pir_rename

Rename the filenames in a <code>pir_params</code>
using a rename function.

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

pir_rename function

<dl><dt>pir_params</dt>
<dd>the parameters of pirouette.
They are created by create_pir_params.</dd>
<dt>rename_fun</dt>
<dd>a function to rename a filename,
as can be checked by check_rename_fun. This function should
have one argument, which will be a filename or <a href="/link/NA?package=pirouette&version=1.6.9" data-mini-rdoc="pirouette::NA">NA</a>. The
function should <a href="/link/return?package=pirouette&version=1.6.9" data-mini-rdoc="pirouette::return">return</a> one filename (when passed one filename) or
one <a href="/link/NA?package=pirouette&version=1.6.9" data-mini-rdoc="pirouette::NA">NA</a> (when passed one <a href="/link/NA?package=pirouette&version=1.6.9" data-mini-rdoc="pirouette::NA">NA</a>).
Example rename functions are:<ul>
<li>get_remove_dir_fun function that removes the directory
 paths from the filenames, in effect turning these into local files</li>
<li>get_replace_dir_fun function that replaces the directory
 paths from the filenames</li>
</ul></dd></dl>

Arguments

Author

Rename the filenames in a pir_params
using a rename function. — pir_rename

<dl>

<dt>pir_params</dt>
<dd>the parameters of pirouette.
They are created by create_pir_params.</dd>


<dt>rename_fun</dt>
<dd>a function to rename a filename,
as can be checked by check_rename_fun. This function should
have one argument, which will be a filename or <a href='https://rdrr.io/r/base/NA.html'>NA</a>. The
function should <a href='https://rdrr.io/r/base/function.html'>return</a> one filename (when passed one filename) or
one <a href='https://rdrr.io/r/base/NA.html'>NA</a> (when passed one <a href='https://rdrr.io/r/base/NA.html'>NA</a>).
Example rename functions are:<ul>
<li>get_remove_dir_fun function that removes the directory
 paths from the filenames, in effect turning these into local files</li>
<li>get_replace_dir_fun function that replaces the directory
 paths from the filenames</li>
</ul></dd>

</dl>

pir_rename: Rename the filenames in a `pir_params` using a rename function.

Description

Usage

Value

Arguments

Author