Package 'babette'

Title: Control 'BEAST2'
Description: 'BEAST2' (<https://www.beast2.org>) is a widely used Bayesian phylogenetic tool, that uses DNA/RNA/protein data and many model priors to create a posterior of jointly estimated phylogenies and parameters. 'BEAST2' is commonly accompanied by 'BEAUti 2', 'Tracer' and 'DensiTree'. 'babette' provides for an alternative workflow of using all these tools separately. This allows doing complex Bayesian phylogenetics easily and reproducibly from 'R'.
Authors: Richèl J.C. Bilderbeek [aut, cre] , Joëlle Barido-Sottani [rev] (Joëlle reviewed the package for rOpenSci, see https://github.com/richelbilderbeek/onboarding/issues/209), David Winter [rev] (David reviewed the package for rOpenSci, see https://github.com/richelbilderbeek/onboarding/issues/209), Jason Griffiths [ctb] , Olivier Roy [ctb], Giovanni Laudanno [ctb]
Maintainer: Richèl J.C. Bilderbeek <[email protected]>
License: GPL-3
Version: 2.3.4
Built: 2024-08-26 05:34:59 UTC
Source: https://github.com/ropensci/babette

Help Index

Continue a BEAST2 run

Description

Do a full run: create a 'BEAST2' configuration file (like 'BEAUti 2'), run 'BEAST2', parse results (like 'Tracer')

Usage

bbt_continue(fasta_filename, inference_model, beast2_options)

Arguments

fasta_filename

a FASTA filename
inference_model

a Bayesian phylogenetic inference model, as returned by create_inference_model
beast2_options

'BEAST2' options, as can be created by create_beast2_options

Value

a list with the following elements:

  • estimates: a data frame with 'BEAST2' parameter estimates

  • [alignment_id]_trees: a multiPhylo containing the phylogenies in the 'BEAST2' posterior. [alignment_id] is the ID of the alignment. For example, when running bbt_run_from_model with anthus_aco.fas, this element will have name anthus_aco_trees

  • operators: a data frame with the 'BEAST2' MCMC operator acceptances

  • output: a numeric vector with the output sent to standard output and error streams

  • ns: (optional) the results of a marginal likelihood estimation, will exist only when create_ns_mcmc was used for mcmc. This structure will contain the following elements:

    • marg_log_lik the marginal log likelihood estimate

    • marg_log_lik_sd the standard deviation around the estimate

    • estimates the parameter estimates created during the marginal likelihood estimation

    • trees the trees created during the marginal likelihood estimation

Author(s)

Richèl J.C. Bilderbeek

See Also

Use remove_burn_ins to remove the burn-ins from the posterior's estimates (posterior$estimates)

Examples

if (beautier::is_on_ci() && is_beast2_installed()) {
  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()

  # A simple FASTA file
  fasta_filename <- beautier::get_beautier_path("test_output_0.fas")

  # Simple short inference
  inference_model <- create_test_inference_model()

  # Default BEAST2 options
  beast2_options <- create_beast2_options()

  bbt_run_from_model(
    fasta_filename = fasta_filename,
    inference_model = inference_model,
    beast2_options = beast2_options
  )

  bbt_continue(
    fasta_filename = fasta_filename,
    inference_model = inference_model,
    beast2_options = beast2_options
  )

  # Cleanup
  bbt_delete_temp_files(
    inference_model = inference_model,
    beast2_options = beast2_options
  )
  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()
}

Delete all the temporary files created by bbt_run_from_model

Description

Delete all the temporary files created by bbt_run_from_model

Usage

bbt_delete_temp_files(inference_model, beast2_options)

Arguments

inference_model

a Bayesian phylogenetic inference model, as returned by create_inference_model
beast2_options

'BEAST2' options, as can be created by create_beast2_options

Value

Nothing.

Author(s)

Richèl J.C. Bilderbeek

Examples

if (beautier::is_on_ci() && is_beast2_installed()) {
  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()

  # Do a minimal run
  inference_model <- create_test_inference_model()
  beast2_options <- create_beast2_options()
  bbt_run_from_model(
    fasta_filename = get_fasta_filename(),
    inference_model = inference_model,
    beast2_options = beast2_options
  )

  # Cleanup
  bbt_delete_temp_files(
    inference_model = inference_model,
    beast2_options = beast2_options
  )

  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()
}

Run BEAST2

Description

Do a full BEAST2 run: create a 'BEAST2' configuration file (like 'BEAUti 2'), run 'BEAST2', parse results (like 'Tracer')

Usage

bbt_run(
  fasta_filename,
  tipdates_filename = NA,
  site_model = beautier::create_jc69_site_model(),
  clock_model = beautier::create_strict_clock_model(),
  tree_prior = beautier::create_yule_tree_prior(),
  mrca_prior = NA,
  mcmc = beautier::create_mcmc(),
  beast2_input_filename = beastier::create_temp_input_filename(),
  rng_seed = 1,
  beast2_output_state_filename = beastier::create_temp_state_filename(),
  beast2_path = beastier::get_default_beast2_path(),
  overwrite = TRUE,
  verbose = FALSE
)

Arguments

fasta_filename

a FASTA filename
tipdates_filename

name of the file containing tip dates
site_model

one site model, see create_site_models
clock_model

one clock model, see create_clock_model
tree_prior

one tree priors, as created by create_tree_prior
mrca_prior

one Most Recent Common Ancestor prior, as returned by create_mrca_prior
mcmc

the MCMC options, see create_mcmc
beast2_input_filename

path of the 'BEAST2' configuration file. By default, this file is put in a temporary folder with a random filename, as the user needs not read it: it is used as input of 'BEAST2'. Specifying a beast2_input_filename allows to store that file in a more permanently stored location.
rng_seed

the random number generator seed. Must be either NA or a positive non-zero value. An RNG seed of NA results in 'BEAST2' picking a random seed.
beast2_output_state_filename

name of the final state file created by 'BEAST2', containing the operator acceptances. By default, this file is put a temporary folder with a random filename, as the user needs not read it: its content is parsed and returned by this function. Specifying a beast2_output_state_filename allows to store that file in a more permanently stored location.
beast2_path

name of either a 'BEAST2' binary file (usually simply beast) or a 'BEAST2' jar file (usually has a .jar extension). Use get_default_beast2_bin_path to get the default BEAST binary file's path Use get_default_beast2_jar_path to get the default BEAST jar file's path
overwrite

will 'BEAST2' overwrite files? Like 'BEAST2', this is set to TRUE by default. If TRUE, 'BEAST2' will overwrite the beast2_options$output_state_filename if its present. If FALSE, 'BEAST2' will not overwrite the beast2_options$output_state_filename if its present and babette will give an error message. Note that if overwrite is set to FALSE when a tracelog (see create_tracelog), screenlog (see create_screenlog) or treelog (see create_treelog) file already exists, 'BEAST2' (and thus babette) will freeze.
verbose

set to TRUE for more output

Details

Prefer using bbt_run_from_model, as it has a cleaner interface.

Value

a list with the following elements:

  • estimates: a data frame with 'BEAST2' parameter estimates

  • [alignment_id]_trees: a multiPhylo containing the phylogenies in the 'BEAST2' posterior. [alignment_id] is the ID of the alignment. For example, when running bbt_run with anthus_aco.fas, this element will have name anthus_aco_trees

  • operators: a data frame with the 'BEAST2' MCMC operator acceptances

  • output: a numeric vector with the output sent to standard output and error streams

  • ns: (optional) the results of a marginal likelihood estimation, will exist only when create_ns_mcmc was used for the MCMC. This structure will contain the following elements:

    • marg_log_lik the marginal log likelihood estimate

    • marg_log_lik_sd the standard deviation around the estimate

    • estimates the parameter estimates created during the marginal likelihood estimation

    • trees the trees created during the marginal likelihood estimation

Author(s)

Richèl J.C. Bilderbeek

See Also

Use remove_burn_ins to remove the burn-ins from the posterior's estimates (posterior$estimates)

Examples

if (beautier::is_on_ci() && is_beast2_installed()) {
  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()

  # Setup for a short run
  mcmc <- create_test_mcmc()

  # Store filenames for cleanup.
  # Note that 'bbt_run_from_model allows for easier cleanup
  mcmc$tracelog$filename <- tempfile()
  mcmc$treelog$filename <- tempfile()
  mcmc$screenlog$filename <- tempfile()
  beast2_input_filename <- tempfile()
  beast2_output_state_filename <- tempfile()

  bbt_run(
    fasta_filename = get_babette_path("anthus_aco.fas"),
    beast2_input_filename = beast2_input_filename,
    beast2_output_state_filename = beast2_output_state_filename,
    mcmc = mcmc
  )

  # Cleanup
  # Again, note that 'bbt_run_from_model allows for easier cleanup
  file.remove(mcmc$tracelog$filename)
  file.remove(mcmc$treelog$filename)
  file.remove(mcmc$screenlog$filename)
  file.remove(beast2_input_filename)
  file.remove(beast2_output_state_filename)
  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()
}

Run BEAST2

Description

Do a full run: create a 'BEAST2' configuration file (like 'BEAUti 2'), run 'BEAST2', parse results (like 'Tracer')

Usage

bbt_run_from_model(
  fasta_filename,
  inference_model = beautier::create_inference_model(),
  beast2_options = beastier::create_beast2_options()
)

Arguments

fasta_filename

a FASTA filename
inference_model

a Bayesian phylogenetic inference model, as returned by create_inference_model
beast2_options

'BEAST2' options, as can be created by create_beast2_options

Value

a list with the following elements:

  • estimates: a data frame with 'BEAST2' parameter estimates

  • [alignment_id]_trees: a multiPhylo containing the phylogenies in the 'BEAST2' posterior. [alignment_id] is the ID of the alignment. For example, when running bbt_run_from_model with anthus_aco.fas, this element will have name anthus_aco_trees

  • operators: a data frame with the 'BEAST2' MCMC operator acceptances

  • output: a numeric vector with the output sent to standard output and error streams

  • ns: (optional) the results of a marginal likelihood estimation, will exist only when create_ns_mcmc was used for mcmc. This structure will contain the following elements:

    • marg_log_lik the marginal log likelihood estimate

    • marg_log_lik_sd the standard deviation around the estimate

    • estimates the parameter estimates created during the marginal likelihood estimation

    • trees the trees created during the marginal likelihood estimation

Author(s)

Richèl J.C. Bilderbeek

See Also

Use remove_burn_ins to remove the burn-ins from the posterior's estimates (posterior$estimates)

Examples

if (beautier::is_on_ci() && is_beast2_installed()) {
  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()

  # Simple short inference
  inference_model <- create_test_inference_model()

  # Default BEAST2 options
  beast2_options <- create_beast2_options()

  bbt_run_from_model(
    fasta_filename = get_babette_path("anthus_aco.fas"),
    inference_model = inference_model,
    beast2_options = beast2_options
  )

  # Cleanup
  bbt_delete_temp_files(
    inference_model = inference_model,
    beast2_options = beast2_options
  )
  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()
}

Do a self test to verify babette that works correctly.

Description

Do a self test to verify babette that works correctly.

Usage

bbt_self_test(beast2_options = beastier::create_beast2_options())

Arguments

beast2_options

'BEAST2' options, as can be created by create_beast2_options

Value

Nothing. Will raise an exception if something is wrong.

Author(s)

Richèl J.C. Bilderbeek

Examples

if (beautier::is_on_ci() && is_beast2_installed()) {
  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()

  bbt_self_test()

  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()
}

Checks if bbt_run has the 'BEAST2' packages needed to process its arguments. Will stop if not.

Description

For example, to use a Nested Sampling MCMC, the 'BEAST2' 'NS' package needs to be installed.

Usage

check_beast2_pkgs(mcmc, beast2_path = get_default_beast2_bin_path())

Arguments

mcmc

the MCMC options, see create_mcmc
beast2_path

name of either a 'BEAST2' binary file (usually simply beast) or a 'BEAST2' jar file (usually has a .jar extension). Use get_default_beast2_bin_path to get the default BEAST binary file's path Use get_default_beast2_jar_path to get the default BEAST jar file's path

Value

Nothing.

Examples

if (beautier::is_on_ci() && is_beast2_installed()) {
  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()

  # Minimal BEAST2 setup
  check_beast2_pkgs(mcmc = create_mcmc())

  # BEAST2 with NS package installed
  if (is_beast2_ns_pkg_installed()) {
    check_beast2_pkgs(mcmc = create_ns_mcmc())
  }

  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()
}

Get an example output of bbt_run or bbt_run_from_model.

Description

This output is used in testing.

Usage

create_test_bbt_run_output()

Value

the same results as bbt_run or bbt_run_from_model

Author(s)

Richèl J.C. Bilderbeek

Examples

beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()

create_test_bbt_run_output()

beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()

Create NS testing output

Description

Create testing output similar to when running a 'BEAST2' run with nested sampling

Usage

create_test_ns_output()

Value

a text of type character vector.

Author(s)

Richèl J.C. Bilderbeek

See Also

Use parse_beast2_output_to_ns to parse this output to a Nested Sampling result. See create_ns_mcmc to see how to do a marginal likelihood estimation using Nested Sampling.

Examples

beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()

create_test_ns_output()

beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()

This function does nothing. It is intended to inherit is parameters' documentation.

Description

This function does nothing. It is intended to inherit is parameters' documentation.

Usage

default_params_doc(
  beast2_input_filename,
  beast2_options,
  beast2_output_log_filename,
  beast2_output_state_filename,
  beast2_output_trees_filenames,
  beast2_path,
  beast2_working_dir,
  cleanup,
  clock_model,
  clock_models,
  fasta_filename,
  fasta_filenames,
  inference_model,
  mcmc,
  mrca_prior,
  mrca_priors,
  overwrite,
  rng_seed,
  site_model,
  site_models,
  tipdates_filename,
  tree_prior,
  tree_priors,
  verbose
)

Arguments

beast2_input_filename

path of the 'BEAST2' configuration file. By default, this file is put in a temporary folder with a random filename, as the user needs not read it: it is used as input of 'BEAST2'. Specifying a beast2_input_filename allows to store that file in a more permanently stored location.
beast2_options

'BEAST2' options, as can be created by create_beast2_options
beast2_output_log_filename

name of the log file created by 'BEAST2', containing the parameter estimates in time. By default, this file is put a temporary folder with a random filename, as the user needs not read it: its content is parsed and returned by this function. Specifying a beast2_output_log_filename allows to store that file in a more permanently stored location.
beast2_output_state_filename

name of the final state file created by 'BEAST2', containing the operator acceptances. By default, this file is put a temporary folder with a random filename, as the user needs not read it: its content is parsed and returned by this function. Specifying a beast2_output_state_filename allows to store that file in a more permanently stored location.
beast2_output_trees_filenames

name of the one or more trees files created by 'BEAST2', one per alignment. By default, these files are put a temporary folder with a random filename, as the user needs not read it: their content is parsed and returned by this function. Specifying beast2_output_trees_filenames allows to store these one or more files in a more permanently stored location.
beast2_path

name of either a 'BEAST2' binary file (usually simply beast) or a 'BEAST2' jar file (usually has a .jar extension). Use get_default_beast2_bin_path to get the default BEAST binary file's path Use get_default_beast2_jar_path to get the default BEAST jar file's path
beast2_working_dir

the folder 'BEAST2' will work in. This is an (empty) temporary folder by default. This allows to call 'BEAST2' in multiple parallel processes, as each process can have its own working directory
cleanup

set to FALSE to keep all temporary files
clock_model

one clock model, see create_clock_model
clock_models

one or more clock models, see create_clock_models
fasta_filename

a FASTA filename
fasta_filenames

one or more FASTA filename, each with one alignment
inference_model

a Bayesian phylogenetic inference model, as returned by create_inference_model
mcmc

the MCMC options, see create_mcmc
mrca_prior

one Most Recent Common Ancestor prior, as returned by create_mrca_prior
mrca_priors

a list of one or more Most Recent Common Ancestor priors, as returned by create_mrca_prior
overwrite

will 'BEAST2' overwrite files? Like 'BEAST2', this is set to TRUE by default. If TRUE, 'BEAST2' will overwrite the beast2_options$output_state_filename if its present. If FALSE, 'BEAST2' will not overwrite the beast2_options$output_state_filename if its present and babette will give an error message. Note that if overwrite is set to FALSE when a tracelog (see create_tracelog), screenlog (see create_screenlog) or treelog (see create_treelog) file already exists, 'BEAST2' (and thus babette) will freeze.
rng_seed

the random number generator seed. Must be either NA or a positive non-zero value. An RNG seed of NA results in 'BEAST2' picking a random seed.
site_model

one site model, see create_site_models
site_models

one or more site models, see create_site_models
tipdates_filename

name of the file containing tip dates
tree_prior

one tree priors, as created by create_tree_prior
tree_priors

one or more tree priors, see create_tree_priors
verbose

set to TRUE for more output

Note

This is an internal function, so it should be marked with @noRd. This is not done, as this will disallow all functions to find the documentation parameters

Author(s)

Richèl J.C. Bilderbeek

Get the alignment IDs from one or more 'BEAST2' XML input files.

Description

Get the alignment IDs from one or more 'BEAST2' XML input files.

Usage

get_alignment_ids_from_xml(xml_filename)

Arguments

xml_filename

name of a 'BEAST2' XML input file.

Value

a character vector with one or more alignment IDs.

Author(s)

Richèl J.C. Bilderbeek

Examples

beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()

alignment_ids <- get_alignment_ids_from_xml(
  get_babette_path("anthus_2_4.xml")
)

beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()

Get the full path of a file in the inst/extdata folder

Description

Get the full path of a file in the inst/extdata folder

Usage

get_babette_path(filename)

Arguments

filename

the file's name, without the path

Value

the full path of the filename, if and only if the file is present. Will stop otherwise.

Author(s)

Richèl J.C. Bilderbeek

See Also

for more files, use get_babette_paths

Examples

beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()

get_babette_path("anthus_aco.fas")

beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()

Get the full paths of files in the inst/extdata folder

Description

Get the full paths of files in the inst/extdata folder

Usage

get_babette_paths(filenames)

Arguments

filenames

the files' names, without the path

Value

the filenames' full paths, if and only if all files are present. Will stop otherwise.

Author(s)

Richèl J.C. Bilderbeek

See Also

for one file, use get_babette_path

Examples

beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()

get_babette_paths(c("anthus_aco.fas", "anthus_nd2.fas"))

beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()

Process the 'BEAST2' output dependent on 'BEAST2' package specifics

Description

Process the 'BEAST2' output dependent on 'BEAST2' package specifics

Usage

parse_beast2_output(out, inference_model)

Arguments

out

a list with the complete babette output, with elements:

  • output textual output of a 'BEAST2' run

inference_model

a Bayesian phylogenetic inference model, as returned by create_inference_model

Value

complete babette output with added attributes, which depends on the 'BEAST2' package.

  • marg_log_lik the marginal log likelihood estimate

  • marg_log_lik_sd the standard deviation around the estimate

  • estimates the parameter estimates created during the marginal likelihood estimation

  • trees the trees created during the marginal likelihood estimation

Author(s)

Richèl J.C. Bilderbeek

Parse BEAST2 NS output

Description

Parse the BEAST2 output when run with the BEAST2 NS ('Nested Sampling') package.

Usage

parse_beast2_output_to_ns(output)

Arguments

output

screen output

Value

a list with the following elements:

  • marg_log_lik the marginal log likelihood estimate

  • marg_log_lik_sd the standard deviation around the estimate

Author(s)

Richèl J.C. Bilderbeek

See Also

use create_test_ns_output to obtain a test screen output.

Examples

beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()

parse_beast2_output_to_ns(
  output = create_test_ns_output()
)

beastier::remove_beaustier_folders()
beastier::check_empty_beaustier_folders()

Draw multiple trees on top of one another.

Description

Draw multiple trees on top of one another.

Usage

plot_densitree(phylos, ...)

Arguments

phylos

one or more phylogenies, must be of class multiPhylo
...

options to be passed to phangorn's densiTree function

Value

nothing. Will produce a plot.

Author(s)

Richèl J.C. Bilderbeek

Examples

if (beautier::is_on_ci() && is_beast2_installed()) {
  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()

  inference_model <- create_test_inference_model()
  beast2_options <- create_beast2_options()

   out <- bbt_run_from_model(
    get_babette_path("anthus_aco.fas"),
    inference_model = inference_model,
    beast2_options = beast2_options
  )
  bbt_delete_temp_files(
    inference_model = inference_model,
    beast2_options = beast2_options
  )

  plot_densitree(out$anthus_aco_trees)

  # Clean up temporary files created by babette
  bbt_delete_temp_files(
    inference_model = inference_model,
    beast2_options = beast2_options
  )
  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()
}

Internal function to prepare for 'BEAST2' creating files

Description

The inference model and 'BEAST2' options contain paths that may point to sub-sub-sub folders. Create those folders and test if these folders can be written to

Usage

prepare_file_creation(inference_model, beast2_options)

Arguments

inference_model

a Bayesian phylogenetic inference model, as returned by create_inference_model
beast2_options

'BEAST2' options, as can be created by create_beast2_options

Value

Nothing.

Examples

# This example will fail on the CRAN
# r-oldrel-macos-x86_64 platform
if (rappdirs::app_dir()$os != "mac") {
  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()

  # For a test inference model, the files can be prepared
  inference_model <- create_test_inference_model()
  beast2_options <- create_beast2_options()
  prepare_file_creation(inference_model, beast2_options)

  beastier::remove_beaustier_folders()
  beastier::check_empty_beaustier_folders()
}

Deprecated function.

Description

Update all babette dependencies, by installing their latest versions.

Usage

update_babette(upgrade = "default")

Arguments

upgrade

Deprecated.

Details

See https://github.com/richelbilderbeek/babetteinstall how to do this.

Value

Nothing.

Author(s)

Giovanni Laudanno, Richèl J.C. Bilderbeek