fun_similarity

Transform a distance matrix into a similarity matrix
Leinster2012divent.
Similarity between two species is defined either by a negative exponential
function of their distance or by the complement to 1 of their normalized
distance (such that the most distant species are 1 apart).

Measurement and partitioning of diversity, based on Tsallis entropy, following Marcon and Herault (2015) <doi:10.18637/jss.v067.i08>.
'divent' provides functions to estimate alpha, beta and gamma diversity of communities, including phylogenetic and functional diversity.

Eric Marcon

divent

Entropy Partitioning to Measure Diversity

Florence Puech

fun_similarity function

<dl><dt>distances</dt>
<dd>a distance matrix or an object of class <a href="/link/stats%3A%3Adist?package=divent&version=0.5-3" data-mini-rdoc="divent::stats::dist">stats::dist</a>.</dd>
<dt>exponential</dt>
<dd>If <code>TRUE</code>, similarity is \(e^{-r \delta}\),
where \(r\) is argument <code>rate</code>.
If <code>FALSE</code>, it is \(1 - \delta / \max(\delta)\).</dd>
<dt>rate</dt>
<dd>the decay rate of the exponential similarity.</dd>
<dt>check_arguments</dt>
<dd>if <code>TRUE</code>, the function arguments are verified.
Should be set to <code>FALSE</code> to save time when the arguments have been checked elsewhere.</dd></dl>

Arguments

Functional similarity — fun_similarity

<dl>

<dt>distances</dt>
<dd>a distance matrix or an object of class <a href='https://rdrr.io/r/stats/dist.html'>stats::dist</a>.</dd>


<dt>exponential</dt>
<dd>If <code>TRUE</code>, similarity is \(e^{-r \delta}\),
where \(r\) is argument <code>rate</code>.
If <code>FALSE</code>, it is \(1 - \delta / \max(\delta)\).</dd>


<dt>rate</dt>
<dd>the decay rate of the exponential similarity.</dd>


<dt>check_arguments</dt>
<dd>if <code>TRUE</code>, the function arguments are verified.
Should be set to <code>FALSE</code> to save time when the arguments have been checked elsewhere.</dd>

</dl>

fun_similarity: Functional similarity

Description

Usage

Value

Arguments

References

Examples