likelihood_sgd

Computes the likelihood of a phylogeny under the SGD model with exponential increasing of the metacommunity, and potentially missing extant species. Notations follow Manceau et al. (2015).

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

likelihood_sgd function

<dl><dt>phylo</dt>
<dd>an object of type 'phylo' (see ape documentation)</dd><dt>tot_time</dt>
<dd>the age of the phylogeny (crown age, or stem age if known). If working with crown ages, tot_time is given by max(node.age(phylo)$ages).</dd><dt>b</dt>
<dd>the (constant) birth rate of individuals in the model.</dd><dt>d</dt>
<dd>the (constant) death rate of individuals in the model.</dd><dt>nu</dt>
<dd>the (constant) mutation rate of individuals in the model.</dd><dt>f</dt>
<dd>the fraction of extant species included in the phylogeny</dd></dl>

Arguments

Author

Likelihood of a phylogeny under the SGD model — likelihood_sgd

<dl>

<dt>phylo</dt>
<dd>an object of type 'phylo' (see ape documentation)</dd>

<dt>tot_time</dt>
<dd>the age of the phylogeny (crown age, or stem age if known). If working with crown ages, tot_time is given by max(node.age(phylo)$ages).</dd>

<dt>b</dt>
<dd>the (constant) birth rate of individuals in the model.</dd>

<dt>d</dt>
<dd>the (constant) death rate of individuals in the model.</dd>

<dt>nu</dt>
<dd>the (constant) mutation rate of individuals in the model.</dd>

<dt>f</dt>
<dd>the fraction of extant species included in the phylogeny</dd>

</dl>

Likelihood of a phylogeny under the SGD model

likelihood_sgd: Likelihood of a phylogeny under the SGD model

Description

Usage

Value

Arguments

Author

References

Examples