doc/faq.md

In richelbilderbeek/pirouette: Create a Bayesian Posterior from a Phylogeny

FAQ

Package

Could you show some examples?

See https://github.com/richelbilderbeek/pirouette_examples for all https://github.com/richelbilderbeek/pirouette examples.

What are the dependencies?

pirouette depends on (non-CRAN) packages like this:

How to set up the experiments?

See How to set up the experiments

Where are the files stored?

pirouette creates a lot of files, that are by default stored in a temp folder. Here are their locations:

File |Where -----------------------------------|----------------------------------------------------------------------- The (true) phylogeny |Unsaved, as the user supplies it The (true) alignment |pir_params$alignment_params$fasta_filename The true evidence |pir_params$evidence_filename The twin phylogeny |pir_params$twinning_params$twin_tree_filename The twin alignment |pir_params$twinning_params$twin_alignment_filename The twin evidence |pir_params$twinning_params$twin_evidence_filename BEAST2 (.xml) input file (1) |pir_params$experiments[[1]]$beast2_options$beast2_input_filename BEAST2 .log output file (1) |pir_params$experiments[[1]]$beast2_options$beast2_output_log_filename BEAST2 .trees output file (1) |pir_params$experiments[[1]]$beast2_options$beast2_output_trees_filename BEAST2 .xml.state output file (1)|pir_params$experiments[[1]]$beast2_options$beast2_output_state_filename

• (1) of the first experiment

Where are the pictures of pir_to_pics stored?

pir_to_pics needs a true tree and pir_params to store it in any folder.

File |Where -----------------------------------|----------------------------------------------------------------------- The (true) phylogeny |true_tree.png The (true) alignment |true_alignment.png The true evidence |None The twin phylogeny |twin_tree.png The twin alignment |twin_alignment.png The twin evidence |None BEAST2 (.xml) input file |None BEAST2 .log output file |None BEAST2 .trees output file |true_posterior_gen.png BEAST2 .trees output file |true_posterior_best.png BEAST2 .trees output file |twin_posterior_gen.png BEAST2 .trees output file |twin_posterior_best.png BEAST2 .xml.state output file |None Errors |true_error_histogram_gen.png Errors |true_error_histogram_best.png Errors |twin_error_histogram_gen.png Errors |twin_error_histogram_best.png Errors |true_error_violin_gen.png Errors |true_error_violin_best.png Errors |twin_error_violin_gen.png Errors |twin_error_violin_best.png

Why the name?

pirouette started out as a working title, as it is an elegant combination of phylogeny and babette. Other name contenders were phyrouette, palette and many more...

The name stuck.

Why is the code coverage less than 100%?

Because too much needs to be done in one hour.

Also, pirouette lacks mocks.

BEAST2

How to install BEAST2?

See how to install BEAST2, or use

beastier::install_beast2()

Development and community

How can I indicate a feature that I miss?

Submit an Issue.

How can I submit code?

See CONTRIBUTING, at 'Submitting code'

How can I submit a bug?

See CONTRIBUTING, at 'Submitting bugs'

How can I indicate something else?

Submit an Issue. Or send an email to Richel Bilderbeek.

How to create the dependency graph from the .dot file?

dot -Tps dependencies.dot -o dependencies.ps; convert dependencies.ps dependencies.png

richelbilderbeek/pirouette documentation built on Oct. 18, 2023, 3:09 p.m.