PhenotypicModel-class

[&lt;-,PhenotypicModel,ANY,ANY,ANY-method

[,PhenotypicModel,ANY,ANY,ANY-method

print,PhenotypicModel-method

show,PhenotypicModel-method

This class describes a model of phenotypic evolution running on a phylogenetic tree, with or without interactions between lineages.

classes

Implements macroevolutionary analyses on phylogenetic trees. See
Morlon et al. (2010) <DOI:10.1371/journal.pbio.1000493>, Morlon et al. (2011)
<DOI:10.1073/pnas.1102543108>, Condamine et al. (2013) <DOI:10.1111/ele.12062>,
Morlon et al. (2014) <DOI:10.1111/ele.12251>, Manceau et al. (2015) <DOI:10.1111/ele.12415>,
Lewitus & Morlon (2016) <DOI:10.1093/sysbio/syv116>, Drury et al. (2016) <DOI:10.1093/sysbio/syw020>,
Manceau et al. (2016) <DOI:10.1093/sysbio/syw115>, Morlon et al. (2016) <DOI:10.1111/2041-210X.12526>, Clavel & Morlon (2017) <DOI:10.1073/pnas.1606868114>,
Drury et al. (2017) <DOI:10.1093/sysbio/syx079>, Lewitus & Morlon (2017) <DOI:10.1093/sysbio/syx095>,
Drury et al. (2018) <DOI:10.1371/journal.pbio.2003563>, Clavel et al. (2019) <DOI:10.1093/sysbio/syy045>, Maliet et al. (2019) <DOI:10.1038/s41559-019-0908-0>,
Billaud et al. (2019) <DOI:10.1093/sysbio/syz057>, Lewitus et al. (2019) <DOI:10.1093/sysbio/syz061>,
Aristide & Morlon (2019) <DOI:10.1111/ele.13385>, Maliet et al. (2020) <DOI:10.1111/ele.13592>, Drury et al. (2021) <DOI:10.1371/journal.pbio.3001270>,
Perez-Lamarque & Morlon (2022) <DOI:10.1111/mec.16478>, Perez-Lamarque et al. (2022) <DOI:10.1101/2021.08.30.458192>, Mazet et al. (2023) <DOI:10.1111/2041-210X.14195>, Drury et al. (2024) <DOI:10.1016/j.cub.2023.12.055>.

H<c3><a9>l<c3><a8>ne Morlon

RPANDA

Phylogenetic ANalyses of DiversificAtion

Hélène Morlon

Eric Lewitus

Fabien Condamine

Marc Manceau

Julien Clavel

Jonathan Drury

Olivier Billaud

Odile Maliet

Leandro Aristide

Benoit Perez-Lamarque

Nathan Mazet

PhenotypicModel-class function

Objects can be created by calls of the form <code>new("PhenotypicModel", ...)</code>.
Alternatively, you may just want to use the "createModel" function for predefined models.

Objects from the Class

<dl>
 <dt><code>name</code>:</dt>
<dd>Object of class <code>"character"</code> ~~</dd> <dt><code>period</code>:</dt>
<dd>Object of class <code>"numeric"</code> ~~</dd> <dt><code>aAGamma</code>:</dt>
<dd>Object of class <code>"function"</code> ~~</dd> <dt><code>numbersCopy</code>:</dt>
<dd>Object of class <code>"numeric"</code> ~~</dd> <dt><code>numbersPaste</code>:</dt>
<dd>Object of class <code>"numeric"</code> ~~</dd> <dt><code>initialCondition</code>:</dt>
<dd>Object of class <code>"function"</code> ~~</dd> <dt><code>paramsNames</code>:</dt>
<dd>Object of class <code>"character"</code> ~~</dd> <dt><code>constraints</code>:</dt>
<dd>Object of class <code>"function"</code> ~~</dd> <dt><code>params0</code>:</dt>
<dd>Object of class <code>"numeric"</code> ~~</dd> <dt><code>tipLabels</code>:</dt>
<dd>Object of class <code>"character"</code> ~~</dd> <dt><code>tipLabelsSimu</code>:</dt>
<dd>Object of class <code>"character"</code> ~~</dd> <dt><code>comment</code>:</dt>
<dd>Object of class <code>"character"</code> ~~</dd> 
</dl>

Slots

<dl>
 <dt>[&lt;-</dt>
<dd><code>signature(x = "PhenotypicModel", i = "ANY", j = "ANY", value = "ANY")</code>: ...</dd> <dt>[</dt>
<dd><code>signature(x = "PhenotypicModel", i = "ANY", j = "ANY", drop = "ANY")</code>: ...</dd> <dt>fitTipData</dt>
<dd><code>signature(object = "PhenotypicModel")</code>: ...</dd> <dt>getDataLikelihood</dt>
<dd><code>signature(object = "PhenotypicModel")</code>: ...</dd> <dt>getTipDistribution</dt>
<dd><code>signature(object = "PhenotypicModel")</code>: ...</dd> <dt>modelSelection</dt>
<dd><code>signature(object = "PhenotypicModel")</code>: ...</dd> <dt>print</dt>
<dd><code>signature(x = "PhenotypicModel")</code>: ...</dd> <dt>show</dt>
<dd><code>signature(object = "PhenotypicModel")</code>: ...</dd> <dt>simulateTipData</dt>
<dd><code>signature(object = "PhenotypicModel")</code>: ...</dd>	 
</dl>

Methods

Author

Class "PhenotypicModel" — PhenotypicModel-class

<dl>
 <dt><code>name</code>:</dt>
<dd>Object of class <code>"character"</code> ~~</dd>

 <dt><code>period</code>:</dt>
<dd>Object of class <code>"numeric"</code> ~~</dd>

 <dt><code>aAGamma</code>:</dt>
<dd>Object of class <code>"function"</code> ~~</dd>

 <dt><code>numbersCopy</code>:</dt>
<dd>Object of class <code>"numeric"</code> ~~</dd>

 <dt><code>numbersPaste</code>:</dt>
<dd>Object of class <code>"numeric"</code> ~~</dd>

 <dt><code>initialCondition</code>:</dt>
<dd>Object of class <code>"function"</code> ~~</dd>

 <dt><code>paramsNames</code>:</dt>
<dd>Object of class <code>"character"</code> ~~</dd>

 <dt><code>constraints</code>:</dt>
<dd>Object of class <code>"function"</code> ~~</dd>

 <dt><code>params0</code>:</dt>
<dd>Object of class <code>"numeric"</code> ~~</dd>

 <dt><code>tipLabels</code>:</dt>
<dd>Object of class <code>"character"</code> ~~</dd>

 <dt><code>tipLabelsSimu</code>:</dt>
<dd>Object of class <code>"character"</code> ~~</dd>

 <dt><code>comment</code>:</dt>
<dd>Object of class <code>"character"</code> ~~</dd>

 
</dl>

<dl>
 <dt>[&lt;-</dt>
<dd><code>signature(x = "PhenotypicModel", i = "ANY", j = "ANY", value = "ANY")</code>: ...</dd>

 <dt>[</dt>
<dd><code>signature(x = "PhenotypicModel", i = "ANY", j = "ANY", drop = "ANY")</code>: ...</dd>

 <dt>fitTipData</dt>
<dd><code>signature(object = "PhenotypicModel")</code>: ...</dd>

 <dt>getDataLikelihood</dt>
<dd><code>signature(object = "PhenotypicModel")</code>: ...</dd>

 <dt>getTipDistribution</dt>
<dd><code>signature(object = "PhenotypicModel")</code>: ...</dd>

 <dt>modelSelection</dt>
<dd><code>signature(object = "PhenotypicModel")</code>: ...</dd>

 <dt>print</dt>
<dd><code>signature(x = "PhenotypicModel")</code>: ...</dd>

 <dt>show</dt>
<dd><code>signature(object = "PhenotypicModel")</code>: ...</dd>

 <dt>simulateTipData</dt>
<dd><code>signature(object = "PhenotypicModel")</code>: ...</dd>

	 
</dl>

PhenotypicModel-class: Class `"PhenotypicModel"`

Description

Arguments

Objects from the Class

Slots

Methods

Author

References

Examples