dd>


</dl>

In the code snippets below, <code>x</code> is an <code>DiversityIndex</code> object.<dl>
<dt><code>as.data.frame(x)</code></dt>
<dd>Coerces to a <code><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></code>.</dd>


</dl>

DiversityIndex-class: Diversity Index

Description

Arguments

Slots

Coerce

Author

See Also