pir_rename_to_std: Rename the 'pir_params' filenames to follow a standard naming...

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

Rename the pir_params filenames to follow a standard naming scheme.

Description

By default, pir_params uses temporary filenames for all files. For pir_run, when only a computer reads those filenames, this is fine. This function conformizes the filenames to a human-friendly form.

Usage

pir_rename_to_std(pir_params, folder_name)

Arguments

pir_params	the parameters of pirouette. They are created by create_pir_params.
folder_name	name of the main folder

Details

The standard naming scheme is this:

• pir_params$alignment_params$fasta_filename becomes [folder_name]/alignment.fas

• pir_params$evidence_filename becomes [folder_name]/evidence.csv, if at least one evidence is measured

For the (zero or one) experiment at index i that is generative:

• pir_params$experiments[[i]]$beast2_options$input_filename becomes [folder_name]/gen.xml

• pir_params$experiments[[i]]$beast2_options$output_state_filename becomes [folder_name]/gen.xml.state

• pir_params$experiments[[i]]$beast2_options$input_filename becomes [folder_name]/gen_errors.csv,

• pir_params$experiments[[i]]$inference_model$mcmc$tracelog$filename becomes [folder_name]/gen.log

• pir_params$experiments[[i]]$inference_model$mcmc$screenlog$filename becomes [folder_name]/gen.csv

• pir_params$experiments[[i]]$inference_model$mcmc$treelog$filename becomes [folder_name]/gen.trees

• pir_params$experiments[[i]]$est_evidence_mcmc$tracelog$filename becomes [folder_name]/gen_evidence.log

• pir_params$experiments[[i]]$est_evidence_mcmc$screenlog$filename becomes [folder_name]/gen_evidence.csv

• pir_params$experiments[[i]]$est_evidence_mcmc$treelog$filename becomes [folder_name]/gen_evidence.trees

For the (zero or more) experiments at index i that is a candidate:

• pir_params$experiments[[i]]$beast2_options$input_filename becomes [folder_name]/best.xml

• pir_params$experiments[[i]]$beast2_options$output_state_filename becomes [folder_name]/best.xml.state

• pir_params$experiments[[i]]$beast2_options$input_filename becomes [folder_name]/best_errors.csv,

• pir_params$experiments[[i]]$inference_model$mcmc$tracelog$filename becomes [folder_name]/best.log

• pir_params$experiments[[i]]$inference_model$mcmc$screenlog$filename becomes [folder_name]/best.csv

• pir_params$experiments[[i]]$inference_model$mcmc$treelog$filename becomes [folder_name]/best.trees

• pir_params$experiments[[i]]$est_evidence_mcmc$tracelog$filename becomes [folder_name]/best_evidence.log

• pir_params$experiments[[i]]$est_evidence_mcmc$screenlog$filename becomes [folder_name]/best_evidence.csv

• pir_params$experiments[[i]]$est_evidence_mcmc$treelog$filename becomes [folder_name]/best_evidence.trees

If twinning is used:

• pir_params$twinning_params$twin_tree_filename becomes [folder_name]/twin.newick

• pir_params$twinning_params$twin_alignment_filename becomes [folder_name]/alignment_twin.fas

• pir_params$twinning_params$twin_evidence_filename becomes [folder_name]/evidence_twin.csv, if at least one evidence is measured

Value

a 'pir_params'

See Also

Use get_pir_params_filenames to obtain all the filenames

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