sim_sgd

Simulates a phylogeny arising from the SGD model with exponentially increasing metapopulation size. 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

sim_sgd function

<dl><dt>tau</dt>
<dd>the simulation time, which corresponds to the length of the phylogeny</dd><dt>b</dt>
<dd>the (constant) per-individual birth rate</dd><dt>d</dt>
<dd>the (constant) per-individual death rate</dd><dt>nu</dt>
<dd>the (constant) per-individual mutation rate</dd></dl>

Arguments

Author

Algorithm for simulating a phylogenetic tree under the SGD model — sim_sgd

<dl>

<dt>tau</dt>
<dd>the simulation time, which corresponds to the length of the phylogeny</dd>

<dt>b</dt>
<dd>the (constant) per-individual birth rate</dd>

<dt>d</dt>
<dd>the (constant) per-individual death rate</dd>

<dt>nu</dt>
<dd>the (constant) per-individual mutation rate</dd>

</dl>

Algorithm for simulating a phylogenetic tree under the SGD model

sim_sgd: Algorithm for simulating a phylogenetic tree under the SGD model

Description

Usage

Value

Arguments

Author

References

Examples