check_sim_tral_fun

Will <a href="/link/stop?package=pirouette&version=1.6.9" data-mini-rdoc="pirouette::stop">stop</a> if not

Theoretical biologists are interested in measuring the extent
at which we can measure the truth. This package allows to
create a Bayesian posterior from a phylogeny that depicts
the true evolutionary relationships. The given and true phylogeny
can than be compared to the posterior phylogenies.
Richèl J. C. Bilderbeek, Giovanni Laudanno, Rampal S. Etienne (2020)
"Quantifying the impact of an inference model in Bayesian phylogenetics"
<doi:10.1111/2041-210X.13514>.

Richel Bilderbeek

pirouette

Create a Bayesian Posterior from a Phylogeny

Richèl J.C. Bilderbeek

Giovanni Laudanno

Thijs Janzen

check_sim_tral_fun function

<dl><dt>sim_tral_fun</dt>
<dd>function to simulate a
true alignment with.
This function must have two arguments,
called <code>true_phylogeny</code> (which will hold the true phylogeny)
and <code>root_sequence</code> (which holds the DNA root sequence).
The return type must be DNAbin.
Use check_sim_tral_fun to verify if the function
has the right signature and output.
Some standard functions: <ul>
<li>Use get_sim_tral_with_std_nsm_fun
 to get a function (sim_tral_with_std_nsm)
 the use a standard site model.</li>
<li>Use
 get_sim_tral_with_lns_nsm_fun
 to get a function
 (sim_tral_with_lns_nsm)
 the use a linked node substitution site model.</li>
<li>Use
 get_sim_tral_with_uns_nsm_fun
 to get a function
 (sim_tral_with_uns_nsm)
 the use an unlinked node substitution site model.</li>
</ul></dd></dl>

Arguments

Author

Will <a href='https://rdrr.io/r/base/stop.html'>stop</a> if not

Check if the function to create a true alignment with (from the
true phylogeny) is valid. — check_sim_tral_fun

<dl>

<dt>sim_tral_fun</dt>
<dd>function to simulate a
true alignment with.
This function must have two arguments,
called <code>true_phylogeny</code> (which will hold the true phylogeny)
and <code>root_sequence</code> (which holds the DNA root sequence).
The return type must be DNAbin.
Use check_sim_tral_fun to verify if the function
has the right signature and output.
Some standard functions: <ul>
<li>Use get_sim_tral_with_std_nsm_fun
 to get a function (sim_tral_with_std_nsm)
 the use a standard site model.</li>
<li>Use
 get_sim_tral_with_lns_nsm_fun
 to get a function
 (sim_tral_with_lns_nsm)
 the use a linked node substitution site model.</li>
<li>Use
 get_sim_tral_with_uns_nsm_fun
 to get a function
 (sim_tral_with_uns_nsm)
 the use an unlinked node substitution site model.</li>
</ul></dd>

</dl>

check_sim_tral_fun: Check if the function to create a true alignment with (from the true phylogeny) is valid.

Description

Usage

Value

Arguments

Author

See Also