faq.md

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