check_experiments_candidates_have_same_mcmcs

If all the candidates share a same MCMC, they share the same
tracelog and treelog. In this way, one can predict where the parameter
estimates (the trace) and posterior trees are written to, as only the
best candidate will run.

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_experiments_candidates_have_same_mcmcs function

<dl><dt>experiments</dt>
<dd>a list of one or more pirouette experiments,
as can be created by create_experiment. If more than one experiment
is provided and a "generative" experiment is part of them, the "generative"
one has to be the first in the list. See also:<ul>
<li>Use check_experiments to check the list of
 experiments for validity</li>
<li>Use create_all_experiments to create experiments with
 all combinations of tree model, clock model and tree priors</li>
<li>Use create_all_bd_experiments to create experiments
 with all combinations of tree model, clock model and tree priors,
 except for only using birth-death tree priors</li>
<li>Use create_all_coal_experiments to create all experiments
 with all combinations of tree model, clock model and tree priors,
 except for only coalescent tree priors</li>
<li>Use shorten_experiments to shorten the run time
 of the list of experiments</li>
</ul></dd></dl>

Arguments

Author

Check that the candidate experiments have a same MCMC — check_experiments_candidates_have_same_mcmcs

<dl>

<dt>experiments</dt>
<dd>a list of one or more pirouette experiments,
as can be created by create_experiment. If more than one experiment
is provided and a "generative" experiment is part of them, the "generative"
one has to be the first in the list. See also:<ul>
<li>Use check_experiments to check the list of
 experiments for validity</li>
<li>Use create_all_experiments to create experiments with
 all combinations of tree model, clock model and tree priors</li>
<li>Use create_all_bd_experiments to create experiments
 with all combinations of tree model, clock model and tree priors,
 except for only using birth-death tree priors</li>
<li>Use create_all_coal_experiments to create all experiments
 with all combinations of tree model, clock model and tree priors,
 except for only coalescent tree priors</li>
<li>Use shorten_experiments to shorten the run time
 of the list of experiments</li>
</ul></dd>

</dl>

check_experiments_candidates_have_same_mcmcs: Check that the candidate experiments have a same MCMC

Description

Usage

Value

Arguments

Author