Help for package babette

Title:

Control 'BEAST2'

Version:

2.3.4

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'.

License:

GPL-3

RoxygenNote:

7.2.3

VignetteBuilder:

knitr

URL:

https://docs.ropensci.org/babette/ (website), https://github.com/ropensci/babette

BugReports:

https://github.com/ropensci/babette/issues

Depends:

beautier (≥ 2.6.12), beastier (≥ 2.5), mauricer (≥ 2.5.2), R (≥ 3.5.0), tracerer

Imports:

phangorn, rlang (≥ 1.1.0), stringr, xml2

Suggests:

ape, ggplot2, knitr, lintr, nLTT, rappdirs, rmarkdown, spelling, testthat (≥ 2.1.0)

Language:

en-US

Encoding:

UTF-8

SystemRequirements:

BEAST2 (https://www.beast2.org/)

NeedsCompilation:

Packaged:

2024-06-24 09:17:09 UTC; richel

Author:

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 <rjcbilderbeek@gmail.com>

Repository:

CRAN

Date/Publication:

2024-06-25 11:20:06 UTC

babette: A package for Bayesian phylogenetics.

Description

'babette' provides for an alternative workflow of using the popular phylogenetics tool 'BEAST2', including it peripheral tools. From an alignment and inference model, a posterior of jointly estimated phylogenies and parameter estimates is generated.

Note

the imports are created by script 'scripts/create_imports.R'

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()

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

  # 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()
}
beastier::remove_beaustier_folders()

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

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

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

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

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

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

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

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

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

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

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

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

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

babette: A package for Bayesian phylogenetics.

Description

Note

Author(s)

See Also

Examples

Continue a BEAST2 run

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Delete all the temporary files created by bbt_run_from_model

Description

Usage

Arguments

Value

Author(s)

Examples

Run BEAST2

Description

Usage

Arguments

Details

Value

Author(s)

See Also

Examples

Run BEAST2

Description

Usage

Arguments

Value

Author(s)

See Also

Examples

Do a self test to verify babette that works correctly.

Description

Usage

Arguments

Value

Author(s)

Examples

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

Description

Usage

Arguments

Value

Examples

Get an example output of bbt_run or bbt_run_from_model.

Description

Usage

Value

Author(s)

Examples

Create NS testing output

Description

Usage

Value

Author(s)

See Also

Examples

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

Description

Usage

Arguments

Note

Author(s)

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

Description

Usage

Arguments

Value

Author(s)

Examples

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

Description

Usage

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

Get an example output of `bbt_run` or `bbt_run_from_model`.

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

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