Title:	'BEAUti' from R
Version:	2.6.12
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. 'BEAUti 2' (which is part of 'BEAST2') is a GUI tool that allows users to specify the many possible setups and generates the XML file 'BEAST2' needs to run. This package provides a way to create 'BEAST2' input files without active user input, but using R function calls instead.
License:	GPL-3
RoxygenNote:	7.2.3
VignetteBuilder:	knitr
URL:	https://docs.ropensci.org/beautier/, https://github.com/ropensci/beautier
BugReports:	https://github.com/ropensci/beautier/issues
Imports:	ape, rappdirs, purrr, rlang (≥ 1.1.0), seqinr, stringr
Suggests:	knitr, markdown, readr, rmarkdown, testthat (≥ 2.1.0)
Language:	en-US
Encoding:	UTF-8
NeedsCompilation:	no
Packaged:	2024-04-01 09:34:18 UTC; richel
Author:	Richèl J.C. Bilderbeek [aut, cre], Joëlle Barido-Sottani [rev] (Joëlle reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209), David Winter [rev] (David reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/209), Paul Van Els [ctb], Raphael Scherrer [ctb], Yacine B. Chehida [ctb], Katharine S. Walter [ctb], Gary Napier [ctb], Jason Griffiths [ctb], Thijs Janzen [ctb], Pedro Taucce [ctb], Olivier Roy [ctb], Jana Riederer [ctb]
Maintainer:	Richèl J.C. Bilderbeek <rjcbilderbeek@gmail.com>
Repository:	CRAN
Date/Publication:	2024-04-01 12:30:02 UTC

beautier: A package to create a BEAST2 input file.

Description

beautier allows to create a BEAST2 input file, using an R interface. beautier closely follows the interface of BEAUti 2, a GUI tool bundled with BEAST2, including its default settings.

Details

See the documentation of create_inference_model to see the features of BEAST2 that beautier supports.

Author(s)

Richèl J.C. Bilderbeek

See Also

These are packages associated with beautier:

• The package beastier can run BEAST2 from R

• The package tracerer can parse BEAST2 output files from R

• The package mauricer manages BEAST2 packages from R

• The package babette combines the functionality of beautier, beastier, mauricer and tracerer into a single workflow

Examples

if (is_on_ci()) {

  check_empty_beautier_folder()

  # Get an example FASTA file
  input_filename <- get_fasta_filename()

  # The file created by beautier, a BEAST2 input file
  output_filename <- get_beautier_tempfilename()

  # Use the default BEAUti settings to create a BEAST2 input file
  create_beast2_input_file_from_model(
    input_filename,
    output_filename,
    inference_model = create_inference_model()
  )

  # Remove the folder that contains the beautier temporary files
  remove_beautier_folder()
  check_empty_beautier_folder()
}

Internal function

Description

Converts an alpha parameter to XML

Usage

alpha_parameter_to_xml(alpha_parameter, beauti_options)

Arguments

Value

the parameter as XML text

Author(s)

Richèl J.C. Bilderbeek

Examples

remove_beautier_folder()
check_empty_beautier_folder()

# The alpha parameter must be initialized, i.e. have an ID
alpha_parameter_to_xml(
  alpha_parameter = create_alpha_param(id = "1"),
  beauti_options = create_beauti_options()
)

check_empty_beautier_folder()

Determine if x consists out of clock_models objects

Description

Determine if x consists out of clock_models objects

Usage

are_clock_models(x)

Arguments

Value

TRUE if x, or all elements of x, are clock_model objects

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

rln_clock_model <- create_rln_clock_model()
strict_clock_model <- create_strict_clock_model()
both_clock_models <- list(rln_clock_model, strict_clock_model)
# TRUE
are_clock_models(rln_clock_model)
are_clock_models(strict_clock_model)
are_clock_models(both_clock_models)

# FALSE
are_clock_models(NA)
are_clock_models(NULL)
are_clock_models("nonsense")
are_clock_models(create_jc69_site_model())

check_empty_beautier_folder()

Determine if two MCMCs are equal.

Description

Will stop if the arguments are not MCMCs.

Usage

are_equal_mcmcs(mcmc_1, mcmc_2)

Arguments

Value

TRUE if the two MCMCs are equal

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_mcmc to create an MCMC

Examples

if (is_on_ci()) {

  check_empty_beautier_folder()

  mcmc_1 <- create_mcmc(chain_length = 1000)
  mcmc_2 <- create_mcmc(chain_length = 314)
  # TRUE
  are_equal_mcmcs(mcmc_1, mcmc_1)
  # FALSE
  are_equal_mcmcs(mcmc_1, mcmc_2)

  check_empty_beautier_folder()
}

Determine if two screenlogs are equal.

Description

Will stop if the arguments are not screenlogs.

Usage

are_equal_screenlogs(screenlog_1, screenlog_2)

Arguments

Value

TRUE if the two screenlogs are equal

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_screenlog to create an screenlog

Examples

check_empty_beautier_folder()

screenlog_1 <- create_screenlog(log_every = 1000)
screenlog_2 <- create_screenlog(log_every = 314)
# TRUE
are_equal_screenlogs(screenlog_1, screenlog_1)
# FALSE
are_equal_screenlogs(screenlog_1, screenlog_2)

check_empty_beautier_folder()

Determine if two tracelogs are equal.

Description

Will stop if the arguments are not tracelogs.

Usage

are_equal_tracelogs(tracelog_1, tracelog_2)

Arguments

Value

TRUE if the two tracelogs are equal

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_tracelog to create an tracelog

Examples

check_empty_beautier_folder()

tracelog_1 <- create_tracelog(log_every = 1000)
tracelog_2 <- create_tracelog(log_every = 314)
# TRUE
are_equal_tracelogs(tracelog_1, tracelog_1)
# FALSE
are_equal_tracelogs(tracelog_1, tracelog_2)

check_empty_beautier_folder()

Determine if two treelogs are equal.

Description

Will stop if the arguments are not treelogs.

Usage

are_equal_treelogs(treelog_1, treelog_2)

Arguments

Value

TRUE if the two treelogs are equal

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_treelog to create an treelog

Examples

check_empty_beautier_folder()

treelog_1 <- create_treelog(log_every = 1000)
treelog_2 <- create_treelog(log_every = 314)
# TRUE
are_equal_treelogs(treelog_1, treelog_1)
# FALSE
are_equal_treelogs(treelog_1, treelog_2)

check_empty_beautier_folder()

Determine if XML files result in equal trees

Description

Determine if XML files result in equal trees

Usage

are_equal_xml_files(filename_1, filename_2, section)

Arguments

Value

TRUE if the two sections of the XML files are equal, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

See Also

to check for equivalence, use are_equivalent_xml_files

Examples

check_empty_beautier_folder()

are_equal_xml_files(
  filename_1 = get_beautier_path("2_4.xml"),
  filename_2 = get_beautier_path("2_6_0.xml"),
  section = "taxonset"
)

check_empty_beautier_folder()

Determine if XML lines result in equal trees

Description

Determine if XML lines result in equal trees

Usage

are_equal_xml_lines(lines_1, lines_2, section)

Arguments

Value

TRUE if the two sections of the XML files are equal, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

are_equal_xml_lines(
  lines_1 = readLines(get_beautier_path("2_4.xml")),
  lines_2 = readLines(get_beautier_path("2_6_0.xml")),
  section = "taxonset"
)

check_empty_beautier_folder()

Internal function

Description

Internal function used for debugging to determine if XML files result in equivalent trees

Usage

are_equivalent_xml_files(filename_1, filename_2, section = NA)

Arguments

Value

TRUE if the two XML files result in equivalent trees, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

See Also

to check for equality, use are_equal_xml_files

Examples

check_empty_beautier_folder()

are_equivalent_xml_files(
  filename_1 = get_beautier_path("2_4.xml"),
  filename_2 = get_beautier_path("2_6_0.xml")
)

check_empty_beautier_folder()

Determine if XML lines result in equivalent trees

Description

Determine if XML lines result in equivalent trees

Usage

are_equivalent_xml_lines(lines_1, lines_2, section = NA, verbose = FALSE)

Arguments

Value

TRUE if the two XML lines result in equivalent trees, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Determine if XML lines result in equivalent trees

Description

Determine if XML lines result in equivalent trees

Usage

are_equivalent_xml_lines_all(lines_1, lines_2, verbose = FALSE)

Arguments

Value

TRUE if the two XML lines result in equivalent trees, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Determine if XML operator lines result in equivalent trees

Description

Determine if XML operator lines result in equivalent trees

Usage

are_equivalent_xml_lines_loggers(lines_1, lines_2, verbose = FALSE)

Arguments

Value

TRUE if the two XML lines result in equivalent trees, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Determine if XML operator lines result in equivalent trees

Description

Determine if XML operator lines result in equivalent trees

Usage

are_equivalent_xml_lines_operators(lines_1, lines_2, verbose = FALSE)

Arguments

Value

TRUE if the two XML lines result in equivalent trees, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Determine if XML lines result in equivalent trees

Description

Determine if XML lines result in equivalent trees

Usage

are_equivalent_xml_lines_section(lines_1, lines_2, section, verbose = FALSE)

Arguments

Value

TRUE if the two XML lines result in equivalent trees, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Checks if all filenames have a FASTA filename extension

Description

Checks if all filenames have a FASTA filename extension

Usage

are_fasta_filenames(filenames)

Arguments

Value

TRUE if all filenames have a FASTA filename extension

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

# TRUE
are_fasta_filenames("1.fas")
are_fasta_filenames("1.fasta")
are_fasta_filenames("1.FAS")
are_fasta_filenames("1.FASTA")
are_fasta_filenames(c("1.fas", "2.fas"))

# FALSE
are_fasta_filenames("")
are_fasta_filenames(NA)
are_fasta_filenames(NULL)
are_fasta_filenames(Inf)
are_fasta_filenames("1.fasX")
are_fasta_filenames(c("1.fas", "2.exe"))
are_fasta_filenames(c("1.bat", "2.exe"))

check_empty_beautier_folder()

Determine if x consists out of IDs

Description

Determine if x consists out of IDs

Usage

are_ids(x)

Arguments

Value

TRUE if x, or all elements of x, are IDs

Author(s)

Richèl J.C. Bilderbeek

See Also

to check one ID, use is_id

Examples

check_empty_beautier_folder()

# TRUE
are_ids("anthus_aco")
are_ids(c("anthus_aco", "anthus_nd2"))
are_ids(list("anthus_aco", "anthus_nd2"))
are_ids(c(1, 2))
are_ids(1)

# FALSE
are_ids(NULL)
are_ids(NA)
are_ids(c())
are_ids(ape::rcoal(3))
are_ids(c(ape::rcoal(3), ape::rcoal(4)))

check_empty_beautier_folder()

Determine if x consists out of initialized clock_models objects

Description

Determine if x consists out of initialized clock_models objects

Usage

are_init_clock_models(x)

Arguments

Value

TRUE if x, or all elements of x, are initialized clock_model objects

Author(s)

Richèl J.C. Bilderbeek

Determine if x consists out of initialized MRCA priors

Description

Determine if x consists out of initialized MRCA priors

Usage

are_init_mrca_priors(x)

Arguments

Value

TRUE if x, or all elements of x, are initialized MRCA priors

Author(s)

Richèl J.C. Bilderbeek

Determine if x consists out of initialized site_models objects

Description

Determine if x consists out of initialized site_models objects

Usage

are_init_site_models(x)

Arguments

Value

TRUE if x, or all elements of x, are initialized site_model objects

Author(s)

Richèl J.C. Bilderbeek

Determine if x consists out of initialized tree_priors objects

Description

Determine if x consists out of initialized tree_priors objects

Usage

are_init_tree_priors(x)

Arguments

Value

TRUE if x, or all elements of x, are initialized tree_prior objects

Author(s)

Richèl J.C. Bilderbeek

Determine if the MRCA priors' alignment IDs are present in the FASTA files

Description

Determine if the MRCA priors' alignment IDs are present in the FASTA files

Usage

are_mrca_align_ids_in_fasta(mrca_prior, fasta_filename)

Arguments

Value

TRUE if all the MRCA priors' alignment IDs are present in the FASTA files. Returns FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Determine if x consists out of MRCA priors

Description

Determine if x consists out of MRCA priors

Usage

are_mrca_priors(mrca_priors)

Arguments

Value

TRUE if x, or all elements of x, are MRCA priors. Returns FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Determine if the MRCA priors' taxa names are present in the FASTA files

Description

Determine if the MRCA priors' taxa names are present in the FASTA files

Usage

are_mrca_taxon_names_in_fasta(mrca_prior, fasta_filename)

Arguments

Value

TRUE if the MRCA priors' taxa names are present in the FASTA files. FALSE otherwise.

Author(s)

Richèl J.C. Bilderbeek

Are the clock models Relaxed Log-Normal clock models?

Description

Are the clock models Relaxed Log-Normal clock models?

Usage

are_rln_clock_models(clock_models)

Arguments

Value

vector of booleans with the same length as the number of clock models in clock_models. Each nth element is TRUE if the nth element in clock_models is a relaxed log-normal clock model, FALSE otherwise

Author(s)

Richèl J.C. Bilderbeek

Determine if x consists out of site_models objects

Description

Determine if x consists out of site_models objects

Usage

are_site_models(x)

Arguments

Value

TRUE if x, or all elements of x, are site_model objects

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_site_model to create a site model

Examples

check_empty_beautier_folder()

jc69_site_model <- create_jc69_site_model()
gtr_site_model <- create_gtr_site_model()
both_site_models <- list(jc69_site_model, gtr_site_model)

# TRUE
are_site_models(jc69_site_model)

# TRUE
are_site_models(gtr_site_model)

# TRUE
are_site_models(both_site_models)

check_empty_beautier_folder()

Determine if x consists out of tree_priors objects

Description

Determine if x consists out of tree_priors objects

Usage

are_tree_priors(x)

Arguments

Value

TRUE if x, or all elements of x, are tree_prior objects

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_yule_tree_prior to create a Yule tree prior

Examples

check_empty_beautier_folder()

yule_tree_prior <- create_yule_tree_prior()
bd_tree_prior <- create_bd_tree_prior()
both_tree_priors <- list(yule_tree_prior, bd_tree_prior)
# TRUE
are_tree_priors(yule_tree_prior)
# TRUE
are_tree_priors(bd_tree_prior)
# TRUE
are_tree_priors(both_tree_priors)

check_empty_beautier_folder()

Internal function

Description

Converts a 'bPopSizes' parameter to XML

Usage

b_pop_sizes_param_to_xml(
  b_pop_sizes_param,
  beauti_options = create_beauti_options()
)

Arguments

Value

the parameter as XML text

Author(s)

Richèl J.C. Bilderbeek

Internal function

Description

Converts a Bayesian population sizes parameter to XML

Usage

b_pop_sizes_parameter_to_xml(
  b_pop_sizes_parameter,
  beauti_options = create_beauti_options()
)

Arguments

Value

the parameter as XML text

Author(s)

Richèl J.C. Bilderbeek

Examples

b_pop_sizes_parameter_to_xml(
  b_pop_sizes_parameter = create_b_pop_sizes_param(id = 42),
  beauti_options = create_beauti_options()
)
b_pop_sizes_parameter_to_xml(
  b_pop_sizes_parameter = create_b_pop_sizes_param(id = 42, upper = Inf),
  beauti_options = create_beauti_options()
)

Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Birth-Death tree prior

Description

Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Birth-Death tree prior

Usage

bd_tree_prior_to_xml_prior_distr(bd_tree_prior, beauti_options)

Arguments

Value

lines of XML text

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

 # <distribution id="posterior" spec="util.CompoundDistribution">
 #     <distribution id="prior" spec="util.CompoundDistribution">
 #       HERE, where the ID of the distribution is 'prior'
 #     </distribution>
 #     <distribution id="likelihood" ...>
 #     </distribution>
 # </distribution>

check_empty_beautier_folder()

Internal function

Description

Converts a beta parameter to XML

Usage

beta_parameter_to_xml(beta_parameter, beauti_options = create_beauti_options())

Arguments

Value

the parameter as XML text

Author(s)

Richèl J.C. Bilderbeek

Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Birth-Death tree prior

Description

Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Birth-Death tree prior

Usage

cbs_tree_prior_to_xml_prior_distr(cbs_tree_prior, beauti_options)

Arguments

Value

lines of XML text

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

 # <distribution id="posterior" spec="util.CompoundDistribution">
 #     <distribution id="prior" spec="util.CompoundDistribution">
 #       HERE, where the ID of the distribution is 'prior'
 #     </distribution>
 #     <distribution id="likelihood" ...>
 #     </distribution>
 # </distribution>

check_empty_beautier_folder()

Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Coalescent Constant Population tree prior

Description

Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Coalescent Constant Population tree prior

Usage

ccp_tree_prior_to_xml_prior_distr(ccp_tree_prior, beauti_options)

Arguments

Value

lines of XML text

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

 # <distribution id="posterior" spec="util.CompoundDistribution">
 #     <distribution id="prior" spec="util.CompoundDistribution">
 #       HERE, where the ID of the distribution is 'prior'
 #     </distribution>
 #     <distribution id="likelihood" ...>
 #     </distribution>
 # </distribution>

check_empty_beautier_folder()

Convert a CCP tree prior to the XML as part of the state section

Description

Convert a CCP tree prior to the XML as part of the state section

Usage

ccp_tree_prior_to_xml_state(inference_model)

Arguments

Value

XML as text

Examples

check_empty_beautier_folder()

# Need an ID and inital value
inference_model <- create_inference_model(
  tree_prior = create_ccp_tree_prior(
    id = "anthus_nd2_sub",
    pop_size_distr = create_normal_distr(
      id = 123,
      value = 3.14
    )
  )
)

ccp_tree_prior_to_xml_state(inference_model)

check_empty_beautier_folder()

Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Coalescent Exponential Population tree prior

Description

Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Coalescent Exponential Population tree prior

Usage

cep_tree_prior_to_xml_prior_distr(cep_tree_prior, beauti_options)

Arguments

Value

lines of XML text

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

 # <distribution id="posterior" spec="util.CompoundDistribution">
 #     <distribution id="prior" spec="util.CompoundDistribution">
 #       HERE, where the ID of the distribution is 'prior'
 #     </distribution>
 #     <distribution id="likelihood" ...>
 #     </distribution>
 # </distribution>

check_empty_beautier_folder()

Check if the alignment_id is valid.

Description

Will stop if not.

Usage

check_alignment_id(alignment_id)

Arguments

Value

nothing, will stop if needed

Examples

check_empty_beautier_folder()

# anthus_aco_sub
alignment_id <- get_alignment_id("/home/homer/anthus_aco_sub.fas")
check_alignment_id(alignment_id)

check_empty_beautier_folder()

Check if the beauti_options is a valid beauti_options object.

Description

Calls stop if the beauti_options object is invalid

Usage

check_beauti_options(beauti_options)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_beauti_options to create a valid BEAUti options setup

Examples

check_empty_beautier_folder()

check_beauti_options(create_beauti_options())

check_empty_beautier_folder()

Check if the clock model is a valid clock model.

Description

Calls stop if the clock model is invalid

Usage

check_clock_model(clock_model)

Arguments

Value

TRUE if clock_model is a valid clock model

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_clock_model to create a valid clock model

Examples

check_empty_beautier_folder()

check_clock_model(create_strict_clock_model())
check_clock_model(create_rln_clock_model())

check_empty_beautier_folder()

Check if the object is a list of one or more clock models.

Description

Will stop if the object is not a list of one or more clock models.

Usage

check_clock_models(clock_models)

Arguments

Value

nothing. Will stop if the object is not a list of one or more clock models.

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_clock_model to create a valid clock model

Examples

check_empty_beautier_folder()

check_clock_models(create_strict_clock_model())
check_clock_models(list(create_strict_clock_model()))
check_clock_models(
  list(create_strict_clock_model(), create_rln_clock_model())
)

check_empty_beautier_folder()

Internal function

Description

Internal function to verify that, if there are 'beautier' temporary files created, these are also cleaned up, as by CRAN policy.

Usage

check_empty_beautier_folder(beautier_folder = get_beautier_folder())

Arguments

Details

If the 'beautier' folder does not exist, this function does nothing. If there are folder and/or files in the 'beautier' folder, an error is given.

Value

No return value, called for side effects.

Author(s)

Richèl J.C. Bilderbeek

See Also

use remove_beautier_folder to remove the default 'beautier' folder

Examples

remove_beautier_folder()

check_empty_beautier_folder()

remove_beautier_folder()

Checks if the input FASTA file and the inference model agree.

Description

Will stop if not

Usage

check_file_and_model_agree(input_filename, inference_model)

Arguments

Value

nothing, will stop if needed

Function to check if a file exists. Calls stop if the file is absent

Description

Function to check if a file exists. Calls stop if the file is absent

Usage

check_file_exists(filename, filename_description = NA)

Arguments

Value

nothing. Will stop if the file is absent, with a proper error message

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

check_file_exists(get_beautier_path("anthus_aco_sub.fas"))

check_empty_beautier_folder()

Check if the 'filename' is valid

Description

Calls stop if the filename is invalid

Usage

check_filename(filename, allow_empty_str = FALSE, allow_na = FALSE)

Arguments

Value

The filename (invisibly)

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

check_filename("trace.log")
check_filename("my.trees")

check_empty_beautier_folder()

Checks if the parameter is a valid gamma site model

Description

Checks if the parameter is a valid gamma site model

Usage

check_gamma_site_model(gamma_site_model)

Arguments

Value

nothing. Will call stop if the argument is not a valid gamma site model

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

check_gamma_site_model(create_gamma_site_model())

check_empty_beautier_folder()

Checks if the gamma site model has the right list elements' names

Description

Checks if the gamma site model has the right list elements' names

Usage

check_gamma_site_model_names(gamma_site_model)

Arguments

Value

nothing. Will call stop if the argument is not a valid gamma site model

Author(s)

Richèl J.C. Bilderbeek

Check if the gtr_site_model is a valid GTR nucleotide substitution model.

Description

Use create_gtr_site_model to create a valid GTR nucleotide substitution model.

Usage

check_gtr_site_model(gtr_site_model)

Arguments

Value

TRUE is the gtr_site_model is a valid GTR nucleotide substitution model, FALSE otherwise

Examples

check_empty_beautier_folder()

check_gtr_site_model(create_gtr_site_model())

check_empty_beautier_folder()

Check if the gtr_site_model has the list elements of a valid gtr_site_model object.

Description

Calls stop if an element is missing

Usage

check_gtr_site_model_names(gtr_site_model)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_gtr_site_model to create a valid gtr_site_model

Check if the supplied object is a valid Bayesian phylogenetic inference model.

Description

Calls stop if the supplied object is not a valid Bayesian phylogenetic inference model.

Usage

check_inference_model(inference_model)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_inference_model to create a valid Bayesian phylogenetic inference model

Examples

check_empty_beautier_folder()

check_inference_model(create_inference_model())

check_empty_beautier_folder()

Check if the inference_model is a valid BEAUti inference model.

Description

Calls stop if not.

Usage

check_inference_models(inference_models)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_inference_model to create a valid BEAST2 options object

Examples

check_empty_beautier_folder()

check_inference_models(list(create_inference_model()))

check_empty_beautier_folder()

Check if is_monophyletic has a valid value.

Description

Will stop if not.

Usage

check_is_monophyletic(is_monophyletic)

Arguments

Value

No return value, called for side effects

Check if the supplied mode is a valid logging mode.

Description

Check if the supplied mode is a valid logging mode.

Usage

check_log_mode(mode)

Arguments

Value

No return value, called for side effects

Check if the supplied sort is a valid logging sorting option.

Description

Check if the supplied sort is a valid logging sorting option.

Usage

check_log_sort(sort)

Arguments

Value

No return value, called for side effects

Check if the MCMC is a valid MCMC object.

Description

Calls stop if the MCMC is invalid

Usage

check_mcmc(mcmc)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_mcmc to create a valid MCMC

Examples

check_empty_beautier_folder()

check_mcmc(create_mcmc())

check_empty_beautier_folder()

Check if the MCMC has the list elements of a valid MCMC object.

Description

Calls stop if an element is missing

Usage

check_mcmc_list_element_names(mcmc)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_mcmc to create a valid MCMC

Check if the MCMC has the list elements with valid values for being a valid MCMC object.

Description

Calls stop if a value is invalid

Usage

check_mcmc_values(mcmc)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_mcmc to create a valid MCMC

Check if the MRCA prior is a valid MRCA prior.

Description

Calls stop if the MRCA prior is invalid.

Usage

check_mrca_prior(mrca_prior)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_mrca_prior to create a valid MRCA prior

Examples

check_empty_beautier_folder()

fasta_filename <- get_beautier_path("anthus_aco.fas")
mrca_prior <- create_mrca_prior(
  alignment_id = get_alignment_id(fasta_filename = fasta_filename),
  taxa_names = get_taxa_names(filename = fasta_filename)
)
mrca_prior <- create_mrca_prior(
 alignment_id = get_alignment_id(fasta_filename = fasta_filename),
 taxa_names = get_taxa_names(filename = fasta_filename)
)
check_mrca_prior(mrca_prior)

check_empty_beautier_folder()

Check if mrca_prior_name is a valid MRCA prior name.

Description

A valid MRCA prior name is either NA or one character string. Will stop if not.

Usage

check_mrca_prior_name(mrca_prior_name)

Arguments

Value

No return value, called for side effects

Check if the MRCA prior, which is a list, has all the named elements.

Description

Calls stop if not.

Usage

check_mrca_prior_names(mrca_prior)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use check_mrca_prior to check the entire MRCA prior

Check the MRCA prior's taxon names are valid.

Description

Will stop if not.

Usage

check_mrca_prior_taxa_names(taxa_names)

Arguments

Value

No return value, called for side effects

Check if this an MCMC that uses Nested Sampling to estimate a marginal likelihood.

Description

Will stop if not, else will do nothing

Usage

check_ns_mcmc(mcmc)

Arguments

Value

No return value, called for side effects

Author(s)

Richèl J.C. Bilderbeek

See Also

use create_ns_mcmc to create an MCMC that uses Nested Sampling to estimate a marginal likelihood

Check if the parameter is a valid parameter

Description

Calls stop if the parameter is invalid

Usage

check_param(param)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_param to create a valid parameter

Examples

check_empty_beautier_folder()

check_param(create_alpha_param())
check_param(create_beta_param())

check_empty_beautier_folder()

Check if the param has the list elements of a valid param object.

Description

Calls stop if an element is missing

Usage

check_param_names(param)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_param to create a valid param

Check if the param has the list elements of the right type for a valid param object.

Description

Calls stop if an element has the incorrect type

Usage

check_param_types(param)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_param to create a valid param

Check if the phylogeny is a valid phylogeny object.

Description

Calls stop if the phylogeny is invalid

Usage

check_phylogeny(phylogeny)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use ape::read.tree to create a phylogeny

Examples

check_empty_beautier_folder()

# Must do nothing on phylogenies
phylogeny <- ape::read.tree(text = "(A:1, B:1):1;")
check_phylogeny(phylogeny)

check_empty_beautier_folder()

Check if the rename function is a valid filename rename function

Description

Will stop if not

Usage

check_rename_fun(rename_fun)

Arguments

Value

No return value, called for side effects

Author(s)

Richèl J.C. Bilderbeek

Check if the clock model is a valid clock model.

Description

Calls stop if the clock model is invalid

Usage

check_rln_clock_model(clock_model)

Arguments

Value

TRUE if clock_model is a valid clock model

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_clock_model to create a valid clock model

Examples

check_empty_beautier_folder()

check_rln_clock_model(create_rln_clock_model())

check_empty_beautier_folder()

Check if a screenlog is valid.

Description

Will call stop if not.

Usage

check_screenlog(screenlog)

Arguments

Value

No return value, called for side effects

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

check_screenlog(create_test_screenlog())

check_empty_beautier_folder()

Check if the screenlog has the list elements of a valid screenlog object.

Description

Calls stop if an element is missing

Usage

check_screenlog_names(screenlog)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_screenlog to create a valid screenlog

Check if the screenlog has the list elements with valid values for being a valid screenlog object.

Description

Calls stop if a value is invalid

Usage

check_screenlog_values(screenlog)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_screenlog to create a valid screenlog

Check if the site model is a valid site model

Description

Calls stop if the site models are invalid

Usage

check_site_model(site_model)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_site_model to create a valid site model

Examples

check_empty_beautier_folder()

check_site_model(create_jc69_site_model())
check_site_model(create_hky_site_model())
check_site_model(create_tn93_site_model())
check_site_model(create_gtr_site_model())

# Can use list of one site model
check_site_model(list(create_jc69_site_model()))

check_empty_beautier_folder()

Check if the site_model has the list elements of a valid site_model object.

Description

Calls stop if an element is missing

Usage

check_site_model_names(site_model)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_site_model to create a valid site_model

Check if the site_model has the list elements of the right type for a valid site_model object.

Description

Calls stop if an element has the incorrect type

Usage

check_site_model_types(site_model)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_site_model to create a valid site_model

Check if the object is a list of one or more site models.

Description

Will stop if the object is not a list of one or more site models.

Usage

check_site_models(site_models)

Arguments

Value

nothing. Will stop if the object is not a list of one or more site models.

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_site_model to create a valid site model

Examples

check_empty_beautier_folder()

check_site_models(create_jc69_site_model())
check_site_models(list(create_jc69_site_model()))
check_site_models(
  list(create_jc69_site_model(), create_gtr_site_model())
)

check_empty_beautier_folder()

Check if store_every holds a valid value

Description

Will stop if not

Usage

check_store_every(store_every)

Arguments

Value

No return value, called for side effects

Check if the clock model is a valid clock model.

Description

Calls stop if the clock model is invalid

Usage

check_strict_clock_model(clock_model)

Arguments

Value

TRUE if clock_model is a valid clock model

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_clock_model to create a valid clock model

Examples

check_empty_beautier_folder()

check_strict_clock_model(create_strict_clock_model())

check_empty_beautier_folder()

Check if the tn93_site_model is a valid TN93 nucleotide substitution model.

Description

Use create_tn93_site_model to create a valid TN93 nucleotide substitution model.

Usage

check_tn93_site_model(tn93_site_model)

Arguments

Value

No return value, called for side effects

Examples

check_empty_beautier_folder()

check_tn93_site_model(create_tn93_site_model())

check_empty_beautier_folder()

Check if the tn93_site_model has the list elements of a valid tn93_site_model object.

Description

Calls stop if an element is missing

Usage

check_tn93_site_model_names(tn93_site_model)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_tn93_site_model to create a valid tn93_site_model

Check if a tracelog is valid.

Description

Will call stop if not.

Usage

check_tracelog(tracelog)

Arguments

Value

No return value, called for side effects

Check if the tracelog has the list elements of a valid tracelog object.

Description

Calls stop if an element is missing

Usage

check_tracelog_names(tracelog)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_tracelog to create a valid tracelog

Check if the tracelog has the list elements with valid values for being a valid tracelog object.

Description

Calls stop if a value is invalid

Usage

check_tracelog_values(tracelog)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_tracelog to create a valid tracelog

Check if the tree prior is a valid tree prior

Description

Calls stop if the tree priors are invalid

Usage

check_tree_prior(tree_prior)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_tree_prior to create a valid tree prior

Examples

check_empty_beautier_folder()

check_tree_prior(create_yule_tree_prior())
check_tree_prior(create_bd_tree_prior())
check_tree_prior(create_cbs_tree_prior())
check_tree_prior(create_ccp_tree_prior())
check_tree_prior(create_cep_tree_prior())

# Can use list of one tree prior
check_tree_prior(list(create_yule_tree_prior()))

check_empty_beautier_folder()

Check if the object is a list of one or more tree priors.

Description

Will stop if the object is not a list of one or more tree priors.

Usage

check_tree_priors(tree_priors)

Arguments

Value

nothing. Will stop if the object is not a list of one or more tree priors.

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_tree_prior to create a valid tree prior

Examples

check_empty_beautier_folder()

check_tree_priors(create_yule_tree_prior())
check_tree_priors(list(create_yule_tree_prior()))
check_tree_priors(list(create_yule_tree_prior(), create_bd_tree_prior()))

check_empty_beautier_folder()

Check if a treelog is valid.

Description

Will call stop if not.

Usage

check_treelog(treelog)

Arguments

Value

No return value, called for side effects

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

check_treelog(create_test_treelog())

check_empty_beautier_folder()

Check if the treelog has the list elements of a valid treelog object.

Description

Calls stop if an element is missing

Usage

check_treelog_names(treelog)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_treelog to create a valid treelog

Check if the treelog has the list elements with valid values for being a valid treelog object.

Description

Calls stop if a value is invalid

Usage

check_treelog_values(treelog)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_treelog to create a valid treelog

Internal function

Description

Converts a clock model to the operators section of the XML as text

Usage

clock_model_to_xml_operators(inference_model)

Arguments

Value

a character vector of XML strings

Author(s)

Richèl J.C. Bilderbeek

Internal function

Description

Internal function to converts a clock model to the prior section of the XML as text

Usage

clock_model_to_xml_prior_distr(inference_model)

Arguments

Value

a character vector of XML strings

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()
 # <distribution id="posterior" spec="util.CompoundDistribution">
 #     <distribution id="prior" spec="util.CompoundDistribution">
 #       HERE, where the ID of the distribution is 'prior'
 #     </distribution>
 #     <distribution id="likelihood" ...>
 #     </distribution>
 # </distribution>
clock_model_to_xml_prior_distr(
  inference_model = create_inference_model()
)
check_empty_beautier_folder()

Internal function

Description

Converts a clock model to the state section of the XML as text

Usage

clock_model_to_xml_state(inference_model)

Arguments

Value

lines of XML text, without indentation nor state tags

Author(s)

Richèl J.C. Bilderbeek

Internal function

Description

Creates the clock model's XML for the tracelog section

Usage

clock_model_to_xml_tracelog(inference_model)

Arguments

Value

a character vector of XML strings

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

# <logger id="tracelog" ...>
#'   # Here
# </logger>

check_empty_beautier_folder()

Convert a clock model to the XML of the TreeLogger

Description

Convert a clock model to the XML of the TreeLogger

Usage

clock_model_to_xml_treelogger(clock_model)

Arguments

Value

a character vector of XML strings

Note

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

Author(s)

Richèl J.C. Bilderbeek

Internal function

Description

Converts a clockRate parameter to XML

Usage

clock_rate_param_to_xml(
  clock_rate_param,
  beauti_options = create_beauti_options()
)

Arguments

Value

the parameter as XML text

Author(s)

Richèl J.C. Bilderbeek

Internal function

Description

Internal debug function to compare the actually created lines to expected lines using any diff tool

Usage

compare_lines(
  lines,
  expected,
  section = NA,
  created_lines_filename = get_beautier_tempfilename(pattern = "created", fileext =
    ".xml"),
  expected_lines_filename = get_beautier_tempfilename(pattern = "expected", fileext =
    ".xml")
)

Arguments

Value

nothing. Instead, two files are created, with the names created_lines_filename and expected_lines_filename that contain the section under investigation, so that a diff tool can compare these

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

# Creates temporary files in beautier folder
compare_lines(
  lines = readLines(get_beautier_path("bd_2_4.xml")),
  expected = readLines(get_beautier_path("bd_2_4.xml"))
)

remove_beautier_folder()
check_empty_beautier_folder()

Count the number of spaces before the first character

Description

Count the number of spaces before the first character

Usage

count_trailing_spaces(line)

Arguments

Value

the number of spaces before the first character

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

# 0
count_trailing_spaces("x")
# 1
count_trailing_spaces(" y")
# 2
count_trailing_spaces("  <")
# 0
count_trailing_spaces("")
# 1
count_trailing_spaces(" ")
# 2
count_trailing_spaces("  ")

check_empty_beautier_folder()

Create a parameter called alpha

Description

Create a parameter called alpha

Usage

create_alpha_param(id = NA, value = 0)

Arguments

Value

a parameter called alpha

Note

this parameter is used in a beta distribution (as returned by create_beta_distr) and gamma distribution (as returned by create_gamma_distr) and inverse-gamma distribution (as returned by create_inv_gamma_distr). It cannot be estimated (as a hyper parameter) yet.

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

if (is_on_ci()) {

  # Create the parameter
  alpha_param <- create_alpha_param()

  # Use the parameter in a distribution
  beta_distr <- create_beta_distr(
    alpha = alpha_param
  )

  # Use the distribution to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = beta_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a parameter called 'b_pop_sizes'.

Description

Create a parameter called 'b_pop_sizes'.

Usage

create_b_pop_sizes_param(id = NA, value = 1, upper = "380000.0")

Arguments

Value

a parameter called b_pop_sizes

Note

this parameter is used in a CBS model, as created by create_cbs_tree_prior

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

# Create the parameter
b_pop_sizes_param <- create_b_pop_sizes_param()

Create a Birth-Death tree prior

Description

Create a Birth-Death tree prior

Usage

create_bd_tree_prior(
  id = NA,
  birth_rate_distr = create_uniform_distr(),
  death_rate_distr = create_uniform_distr()
)

Arguments

Value

a Birth-Death tree_prior

Author(s)

Richèl J.C. Bilderbeek

See Also

An alignment ID can be extracted from its FASTA filename using get_alignment_id

Examples

if (is_on_ci()) {

  bd_tree_prior <- create_bd_tree_prior()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = bd_tree_prior
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create the <beast ...> XML

Description

The <beast ...> XML is the XML at the start of a BEAST2 XML input file, directly after the general XML declaration (as created by create_xml_declaration).

Usage

create_beast2_beast_xml(beauti_options)

Arguments

Value

the XML

Author(s)

Richèl J.C. Bilderbeek

Examples

remove_beautier_folder()

create_beast2_beast_xml(
  beauti_options = create_beauti_options_v2_6()
)

check_empty_beautier_folder()

Create a BEAST2 XML input text

Description

Create a BEAST2 XML input text

Usage

create_beast2_input(
  input_filename,
  tipdates_filename = NA,
  site_model = create_jc69_site_model(),
  clock_model = create_strict_clock_model(),
  tree_prior = create_yule_tree_prior(),
  mrca_prior = NA,
  mcmc = create_mcmc(),
  beauti_options = create_beauti_options()
)

Arguments

Value

a character vector of XML strings

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_beast2_input_from_model to create the BEAST2 XML input text from an inference model Use create_beast2_input_file to also save it to file.

create_beast2_input_file shows more examples

Examples

if (is_on_ci()) {
  create_beast2_input(
    input_filename = get_fasta_filename()
  )
}

Creates the XML text for the beast tag of a BEAST2 parameter file.

Description

Creates the XML text for the beast tag of a BEAST2 parameter file, which is directly after the XML declaration (created by create_xml_declaration.

Usage

create_beast2_input_beast(
  input_filename,
  inference_model = create_inference_model()
)

Arguments

Details

The beast tag has these elements:

  <beast[...]>
      <data
      [...]
      </data>
      [map names]
      <run[...]>
      [...]
      </run>
  </beast>

Value

lines of XML text

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_beast2_input_from_model to create the complete XML text. Use create_beast2_input_data to create the XML text for the data tag only. Use create_beast2_input_map to create the XML text for the [map names] part. Use create_beast2_input_run to create the XML text for the run tag only.

Creates the data section of a BEAST2 XML parameter file

Description

Creates the data section of a BEAST2 XML parameter file

Usage

create_beast2_input_data(
  input_filename,
  beauti_options = create_beauti_options()
)

Arguments

Value

lines of XML text

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

create_beast2_input_data(
  input_filename = get_fasta_filename(),
  beauti_options = create_beauti_options_v2_4()
)

check_empty_beautier_folder()

Creates the data section of a BEAST2 XML parameter file

Description

Creates the data section of a BEAST2 XML parameter file

Usage

create_beast2_input_data_sequences(
  input_fasta_filename,
  beauti_options = create_beauti_options()
)

Arguments

Value

lines of XML text

Author(s)

Richèl J.C. Bilderbeek

Creates the distribution section of a BEAST2 XML parameter file.

Description

Creates the distribution section of a BEAST2 XML parameter file.

Usage

create_beast2_input_distr(inference_model)

Arguments

Value

lines of XML text

Note

this function is not intended for regular use, thus its long name length is accepted

Author(s)

Richèl J.C. Bilderbeek

See Also

create_beast2_input

Examples

check_empty_beautier_folder()

inference_model <- init_inference_model(
  input_filename = get_fasta_filename(),
  inference_model = create_inference_model(
    beauti_options = create_beauti_options_v2_4()
  )
)
create_beast2_input_distr(
  inference_model = inference_model
)
 # <distribution id="posterior" spec="util.CompoundDistribution">
 #     <distribution id="prior" spec="util.CompoundDistribution">
 #       HERE, where the ID of the distribution is 'prior'
 #     </distribution>
 #     <distribution id="likelihood" ...>
 #     </distribution>
 # </distribution>

check_empty_beautier_folder()

Creates the XML text for the distribution tag with the likelihood ID, of a BEAST2 parameter file.

Description

Creates the XML text for the distribution tag with the likelihood ID, of a BEAST2 parameter file, in an unindented form

Usage

create_beast2_input_distr_lh(inference_model)

Arguments

Details

The distribution tag (with ID equals likelihood) has these elements:

  <distribution id="likelihood"[...]>
     <distribution id="treeLikelihood"[...]>
       [...]
     </distribution>
  </distribution>

The distribution section with ID treeLikelihood is created by create_tree_likelihood_distr_xml.

Zooming out:

  <beast[...]>
    <run[...]>
      <distribution id="posterior"[...]>
        <distribution id="likelihood"[...]>
          [this section]
        </distribution>
      </distribution>
    </run>
  </beast>

Value

lines of XML text

Note

this function is not intended for regular use, thus its long name length is accepted

Author(s)

Richèl J.C. Bilderbeek

See Also

this function is called by create_beast2_input_distr, together with create_beast2_input_distr_prior

Creates the prior section in the distribution section of a BEAST2 XML parameter file

Description

Creates the prior section in the distribution section of a BEAST2 XML parameter file

Usage

create_beast2_input_distr_prior(inference_model)

Arguments

Value

lines of XML text

Note

this function is not intended for regular use, thus its long name length is accepted

Author(s)

Richèl J.C. Bilderbeek

See Also

this function is called by create_beast2_input_distr, together with create_beast2_input_distr_lh

Examples

check_empty_beautier_folder()

 # <distribution id="posterior" spec="util.CompoundDistribution">
 #     <distribution id="prior" spec="util.CompoundDistribution">
 #       HERE, where the ID of the distribution is 'prior'
 #     </distribution>
 #     <distribution id="likelihood" ...>
 #     </distribution>
 # </distribution>

check_empty_beautier_folder()

Create a BEAST2 input file

Description

Create a BEAST2 input file

Usage

create_beast2_input_file(
  input_filename,
  output_filename,
  site_model = create_jc69_site_model(),
  clock_model = create_strict_clock_model(),
  tree_prior = create_yule_tree_prior(),
  mrca_prior = NA,
  mcmc = create_mcmc(),
  beauti_options = create_beauti_options(),
  tipdates_filename = NA
)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_beast2_input_file_from_model to do the same with an inference model. See create_site_model for examples with different site models. See create_clock_model for examples with clock models. See create_tree_prior for examples with different tree priors. See create_mcmc for examples with a different MCMC setup.

Examples

if (is_on_ci()) {

  check_empty_beautier_folder()

  # Get an example FASTA file
  input_filename <- get_fasta_filename()

  # The file created by beautier, a BEAST2 input file
  output_filename <- get_beautier_tempfilename()

  create_beast2_input_file(
    input_filename,
    output_filename
  )
  file.remove(output_filename)

  remove_beautier_folder()
  check_empty_beautier_folder()
}

Create a BEAST2 input file from an inference model

Description

Create a BEAST2 input file from an inference model

Usage

create_beast2_input_file_from_model(
  input_filename,
  output_filename,
  inference_model = create_inference_model()
)

Arguments

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

See Also

use create_beast2_input_from_model to get the BEAST2 input file as text

See create_site_model for examples with different site models. See create_clock_model for examples with clock models. See create_tree_prior for examples with different tree priors. See create_mcmc for examples with a different MCMC setup. Use create_beast2_input_file to do the same with the elements of an inference model.

Examples

if (is_on_ci()) {
  check_empty_beautier_folder()

  output_filename <- get_beautier_tempfilename()
  create_beast2_input_file_from_model(
    input_filename = get_fasta_filename(),
    output_filename = output_filename,
    inference_model = create_inference_model()
  )
  file.remove(output_filename)

  remove_beautier_folder()
  check_empty_beautier_folder()
}

Create a BEAST2 XML input text from an inference model

Description

The main two XML tags are these:

  <?xml[...]?><beast[...]>
  [...]
  </beast>

Usage

create_beast2_input_from_model(input_filename, inference_model)

Arguments

Value

a character vector of XML strings

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_beast2_input_file_from_model to also save it to file. Use create_xml_declaration to create the XML text of the XML declaration. Use create_beast2_input_beast to create to create the XML text of the beast tag.

Examples

if (is_on_ci()) {

  check_empty_beautier_folder()

  text <- create_beast2_input_from_model(
    input_filename = get_fasta_filename(),
    inference_model = create_inference_model()
  )

  check_empty_beautier_folder()
}

Creates the init section of a BEAST2 XML parameter file

Description

Creates the init section of a BEAST2 XML parameter file

Usage

create_beast2_input_init(inference_model)

Arguments

Value

lines of XML text

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

inference_model <- init_inference_model(
  input_filename = get_fasta_filename(),
  inference_model = create_test_inference_model()
)
xml <- create_beast2_input_init(
  inference_model = inference_model
)

check_empty_beautier_folder()

Creates the map section of a BEAST2 XML parameter file

Description

Creates the map section of a BEAST2 XML parameter file

Usage

create_beast2_input_map(beauti_options)

Arguments

Value

lines of XML text

Author(s)

Richèl J.C. Bilderbeek

Creates the operators section of a BEAST2 XML parameter file

Description

Creates the operators section of a BEAST2 XML parameter file

Usage

create_beast2_input_operators(inference_model)

Arguments

Value

lines of XML text

Author(s)

Richèl J.C. Bilderbeek

Creates the 'run' section of a BEAST2 XML parameter file

Description

Creates the 'run' section of a BEAST2 XML parameter file, without being indented.

Usage

create_beast2_input_run(
  input_filename,
  inference_model = create_inference_model()
)

Arguments

Details

The run tag has these elements:

   <run[...]>
       <state[...]>
       [...]
       </state>
       <init[...]>
       [...]
       </init>
       <distribution[...]>
       [...]
       </distribution>
       [operator ids]
       [loggers]
    </run>

Value

lines of XML text

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_beast2_input_state to create the XML text of the state tag. Use create_beast2_input_init to create the XML text of the init tag. Use create_beast2_input_distr to create the XML text of the distribution tag. Use create_beast2_input_operators to create the XML text of the [operator ids] section. Use create_loggers_xml to create the XML text of the [loggers] part.

Creates the 'state' section of a BEAST2 XML parameter file

Description

Creates the 'state' section of a BEAST2 XML parameter file, without being indented.

Usage

create_beast2_input_state(inference_model)

Arguments

Details

The state tag has these elements:

   <state[...]>
       <tree[...]>
       [...]
       </tree>
       [parameters]
    </run>

Value

lines of XML text

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_beast2_input_state to create the XML text of the tree tag. to create the XML text of the [parameters] section.

Function to create a set of 'BEAUti' options.

Description

'BEAUti' options are settings that differ between 'BEAUti' version. The use of these options is mostly for testing older versions Whatever option chosen here, the created XML file will be valid.

Usage

create_beauti_options(
  capitalize_first_char_id = FALSE,
  nucleotides_uppercase = FALSE,
  beast2_version = "2.4",
  required = "",
  sequence_indent = 20,
  status = "",
  namespace = get_default_beast_namespace_v2_4()
)

Arguments

Details

Available BEAUti options are:
* create_beauti_options_v2_4 * create_beauti_options_v2_6

'beautier' uses v2.4 by default, as this is when the first tests were written.

Value

a BEAUti options structure

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  check_empty_beautier_folder()

  beauti_options <- create_beauti_options_v2_4()
  xml <- create_beast2_input(
    get_fasta_filename(),
    beauti_options = beauti_options
  )

  check_empty_beautier_folder()
}

Function to create the BEAUti options for version 2.4.

Description

Function to create the BEAUti options for version 2.4, by calling create_beauti_options.

Usage

create_beauti_options_v2_4()

Value

a BEAUti options structure

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {
  check_empty_beautier_folder()

  beauti_options <- create_beauti_options_v2_4()
  xml <- create_beast2_input(
    get_fasta_filename(),
    beauti_options = beauti_options
  )

  check_empty_beautier_folder()
}

Function to create the BEAUti options for version 2.6.

Description

Function to create the BEAUti options for version 2.6, by calling create_beauti_options.

Usage

create_beauti_options_v2_6(
  beast2_version = "2.6",
  sequence_indent = 8,
  nucleotides_uppercase = FALSE,
  status = "",
  namespace = get_default_beast_namespace_v2_6(),
  required = ""
)

Arguments

Value

a BEAUti options structure

Author(s)

Richèl J.C. Bilderbeek

See Also

see create_beauti_options_v2_4 for using the older v2.4

Examples

if (is_on_ci()) {

  check_empty_beautier_folder()

  beauti_options <- create_beauti_options_v2_6()
  xml <- create_beast2_input(
    get_fasta_filename(),
    beauti_options = beauti_options
  )

  check_empty_beautier_folder()
}

Create the default 'beautier' temporary folder

Description

Create the default 'beautier' temporary folder

Usage

create_beautier_tempfolder()

Value

nothing

Author(s)

Richèl J.C. Bilderbeek

Examples

create_beautier_tempfolder()

remove_beautier_folder()

check_empty_beautier_folder()

Create a beta distribution

Description

Create a beta distribution

Usage

create_beta_distr(
  id = NA,
  alpha = 0,
  beta = 1,
  value = NA,
  lower = NA,
  upper = NA
)

Arguments

Value

a beta distribution

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_distr shows an overview of all supported distributions

Examples

if (is_on_ci()) {

  beta_distr <- create_beta_distr()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = beta_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a parameter called beta

Description

Create a parameter called beta

Usage

create_beta_param(id = NA, value = 1)

Arguments

Value

a parameter called beta

Note

this parameter is used in a beta distribution (as returned by create_beta_distr) and gamma distribution (as returned by create_gamma_distr) and inverse-gamma distribution (as returned by create_inv_gamma_distr). It cannot be estimated (as a hyper parameter) yet.

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

if (is_on_ci()) {

  # Create the parameter
  beta_param <- create_beta_param()

  # Use the parameter in a distribution
  gamma_distr <- create_gamma_distr(
    beta = beta_param
  )

  # Use the distribution to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = gamma_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Internal function to create the branchRateModel section of the XML as text.

Description

Creates the branchRateModel section of the XML as text.

Usage

create_branch_rate_model_xml(inference_model)

Arguments

Details

The distribution tag (with ID equals treeLikelihood) has these elements:

  <branchRateModel[...]>
    [...]
  </branchRateModel>

When there is a strict clock, create_strict_clock_branch_rate_model_xml is called. When there is an RLN clock, create_rln_clock_branch_rate_model_xml is called.

Zooming out:

  <beast[...]>
    <run[...]>
      <distribution id="posterior"[...]>
        <distribution id="likelihood"[...]>
          <distribution id="treeLikelihood"[...]>
             [...]

             [this section]
          </distribution>
        </distribution>
      </distribution>
    </run>
  </beast>

Value

a character vector of XML strings

Author(s)

Richèl J.C. Bilderbeek

Create a Coalescent Bayesian Skyline tree prior

Description

Create a Coalescent Bayesian Skyline tree prior

Usage

create_cbs_tree_prior(
  id = NA,
  group_sizes_dimension = 5,
  b_pop_sizes_param = create_b_pop_sizes_param(),
  pop_sizes_scaler_scale_factor = ""
)

Arguments

Value

a Coalescent Bayesian Skyline tree_prior

Author(s)

Richèl J.C. Bilderbeek

See Also

An alignment ID can be extracted from its FASTA filename using get_alignment_id

Examples

if (is_on_ci()) {

  cbs_tree_prior <- create_cbs_tree_prior()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_beautier_path("test_output_6.fas"),
    beast2_input_file,
    tree_prior = cbs_tree_prior
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a Coalescent Constant Population tree prior

Description

Create a Coalescent Constant Population tree prior

Usage

create_ccp_tree_prior(
  id = NA,
  pop_size_distr = create_one_div_x_distr(value = 0.3)
)

Arguments

Value

a Coalescent Constant Population tree_prior

Author(s)

Richèl J.C. Bilderbeek

See Also

An alignment ID can be extracted from its FASTA filename using get_alignment_id

Examples

if (is_on_ci()) {

  ccp_tree_prior <- create_ccp_tree_prior()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = ccp_tree_prior
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a Coalescent Exponential Population tree prior

Description

Create a Coalescent Exponential Population tree prior

Usage

create_cep_tree_prior(
  id = NA,
  pop_size_distr = create_one_div_x_distr(),
  growth_rate_distr = create_laplace_distr()
)

Arguments

Value

a Coalescent Exponential Population tree_prior

Author(s)

Richèl J.C. Bilderbeek

See Also

An alignment ID can be extracted from its FASTA filename using get_alignment_id

Examples

if (is_on_ci()) {

  cep_tree_prior <- create_cep_tree_prior()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = cep_tree_prior
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

General function to create a clock model

Description

General function to create a clock model

Usage

create_clock_model(name, id, ...)

Arguments

Value

a valid clock model

Note

Prefer using the named function create_rln_clock_model and create_strict_clock_model

Author(s)

Richèl J.C. Bilderbeek

See Also

An alignment ID can be extracted from its FASTA filename using get_alignment_id. For more examples about creating a relaxed log-normal clock model, see create_rln_clock_model. For more examples about creating a strict clock model, see create_strict_clock_model.

Examples

if (is_on_ci()) {
  # Can use any of these models
  strict_clock_model <- create_strict_clock_model()
  rln_clock_model <- create_rln_clock_model()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    get_fasta_filename(),
    beast2_input_file,
    clock_model = strict_clock_model
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a clock model from name

Description

Create a clock model from name

Usage

create_clock_model_from_name(clock_model_name)

Arguments

Value

a clock model, as can be created by create_clock_model

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_clock_model to create a clock model

Examples

check_empty_beautier_folder()

create_clock_model_from_name(get_clock_model_names()[1])

check_empty_beautier_folder()

Creates all supported clock models, which is a list of the types returned by create_rln_clock_model, and create_strict_clock_model

Description

Creates all supported clock models, which is a list of the types returned by create_rln_clock_model, and create_strict_clock_model

Usage

create_clock_models()

Value

a list of site_models

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_clock_model to create a clock model

Examples

check_empty_beautier_folder()

clock_models <- create_clock_models()
is_rln_clock_model(clock_models[[1]])
is_strict_clock_model(clock_models[[2]])

check_empty_beautier_folder()

Create clock models from their names

Description

Create clock models from their names

Usage

create_clock_models_from_names(clock_model_names)

Arguments

Value

a list of one or more clock models

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_clock_models to get all clock models

Examples

check_empty_beautier_folder()

create_clock_models_from_names(get_clock_model_names())

check_empty_beautier_folder()

Create a parameter called clock_rate, as needed by create_strict_clock_model

Description

Create a parameter called clock_rate, as needed by create_strict_clock_model

Usage

create_clock_rate_param(value = "1.0", estimate = FALSE, id = NA)

Arguments

Value

a parameter called rate

Note

It cannot be estimated (as a hyper parameter) yet.

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

if (is_on_ci()) {

  clock_rate_param <- create_clock_rate_param(
    id = "anthus_aco", value = 1.0
  )

  # Use the parameter in a clock model
  strict_clock_model <- create_strict_clock_model(
    clock_rate_param = clock_rate_param
  )

  # Use the distribution to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    clock_model = strict_clock_model
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Internal function

Description

Creates the clockRate parameter with the name stateNode, such as: <parameter id="ucldStdev.c:[id]" [...] name="stateNode">0.1</parameter>

Usage

create_clock_rate_state_node_parameter_xml(inference_model)

Arguments

Value

the following XML: <parameter id="ucldStdev.c:[id]" lower="0.0" name="stateNode"> 0.1 </parameter>

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

create_ucld_stdev_state_node_param_xml(
  create_inference_model(
    clock_model = create_rln_clock_model(id = 314)
  )
)

check_empty_beautier_folder()

Create the <data ..> XML

Description

Create the <data ..> XML

Usage

create_data_xml(id, beast2_version)

Arguments

Value

lines of XML text

Author(s)

Richèl J.C. Bilderbeek

General function to create a distribution.

Description

General function to create a distribution.

Usage

create_distr(name, id, value = NA, lower = NA, upper = NA, ...)

Arguments

Value

a distribution

Note

Prefer using the named functions create_beta_distr, create_exp_distr, create_gamma_distr, create_inv_gamma_distr, create_laplace_distr, create_log_normal_distr, create_normal_distr, create_one_div_x_distr, create_poisson_distr and create_uniform_distr

See create_beta_distr, create_exp_distr, create_gamma_distr, create_inv_gamma_distr, create_laplace_distr, create_log_normal_distr, create_normal_distr, create_one_div_x_distr, create_poisson_distr and create_uniform_distr for examples how to use those distributions

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  # Use any distribution
  distr <- create_beta_distr()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create an exponential distribution

Description

Create an exponential distribution

Usage

create_exp_distr(id = NA, mean = 1, value = NA, lower = NA, upper = NA)

Arguments

Value

an exponential distribution

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_distr shows an overview of all supported distributions

Examples

if (is_on_ci()) {

  exp_distr <- create_exp_distr()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = exp_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a parameter called freq

Description

Create a parameter called freq

Usage

create_freq_param(
  id = NA,
  lower = "0.0",
  upper = "1.0",
  value = "0.25",
  estimate = TRUE,
  dimension = 4
)

Arguments

Value

a parameter called freq

Author(s)

Richèl J.C. Bilderbeek

Create a gamma distribution

Description

Create a gamma distribution

Usage

create_gamma_distr(
  id = NA,
  alpha = 0.5396,
  beta = 0.3819,
  value = NA,
  lower = NA,
  upper = NA
)

Arguments

Value

a gamma distribution

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_distr shows an overview of all supported distributions

Examples

if (is_on_ci()) {

  gamma_distr <- create_gamma_distr(
    alpha = 0.05,
    beta = 10.0
  )

  gtr_site_model <- create_gtr_site_model(
    rate_ac_prior_distr = gamma_distr
  )

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    site_model = gtr_site_model
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a gamma site model, part of a site model

Description

Create a gamma site model, part of a site model

Usage

create_gamma_site_model(
  gamma_cat_count = "0",
  gamma_shape = "1.0",
  prop_invariant = "0.0",
  gamma_shape_prior_distr = NA,
  freq_equilibrium = "estimated",
  freq_prior_uniform_distr_id = 1000
)

Arguments

Value

a gamma site model

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_gamma_site_model to create a gamma site model

Examples

if (is_on_ci()) {

  gamma_site_model <- create_gamma_site_model(prop_invariant = 0.5)

  site_model <- create_hky_site_model(gamma_site_model = gamma_site_model)

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    get_fasta_filename(),
    beast2_input_file,
    site_model = site_model
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a GTR site model

Description

Create a GTR site model

Usage

create_gtr_site_model(
  id = NA,
  gamma_site_model = create_gamma_site_model(),
  rate_ac_prior_distr = create_gamma_distr(alpha = 0.05, beta = create_beta_param(value =
    "10.0")),
  rate_ag_prior_distr = create_gamma_distr(alpha = 0.05, beta = create_beta_param(value =
    "20.0")),
  rate_at_prior_distr = create_gamma_distr(alpha = 0.05, beta = create_beta_param(value =
    "10.0")),
  rate_cg_prior_distr = create_gamma_distr(alpha = 0.05, beta = create_beta_param(value =
    "10.0")),
  rate_gt_prior_distr = create_gamma_distr(alpha = 0.05, beta = create_beta_param(value =
    "10.0")),
  rate_ac_param = create_rate_ac_param(),
  rate_ag_param = create_rate_ag_param(),
  rate_at_param = create_rate_at_param(),
  rate_cg_param = create_rate_cg_param(),
  rate_ct_param = create_rate_ct_param(),
  rate_gt_param = create_rate_gt_param(),
  freq_equilibrium = "estimated",
  freq_param = create_freq_param()
)

Arguments

Value

a GTR site_model

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  gtr_site_model <- create_gtr_site_model(
    rate_ac_param = 1.2,
    rate_ag_param = 2.3,
    rate_at_param = 3.4,
    rate_cg_param = 4.5,
    rate_ct_param = 5.6,
    rate_gt_param = 6.7
  )

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    site_model = gtr_site_model
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Converts a GTR site model to XML, used in the substModel section

Description

Converts a GTR site model to XML, used in the substModel section

Usage

create_gtr_subst_model_xml(site_model)

Arguments

Value

the site model as XML text

Author(s)

Richèl J.C. Bilderbeek

Create an HKY site model

Description

Create an HKY site model

Usage

create_hky_site_model(
  id = NA,
  kappa = "obsolete",
  kappa_param = create_kappa_param(value = "2.0"),
  gamma_site_model = create_gamma_site_model(),
  kappa_prior_distr = create_log_normal_distr(m = create_m_param(value = "1.0"), s =
    1.25),
  freq_equilibrium = "estimated",
  freq_param = create_freq_param()
)

Arguments

Value

an HKY site_model

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  hky_site_model <- create_hky_site_model()
  output_filename <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    output_filename = output_filename,
    site_model = hky_site_model
  )
  file.remove(output_filename)

  remove_beautier_folder()
}

Converts a site model to XML, used in the substModel section

Description

Converts a site model to XML, used in the substModel section

Usage

create_hky_subst_model_xml(site_model)

Arguments

Value

the site model as XML text

Author(s)

Richèl J.C. Bilderbeek

Create a Bayesian phylogenetic inference model.

Description

Create a Bayesian phylogenetic inference model, as can be done by BEAUti.

Usage

create_inference_model(
  site_model = create_jc69_site_model(),
  clock_model = create_strict_clock_model(),
  tree_prior = create_yule_tree_prior(),
  mrca_prior = NA,
  mcmc = create_mcmc(),
  beauti_options = create_beauti_options(),
  tipdates_filename = NA
)

Arguments

Value

an inference model

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_test_inference_model to create an inference model with a short MCMC, to be used in testing. Use create_ns_inference_model to create an inference model to estimate the marginal likelihood (aka evidence) using a nested sampling approach.

Examples

if (is_on_ci()) {

  check_empty_beautier_folder()

  # Create an MCMC chain with 50 states
  inference_model <- create_inference_model(
    mcmc = create_mcmc(chain_length = 50000, store_every = 1000)
  )

  output_filename <- get_beautier_tempfilename()
  create_beast2_input_file_from_model(
    input_filename = get_fasta_filename(),
    output_filename = output_filename,
    inference_model = inference_model
  )
  file.remove(output_filename)

  remove_beautier_folder()
  check_empty_beautier_folder()
}

Create an inverse-gamma distribution

Description

Create an inverse-gamma distribution

Usage

create_inv_gamma_distr(
  id = NA,
  alpha = 0,
  beta = 1,
  value = NA,
  lower = NA,
  upper = NA
)

Arguments

Value

an inverse-gamma distribution

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_distr shows an overview of all supported distributions

Examples

if (is_on_ci()) {

  inv_gamma_distr <- create_inv_gamma_distr()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = inv_gamma_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a JC69 site model

Description

Create a JC69 site model

Usage

create_jc69_site_model(id = NA, gamma_site_model = create_gamma_site_model())

Arguments

Value

a JC69 site_model

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  jc69_site_model <- create_jc69_site_model()

  output_filename <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    output_filename = output_filename,
    site_model = jc69_site_model
  )
  file.remove(output_filename)

  remove_beautier_folder()
}

Converts a JC69 site model to XML, used in the substModel section

Description

Converts a JC69 site model to XML, used in the substModel section

Usage

create_jc69_subst_model_xml(site_model)

Arguments

Value

the site model as XML text

Author(s)

Richèl J.C. Bilderbeek

Create a parameter called kappa 1

Description

Create a parameter called kappa 1

Usage

create_kappa_1_param(id = NA, lower = "0.0", value = "2.0", estimate = TRUE)

Arguments

Value

a parameter called kappa 1

Author(s)

Richèl J.C. Bilderbeek

Create a parameter called kappa 2

Description

Create a parameter called kappa 2

Usage

create_kappa_2_param(id = NA, lower = "0.0", value = "2.0", estimate = TRUE)

Arguments

Value

a parameter called kappa 2

Author(s)

Richèl J.C. Bilderbeek

Create a parameter called kappa

Description

Create a parameter called kappa

Usage

create_kappa_param(id = NA, lower = "0.0", value = "2.0", estimate = TRUE)

Arguments

Value

a parameter called kappa

Author(s)

Richèl J.C. Bilderbeek

Create a parameter called lambda

Description

Create a parameter called lambda

Usage

create_lambda_param(id = NA, value = 0)

Arguments

Value

a parameter called lambda

Note

this parameter is used in a Poisson distribution (as returned by create_poisson_distr)

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

if (is_on_ci()) {

  # Create the parameter
  lambda_param <- create_lambda_param()

  # Use the parameter in a distribution
  poisson_distr <- create_poisson_distr(
    lambda = lambda_param
  )

  # Use the distribution to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = poisson_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a Laplace distribution

Description

Create a Laplace distribution

Usage

create_laplace_distr(
  id = NA,
  mu = 0,
  scale = 1,
  value = NA,
  lower = NA,
  upper = NA
)

Arguments

Value

a Laplace distribution

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_distr shows an overview of all supported distributions

Examples

if (is_on_ci()) {

  laplace_distr <- create_laplace_distr()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = laplace_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a log-normal distribution

Description

Create a log-normal distribution

Usage

create_log_normal_distr(
  id = NA,
  m = 0,
  s = 0,
  value = NA,
  lower = NA,
  upper = NA
)

Arguments

Value

a log-normal distribution

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_distr shows an overview of all supported distributions

Examples

if (is_on_ci()) {

  log_normal_distr <- create_log_normal_distr()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = log_normal_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Creates the three logger sections of a BEAST2 XML parameter file

Description

The logger section has these elements:

 <logger id="tracelog" [...]>
     [...]
 </logger>
 <logger id="screenlog" [...]>
     [...]
 </logger>
 <logger id="treelog.t:[alignment ID]"  [...]>
     [...]
 </logger>

Usage

create_loggers_xml(input_filename, inference_model)

Arguments

Value

lines of XML text

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_tracelog_xml to create the XML text of the logger with the tracelog ID. Use create_screenlog_xml to create the XML text of the logger with the screenlog ID. Use create_treelog_xml to create the XML text of the loggers with the treelog ID.

Create a parameter called m

Description

Create a parameter called m

Usage

create_m_param(id = NA, estimate = FALSE, lower = NA, upper = NA, value = 0)

Arguments

Value

a parameter called m

Note

this parameter is used in a log-normal distribution (as returned by create_log_normal_distr) It cannot be estimated (as a hyper parameter) yet.

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

if (is_on_ci()) {

  # Create the parameter
  m_param <- create_m_param()

  # Use the parameter in a distribution
  log_normal_distr <- create_log_normal_distr(
    m = m_param
  )

  # Use the distribution to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = log_normal_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()

}

Create an MCMC configuration.

Description

Create an MCMC configuration, as in the BEAUti MCMC tab.

Usage

create_mcmc(
  chain_length = 1e+07,
  store_every = -1,
  pre_burnin = 0,
  n_init_attempts = 10,
  sample_from_prior = FALSE,
  tracelog = create_tracelog(),
  screenlog = create_screenlog(),
  treelog = create_treelog()
)

Arguments

Details

There are four things that can be saved: * store_every: saves the state of the MCMC to file, as a .state.xml file * tracelog: stores the trace of the state of the MCMC to file. See create_tracelog how to specify the filename * screenlog: stores the screen output to file. See create_screenlog how to specify the filename * treelog: stores the estimated phylogenies to file. See create_treelog how to specify the filename

Value

an MCMC configuration

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_test_mcmc to create a short regular MCMC, that can be used for testing runs. Use create_ns_mcmc to create an MCMC for a Nested Sampling run. Use check_mcmc to check if an MCMC is valid. Use rename_mcmc_filenames to rename the filenames in an MCMC.

Examples

if (is_on_ci()) {

  # Create an MCMC chain with 50 states
  mcmc <- create_mcmc(chain_length = 50000, store_every = 1000)

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    get_fasta_filename(),
    beast2_input_file,
    mcmc = mcmc
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a parameter called mean

Description

Create a parameter called mean

Usage

create_mean_param(id = NA, value = 0)

Arguments

Value

a parameter called mean

Note

this parameter is used in an exponential distribution (as returned by create_exp_distr) and normal distribution (as returned by create_normal_distr). It cannot be estimated (as a hyper parameter) yet.

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

if (is_on_ci()) {

  # Create the parameter
  mean_param <- create_mean_param(value = 1.0)

  # Use the parameter in a distribution
  exp_distr <- create_exp_distr(
    mean = mean_param
  )

  # Use the distribution to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = exp_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a Most Recent Common Ancestor prior

Description

Create a Most Recent Common Ancestor prior

Usage

create_mrca_prior(
  alignment_id = NA,
  taxa_names = NA,
  is_monophyletic = FALSE,
  mrca_distr = NA,
  name = NA,
  clock_prior_distr_id = NA
)

Arguments

Value

an MRCA prior

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

fasta_filename <- get_beautier_path("anthus_aco.fas")

 # The first two taxa are sister species
 mrca_prior <- create_mrca_prior(
   taxa_names = get_taxa_names(filename = fasta_filename)[1:2]
 )

 # The taxa are monophyletic
 mrca_prior <- create_mrca_prior(
   taxa_names = get_taxa_names(filename = fasta_filename),
   is_monophyletic = TRUE
 )

 # Set the crown age to 10
 mrca_prior <- create_mrca_prior(
   taxa_names = get_taxa_names(fasta_filename),
   mrca_distr = create_normal_distr(mean = 10, sigma = 0.1)
 )

check_empty_beautier_folder()

Create a parameter called mu

Description

Create a parameter called mu

Usage

create_mu_param(id = NA, value = 0)

Arguments

Value

a parameter called mu

Note

this parameter is used in a Laplace distribution (as returned by create_laplace_distr). It cannot be estimated (as a hyper parameter) yet.

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

if (is_on_ci()) {

  # Create the parameter
  mu_param <- create_mu_param()

  # Use the parameter in a distribution
  laplace_distr <- create_laplace_distr(
    mu = mu_param
  )

  # Use the distribution to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = laplace_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create an normal distribution

Description

Create an normal distribution

Usage

create_normal_distr(
  id = NA,
  mean = 0,
  sigma = 1,
  value = NA,
  lower = NA,
  upper = NA
)

Arguments

Value

a normal distribution

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_distr shows an overview of all supported distributions

Examples

if (is_on_ci()) {

  normal_distr <- create_normal_distr()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = normal_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create an inference model to measure the evidence of.

Description

Create an inference model to measure the evidence of. To do so, the inference model is created as usual (see create_inference_model), except for using a Nested Sampling MCMC (see create_ns_mcmc)

Usage

create_ns_inference_model(
  site_model = create_jc69_site_model(),
  clock_model = create_strict_clock_model(),
  tree_prior = create_yule_tree_prior(),
  mcmc = create_ns_mcmc()
)

Arguments

Value

an inference model

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_inference_model to create a regular inference model. Use create_test_ns_inference_model to create an inference model to estimate the marginal likelihood with a short MCMC, to be used in testing.

Examples

check_empty_beautier_folder()

inference_model <- create_ns_inference_model()

check_empty_beautier_folder()

Create an MCMC object to estimate the marginal likelihood using Nested Sampling.

Description

This will result in a BEAST run that estimates the marginal likelihood until convergence is achieved. In this context, chain_length is only an upper bound to the length of that run.

Usage

create_ns_mcmc(
  chain_length = 1e+07,
  store_every = -1,
  pre_burnin = 0,
  n_init_attempts = 3,
  particle_count = 1,
  sub_chain_length = 5000,
  epsilon = "1e-12",
  tracelog = create_tracelog(),
  screenlog = create_screenlog(),
  treelog = create_treelog()
)

Arguments

Value

an MCMC object

Author(s)

Richèl J.C. Bilderbeek

References

* [1] Patricio Maturana Russel, Brendon J Brewer, Steffen Klaere, Remco R Bouckaert; Model Selection and Parameter Inference in Phylogenetics Using Nested Sampling, Systematic Biology, 2018, syy050, https://doi.org/10.1093/sysbio/syy050

See Also

Use create_mcmc to create a regular MCMC. Use create_test_ns_mcmc to create an NS MCMC for testing, with, among others, a short MCMC chain length. Use check_ns_mcmc to check that an NS MCMC object is valid.

Examples

if (is_on_ci()) {

  mcmc <- create_ns_mcmc(
    chain_length = 1e7,
    store_every = 1000,
    particle_count = 1,
    sub_chain_length = 1000,
    epsilon = 1e-12
  )

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    get_fasta_filename(),
    beast2_input_file,
    mcmc = mcmc
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a 1/x distribution

Description

Create a 1/x distribution

Usage

create_one_div_x_distr(id = NA, value = NA, lower = NA, upper = NA)

Arguments

Value

a 1/x distribution

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_distr shows an overview of all supported distributions

Examples

if (is_on_ci()) {

  one_div_x_distr <- create_one_div_x_distr()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = one_div_x_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

General function to create a parameter.

Description

General function to create a parameter.

Usage

create_param(name, id, value, ...)

Arguments

Value

a parameter

Note

Prefer using the named functions create_alpha_param, create_beta_param, create_clock_rate_param, create_kappa_1_param, create_kappa_2_param, create_lambda_param, create_m_param, create_mean_param, create_mu_param, create_rate_ac_param, create_rate_ag_param, create_rate_at_param, create_rate_cg_param, create_rate_ct_param, create_rate_gt_param, create_s_param, create_scale_param, and create_sigma_param

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  # Create an alpha parameter
  alpha_param <- create_alpha_param()

  # Use the parameter in a distribution
  beta_distr <- create_beta_distr(
    alpha = alpha_param
  )

  # Use the distribution to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = beta_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a Poisson distribution

Description

Create a Poisson distribution

Usage

create_poisson_distr(id = NA, lambda = 0, value = NA, lower = NA, upper = NA)

Arguments

Value

a Poisson distribution

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_distr shows an overview of all supported distributions

Examples

if (is_on_ci()) {

  poisson_distr <- create_poisson_distr()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = poisson_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a parameter called 'rate AC'

Description

Create a parameter called 'rate AC'

Usage

create_rate_ac_param(id = NA, estimate = TRUE, value = "1.0", lower = "0.0")

Arguments

Value

a parameter called 'rate AC'

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

if (is_on_ci()) {

  # Create parameter
  rate_ac_param <- create_rate_ac_param(value = 1, estimate = FALSE)

  # Use the parameter to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    site_model = create_gtr_site_model(
      rate_ac_param = rate_ac_param
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a parameter called 'rate AG'

Description

Create a parameter called 'rate AG'

Usage

create_rate_ag_param(id = NA, estimate = TRUE, value = "1.0", lower = "0.0")

Arguments

Value

a parameter called 'rate AG'

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

if (is_on_ci()) {

  # Create parameter
  rate_ag_param <- create_rate_ag_param(value = 1, estimate = FALSE)

  # Use the parameter to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    site_model = create_gtr_site_model(
      rate_ag_param = rate_ag_param
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a parameter called 'rate AT'

Description

Create a parameter called 'rate AT'

Usage

create_rate_at_param(id = NA, estimate = TRUE, value = "1.0", lower = "0.0")

Arguments

Value

a parameter called 'rate AT'

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

if (is_on_ci()) {

  # Create parameter
  rate_at_param <- create_rate_at_param(value = 1, estimate = FALSE)

  # Use the parameter to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    site_model = create_gtr_site_model(
      rate_at_param = rate_at_param
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Internal function

Description

Creates the rateCategories state node, such as: "<stateNode id=\"rateCategories.c:[id]\" spec=\"parameter.IntegerParameter\" dimension=\"[dimension]\"> 1 </stateNode>"

Usage

create_rate_categories_state_node_xml(inference_model)

Arguments

Value

the following XML: "<stateNode id=\"rateCategories.c:[id]\" spec=\"parameter.IntegerParameter\" dimension=\"[dimension]\"> 1 </stateNode>"

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

create_rate_categories_state_node_xml(
  create_inference_model(
    clock_model = create_rln_clock_model(
      id = 314,
      dimension = 1
    )
  )
)

check_empty_beautier_folder()

Create a parameter called 'rate CG'

Description

Create a parameter called 'rate CG'

Usage

create_rate_cg_param(id = NA, estimate = TRUE, value = "1.0", lower = "0.0")

Arguments

Value

a parameter called 'rate CG'

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

if (is_on_ci()) {

  # Create parameter
  rate_cg_param <- create_rate_cg_param(value = 1, estimate = FALSE)

  # Use the parameter to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    site_model = create_gtr_site_model(
      rate_cg_param = rate_cg_param
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a parameter called 'rate CT'

Description

Create a parameter called 'rate CT'

Usage

create_rate_ct_param(id = NA, value = "1.0", lower = "0.0")

Arguments

Value

a parameter called 'rate CT'

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

if (is_on_ci()) {

  # Create parameter
  rate_ct_param <- create_rate_ct_param(value = 1)

  # Use the parameter to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    site_model = create_gtr_site_model(
      rate_ct_param = rate_ct_param
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a parameter called 'rate GT'

Description

Create a parameter called 'rate GT'

Usage

create_rate_gt_param(id = NA, estimate = TRUE, value = "1.0", lower = "0.0")

Arguments

Value

a parameter called 'rate GT'

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

if (is_on_ci()) {

  # Create parameter
  rate_gt_param <- create_rate_gt_param(value = 1, estimate = FALSE)

  # Use the parameter to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    site_model = create_gtr_site_model(
      rate_gt_param = rate_gt_param
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Internal function

Description

Internal function to call create_branch_rate_model_xml for a relaxed log-normal clock.

Usage

create_rln_clock_branch_rate_model_xml(inference_model)

Arguments

Value

a character vector of XML strings

Author(s)

Richèl J.C. Bilderbeek

Create a relaxed log-normal clock model

Description

Create a relaxed log-normal clock model

Usage

create_rln_clock_model(
  id = NA,
  mean_rate_prior_distr = create_uniform_distr(),
  ucldstdev_distr = create_gamma_distr(),
  mparam_id = NA,
  mean_clock_rate = "1.0",
  n_rate_categories = -1,
  normalize_mean_clock_rate = FALSE,
  dimension = NA,
  rate_scaler_factor = 0.75
)

Arguments

Value

a relaxed log-normal clock_model

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  rln_clock_model <- create_rln_clock_model()

  beast2_input_file <- get_beautier_tempfilename()

  create_beast2_input_file(
    get_fasta_filename(),
    beast2_input_file,
    clock_model = rln_clock_model
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a parameter called s

Description

Create a parameter called s

Usage

create_s_param(id = NA, value = 0, lower = 0, upper = Inf)

Arguments

Value

a parameter called s

Note

this parameter is used in a log-normal distribution (as returned by create_log_normal_distr)

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

if (is_on_ci()) {

  # Create the parameter
  s_param <- create_s_param()

  # Use the parameter in a distribution
  log_normal_distr <- create_log_normal_distr(
    s = s_param
  )

  # Use the distribution to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = log_normal_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a parameter called scale

Description

Create a parameter called scale

Usage

create_scale_param(id = NA, value = 0)

Arguments

Value

a parameter called scale

Note

this parameter is used in a Laplace distribution (as returned by create_laplace_distr)

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

if (is_on_ci()) {
  # Create the parameter
  scale_param <- create_scale_param()

  # Use the parameter in a distribution
  laplace_distr <- create_laplace_distr(
    scale = scale_param
  )

  # Use the distribution to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = laplace_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a screenlog object

Description

Create a screenlog object

Usage

create_screenlog(
  filename = "",
  log_every = 1000,
  mode = "autodetect",
  sanitise_headers = FALSE,
  sort = "none"
)

Arguments

Value

a screenlog object

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

create_screenlog()

check_empty_beautier_folder()

Creates the screenlog section of the logger section of a BEAST2 XML parameter file

Description

Creates the screenlog section of the logger section of a BEAST2 XML parameter file

Usage

create_screenlog_xml(inference_model = create_inference_model())

Arguments

Value

the XML text

Author(s)

Richèl J.C. Bilderbeek

Create a parameter called sigma

Description

Create a parameter called sigma

Usage

create_sigma_param(id = NA, value = 1)

Arguments

Value

a parameter called sigma

Note

this parameter is used in a normal distribution (as returned by create_normal_distr)

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_param contains a list of all parameters that can be created

Examples

if (is_on_ci()) {

  # Create the parameter
  sigma_param <- create_sigma_param()

  # Use the parameter in a distribution
  normal_distr <- create_normal_distr(
    sigma = sigma_param
  )

  # Use the distribution to create a BEAST2 input file
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = normal_distr
    )
  )
 file.remove(beast2_input_file)

  remove_beautier_folder()
}

General function to create a site model.

Description

General function to create a site model.

Usage

create_site_model(name, id, gamma_site_model = create_gamma_site_model(), ...)

Arguments

Value

a site_model

Note

Prefer using the named functions create_gtr_site_model, create_hky_site_model,, create_jc69_site_model, and create_tn93_site_model

Author(s)

Richèl J.C. Bilderbeek

See Also

See create_gtr_site_model for more examples with a GTR site model. See create_hky_site_model for more examples with an HKY site model. See create_jc69_site_model for more examples with a JC69 site model. See create_tn93_site_model for more examples with a TN93 site model

Examples

if (is_on_ci()) {

  check_empty_beautier_folder()

  input_filename <- get_fasta_filename()
  gtr_site_model <- create_gtr_site_model()
  hk_site_model <- create_hky_site_model()
  jc69_site_model <- create_jc69_site_model()
  tn93_site_model <- create_tn93_site_model()

  # Can use any site model
  output_filename <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = input_filename,
    output_filename = output_filename,
    site_model = jc69_site_model
  )
  file.remove(output_filename)

  remove_beautier_folder()
  check_empty_beautier_folder()
}

Create a site model from name

Description

Create a site model from name

Usage

create_site_model_from_name(site_model_name)

Arguments

Value

a site model

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_site_model to create a site model

Examples

check_empty_beautier_folder()

site_model <- create_site_model_from_name(get_site_model_names()[1])

check_empty_beautier_folder()

Internal function to creates the XML text for the parameters within the siteModel section of a BEAST2 parameter file.

Description

Internal function to creates the XML text for the parameters within the siteModel section, which is part of the siteModel section of a BEAST2 parameter file.

Usage

create_site_model_parameters_xml(inference_model)

Arguments

Details

The parameters sections has these elements:

   [parameters]

[parameters] can be a combination of these:

  <parameter id="mutationRate.s[...]>
  <parameter id="gammaShape.s[...]>
  <parameter id="proportionInvariant.s[...]>

Value

the site model as XML text

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

Internal function to creates the XML text for the siteModel tag of a BEAST2 parameter file.

Description

Creates the XML text for the siteModel tag of a BEAST2 parameter file, which is part of the distribution node for the treeLikelihood ID.

Usage

create_site_model_xml(inference_model)

Arguments

Details

The siteModel tag has these elements:

  <siteModel[...]>

      [parameters]

      <substModel[...]>
        [...]
      </substModel>
  </siteModel>

The parameter section is created by create_site_model_parameters_xml The substModel section is created by create_subst_model_xml

Value

the site model as XML text

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()
 # <distribution id="posterior"[...]">
 #     <distribution id="likelihood" [...]>
 #       <siteModel...>
 #         [parameters]
 #       </siteModel>
 #     </distribution>
 # </distribution>

check_empty_beautier_folder()

Creates all supported site models which is a list of the types returned by create_gtr_site_model, create_hky_site_model, create_jc69_site_model and create_tn93_site_model

Description

Creates all supported site models which is a list of the types returned by create_gtr_site_model, create_hky_site_model, create_jc69_site_model and create_tn93_site_model

Usage

create_site_models()

Value

a list of site_models

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_site_model to create a site model

Examples

check_empty_beautier_folder()

# All created site models are a kind of site model
site_models <- create_site_models()

# TRUE
is_gtr_site_model(site_models[[1]])
is_hky_site_model(site_models[[2]])
is_jc69_site_model(site_models[[3]])
is_tn93_site_model(site_models[[4]])

check_empty_beautier_folder()

Create site models from their names

Description

Create site models from their names

Usage

create_site_models_from_names(site_model_names)

Arguments

Value

one or more site models

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_site_model to create a site model

Examples

check_empty_beautier_folder()

create_site_models_from_names(get_site_model_names())

check_empty_beautier_folder()

Internal function.

Description

Internal function to create the branchRateModel section of the XML as text, for a strict clock model

Usage

create_strict_clock_branch_rate_model_xml(inference_model)

Arguments

Value

a character vector of XML strings

Author(s)

Richèl J.C. Bilderbeek

Create a strict clock model

Description

Create a strict clock model

Usage

create_strict_clock_model(
  id = NA,
  clock_rate_param = create_clock_rate_param(),
  clock_rate_distr = create_uniform_distr(),
  rate_scaler_factor = 0.75
)

Arguments

Value

a strict clock_model

Note

I am unsure about the relationship between 'clock_rate_param' and 'clock_rate_distr'. Please contact me if you know the most natural architecture

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {
  strict_clock_model <- create_strict_clock_model(
    clock_rate_param = 1.0,
    clock_rate_distr = create_uniform_distr()
  )

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    get_fasta_filename(),
    beast2_input_file,
    clock_model = strict_clock_model
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Internal function

Description

Creates the StrictClockRateScaler operator such as: ...

Usage

create_strict_clock_rate_scaler_operator_xml(inference_model)

Arguments

Value

the following XML: ...

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

create_strict_clock_rate_scaler_operator_xml(
  create_inference_model(
    clock_model = create_strict_clock_model(id = 314)
  )
)

check_empty_beautier_folder()

Internal function to create the substModel section

Description

Internal function to create the substModel section

Usage

create_subst_model_xml(inference_model)

Arguments

Value

the substModel section as XML text

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

# Inference model must be initialized
inference_model <- create_inference_model(
  site_model = create_jc69_site_model(id = 123)
)
create_subst_model_xml(
  inference_model = inference_model
)

check_empty_beautier_folder()

Create a filename for a temporary 'screenlog' file

Description

Create a filename for a temporary 'screenlog' file

Usage

create_temp_screenlog_filename()

Value

a filename for a temporary 'screenlog' file

Author(s)

Richèl J.C. Bilderbeek

See Also

use create_screenlog to create a screenlog.

Examples

check_empty_beautier_folder()

create_temp_screenlog_filename()

check_empty_beautier_folder()

Create a filename for a temporary 'tracelog' file

Description

Create a filename for a temporary 'tracelog' file

Usage

create_temp_tracelog_filename()

Value

a filename for a temporary 'tracelog' file

Author(s)

Richèl J.C. Bilderbeek

See Also

use create_tracelog to create a tracelog.

Examples

check_empty_beautier_folder()

create_temp_tracelog_filename()

check_empty_beautier_folder()

Create a filename for a temporary 'treelog' file

Description

Create a filename for a temporary 'treelog' file

Usage

create_temp_treelog_filename()

Value

a filename for a temporary 'treelog' file

Author(s)

Richèl J.C. Bilderbeek

See Also

use create_treelog to create a treelog.

Examples

check_empty_beautier_folder()

create_temp_treelog_filename()

check_empty_beautier_folder()

Create a testing inference model.

Description

Creates a simple inference model with a short MCMC chain, to be used in testing.

Usage

create_test_inference_model(
  site_model = create_jc69_site_model(),
  clock_model = create_strict_clock_model(),
  tree_prior = create_yule_tree_prior(),
  mrca_prior = NA,
  mcmc = create_test_mcmc(),
  beauti_options = create_beauti_options(),
  tipdates_filename = NA
)

Arguments

Value

an inference model

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_inference_model to create a regular inference model. Use create_test_ns_inference_model to create an inference model to estimate the marginal likelihood with a short MCMC, to be used in testing

Examples

if (is_on_ci()) {
  check_empty_beautier_folder()

  inference_model <- create_test_inference_model()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file_from_model(
    get_fasta_filename(),
    beast2_input_file,
    inference_model = inference_model
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
  check_empty_beautier_folder()
}

Create an MCMC configuration for testing.

Description

Create an MCMC configuration for testing.

Usage

create_test_mcmc(
  chain_length = 3000,
  store_every = 1000,
  pre_burnin = 0,
  n_init_attempts = 10,
  sample_from_prior = FALSE,
  tracelog = create_test_tracelog(),
  screenlog = create_test_screenlog(),
  treelog = create_test_treelog()
)

Arguments

Value

an MCMC configuration

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_mcmc to create a default BEAST2 MCMC

Examples

if (is_on_ci()) {

  # Create an MCMC chain with 50 states
  mcmc <- create_test_mcmc()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    get_fasta_filename(),
    beast2_input_file,
    mcmc = mcmc
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create an inference model to be tested by Nested Sampling

Description

Create an inference model to be tested by Nested Sampling

Usage

create_test_ns_inference_model(
  site_model = create_jc69_site_model(),
  clock_model = create_strict_clock_model(),
  tree_prior = create_yule_tree_prior(),
  mcmc = create_test_ns_mcmc()
)

Arguments

Value

an inference model

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_test_inference_model to create a regular inference model with a short MCMC, to be used in testing. Use create_ns_inference_model to create an inference model to estimate the marginal likelihood.

Examples

check_empty_beautier_folder()

inference_model <- create_test_ns_inference_model()

check_empty_beautier_folder()

Create an NS MCMC object for testing

Description

Create an NS MCMC object for testing

Usage

create_test_ns_mcmc(
  chain_length = 2000,
  store_every = 1000,
  pre_burnin = 0,
  n_init_attempts = 3,
  particle_count = 1,
  sub_chain_length = 500,
  epsilon = 1e-12,
  tracelog = create_test_tracelog(),
  screenlog = create_test_screenlog(),
  treelog = create_test_treelog()
)

Arguments

Value

an MCMC object

Author(s)

Richèl J.C. Bilderbeek

See Also

Use create_ns_mcmc to create a default nested sampling MCMC

Examples

if (is_on_ci()) {

  mcmc <- create_test_ns_mcmc()
  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    get_fasta_filename(),
    beast2_input_file,
    mcmc = mcmc
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create a screenlog object, to be used in testing

Description

Create a screenlog object, to be used in testing

Usage

create_test_screenlog(
  filename = create_temp_screenlog_filename(),
  log_every = 1000,
  mode = "autodetect",
  sanitise_headers = FALSE,
  sort = "none"
)

Arguments

Value

a screenlog object

Author(s)

Richèl J.C. Bilderbeek

Examples

create_test_screenlog()

Create a tracelog object, as used for testing

Description

Create a tracelog object, as used for testing

Usage

create_test_tracelog(
  filename = create_temp_tracelog_filename(),
  log_every = 1000,
  mode = "autodetect",
  sanitise_headers = TRUE,
  sort = "smart"
)

Arguments

Value

a tracelog object

Author(s)

Richèl J.C. Bilderbeek

Examples

create_test_tracelog()

Create a treelog object to be used in testing

Description

Create a treelog object to be used in testing

Usage

create_test_treelog(
  filename = create_temp_treelog_filename(),
  log_every = 1000,
  mode = "tree",
  sanitise_headers = FALSE,
  sort = "none"
)

Arguments

Value

a treelog object

Author(s)

Richèl J.C. Bilderbeek

Examples

create_test_treelog()

Create a TN93 site model

Description

Create a TN93 site model

Usage

create_tn93_site_model(
  id = NA,
  gamma_site_model = create_gamma_site_model(),
  kappa_1_param = create_kappa_1_param(),
  kappa_2_param = create_kappa_2_param(),
  kappa_1_prior_distr = create_log_normal_distr(m = 1, s = 1.25),
  kappa_2_prior_distr = create_log_normal_distr(m = 1, s = 1.25),
  freq_equilibrium = "estimated",
  freq_param = create_freq_param()
)

Arguments

Value

a TN93 site_model

Author(s)

Richèl J.C. Bilderbeek

Examples

if (is_on_ci()) {

  tn93_site_model <- create_tn93_site_model(
    kappa_1_param = 2.0,
    kappa_2_param = 2.0
  )

  output_filename <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    output_filename = output_filename,
    site_model = tn93_site_model
  )
  file.remove(output_filename)

  remove_beautier_folder()
}

Converts a TN93 site model to XML, used in the substModel section

Description

Converts a TN93 site model to XML, used in the substModel section

Usage

create_tn93_subst_model_xml(site_model)

Arguments

Value

the site model as XML text

Author(s)

Richèl J.C. Bilderbeek

Create a tracelog object

Description

Create a tracelog object

Usage

create_tracelog(
  filename = NA,
  log_every = 1000,
  mode = "autodetect",
  sanitise_headers = TRUE,
  sort = "smart"
)

Arguments

Value

a tracelog object

Author(s)

Richèl J.C. Bilderbeek

Examples

create_tracelog()

Internal function

Description

Creates the tracelog section of the logger section of a BEAST2 XML parameter file

Usage

create_tracelog_xml(input_filename, inference_model)

Arguments

Value

lines of XML text

Author(s)

Richèl J.C. Bilderbeek

Create a trait set string.

Description

For example, a data frame with row A 1 and another row B 2, the trait set string will be A=1,B=2

Usage

create_trait_set_string(df)

Arguments

Value

the trait set string

Author(s)

Richèl J.C. Bilderbeek

Creates the XML text for the distribution tag with the treeLikelihood ID, of a BEAST2 parameter file.

Description

Creates the XML text for the distribution tag with the treeLikelihood ID, of a BEAST2 parameter file, in an unindented form

Usage

create_tree_likelihood_distr_xml(inference_model)

Arguments

Details

The distribution tag (with ID equals treeLikelihood) has these elements:

   <distribution id="treeLikelihood"[...]>
      <siteModel[...]>
        [...]
      </siteModel>
      <branchRateModel[...]>
        [...]
      </branchRateModel>
   </distribution>

The siteModel section is created by create_site_model_xml. The branchRateModel section is created by create_branch_rate_model_xml.

Zooming out:

  <beast[...]>
    <run[...]>
      <distribution id="posterior"[...]>
        <distribution id="likelihood"[...]>
          [this section]
        </distribution>
      </distribution>
    </run>
  </beast>

Value

lines of XML text

Note

this function is not intended for regular use, thus its long name length is accepted

Author(s)

Richèl J.C. Bilderbeek

See Also

this function is called by create_beast2_input_distr, together with create_beast2_input_distr_prior

Internal function to create a tree prior

Description

Internal function to create a tree prior

Usage

create_tree_prior(name, id, ...)

Arguments

Value

a tree_prior

Note

Prefer the use the named functions create_bd_tree_prior, create_cbs_tree_prior, create_ccp_tree_prior create_cep_tree_prior and create_yule_tree_prior instead

Author(s)

Richèl J.C. Bilderbeek

See Also

See create_bd_tree_prior, create_cbs_tree_prior, create_ccp_tree_prior create_cep_tree_prior and create_yule_tree_prior for more examples using those functions

Examples

if (is_on_ci()) {

  check_empty_beautier_folder()

  beast2_input_file <- get_beautier_tempfilename()

  bd_tree_prior <- create_bd_tree_prior()
  cbs_tree_prior <- create_cbs_tree_prior()
  ccp_tree_prior <- create_ccp_tree_prior()
  cep_tree_prior <- create_cep_tree_prior()
  yule_tree_prior <- create_yule_tree_prior()

  # Use any of the above tree priors
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = bd_tree_prior
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
  check_empty_beautier_folder()
}

Creates all supported tree priors, which is a list of the types returned by create_bd_tree_prior, create_cbs_tree_prior, create_ccp_tree_prior, create_cep_tree_prior and create_yule_tree_prior

Description

Creates all supported tree priors, which is a list of the types returned by create_bd_tree_prior, create_cbs_tree_prior, create_ccp_tree_prior, create_cep_tree_prior and create_yule_tree_prior

Usage

create_tree_priors()

Value

a list of tree_priors

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

tree_priors <- create_tree_priors()
# TRUE
is_bd_tree_prior(tree_priors[[1]])
is_cbs_tree_prior(tree_priors[[2]])
is_ccp_tree_prior(tree_priors[[3]])
is_cep_tree_prior(tree_priors[[4]])
is_yule_tree_prior(tree_priors[[5]])

check_empty_beautier_folder()

Create a treelog object

Description

Create a treelog object

Usage

create_treelog(
  filename = "$(tree).trees",
  log_every = 1000,
  mode = "tree",
  sanitise_headers = FALSE,
  sort = "none"
)

Arguments

Value

a 'treelog', as can be checked by check_treelog

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

create_treelog()

check_empty_beautier_folder()

Creates the XML text for the 'logger' tag with ID 'treelog'. This section has these elements: “' <logger id="treelog.t:test_output_0" spec="Logger" fileName="my_treelog.trees" logEvery="345000" mode="tree" sanitiseHeaders="true" sort="smart"> # nolint indeed long <log id="TreeWithMetaDataLogger.t:test_output_0" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:test_output_0"/> # nolint indeed long </logger> “'

Description

Creates the XML text for the 'logger' tag with ID 'treelog'. This section has these elements: “' <logger id="treelog.t:test_output_0" spec="Logger" fileName="my_treelog.trees" logEvery="345000" mode="tree" sanitiseHeaders="true" sort="smart"> # nolint indeed long <log id="TreeWithMetaDataLogger.t:test_output_0" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:test_output_0"/> # nolint indeed long </logger> “'

Usage

create_treelog_xml(inference_model)

Arguments

Value

lines of XML text

Author(s)

Richèl J.C. Bilderbeek

Internal function

Description

Creates the ucldMean.c parameter with the name stateNode, such as: <parameter id=\"ucldMean.c:[id]\" spec=\"parameter.RealParameter\" name=\"stateNode\">1.0</parameter>

Usage

create_ucld_mean_state_node_param_xml(inference_model)

Arguments

Value

the XML <parameter id=\"ucldMean.c:[id]\" spec=\"parameter.RealParameter\" name=\"stateNode\">1.0</parameter>

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

create_ucld_mean_state_node_param_xml(
  create_inference_model(
    clock_model = create_rln_clock_model(id = 314),
    beauti_options = create_beauti_options_v2_6()
  )
)

check_empty_beautier_folder()

Internal function

Description

Creates the ucldStdev parameter with the name stateNode, such as: <parameter id="ucldStdev.c:[id]" [...] name="stateNode">0.1</parameter>

Usage

create_ucld_stdev_state_node_param_xml(inference_model)

Arguments

Value

the following XML: <parameter id="ucldStdev.c:[id]" lower="0.0" name="stateNode"> 0.1 </parameter>

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

create_ucld_stdev_state_node_param_xml(
  create_inference_model(
    clock_model = create_rln_clock_model(id = 314)
  )
)

check_empty_beautier_folder()

Create a uniform distribution

Description

Create a uniform distribution

Usage

create_uniform_distr(id = NA, value = NA, lower = NA, upper = Inf)

Arguments

Value

a uniform distribution

Author(s)

Richèl J.C. Bilderbeek

See Also

the function create_distr shows an overview of all supported distributions

Examples

if (is_on_ci()) {

  uniform_distr <- create_uniform_distr()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
    input_filename = get_fasta_filename(),
    beast2_input_file,
    tree_prior = create_yule_tree_prior(
      birth_rate_distr = uniform_distr
    )
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Create the XML declaration of the BEAST2 XML input file

Description

Create the XML declaration of the BEAST2 XML input file

Usage

create_xml_declaration()

Value

one line of XML text

Author(s)

Richèl J.C. Bilderbeek

Examples

check_empty_beautier_folder()

create_xml_declaration()

check_empty_beautier_folder()

Create a Yule tree prior

Description

Create a Yule tree prior

Usage

create_yule_tree_prior(
  id = NA,
  birth_rate_distr = create_uniform_distr()
)

Arguments

Value

a Yule tree_prior

Author(s)

Richèl J.C. Bilderbeek

See Also

An alignment ID can be extracted from its FASTA filename using get_alignment_id

Examples

if (is_on_ci()) {

  yule_tree_prior <- create_yule_tree_prior()

  beast2_input_file <- get_beautier_tempfilename()
  create_beast2_input_file(
     input_filename = get_fasta_filename(),
     beast2_input_file,
     tree_prior = yule_tree_prior
  )
  file.remove(beast2_input_file)

  remove_beautier_folder()
}

Documentation of parameters (for example, create_param. This function does nothing. It is intended to inherit documentation from.

Description

Documentation of parameters (for example, create_param. This function does nothing. It is intended to inherit documentation from.

Usage

default_parameters_doc(dimension, estimate, id, lower, name, upper, value, ...)

Arguments

Note

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

Author(s)

Richèl J.C. Bilderbeek

Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.

Description

Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.

Usage

default_params_doc(
  alignment_id,
  allow_empty_str,
  allow_na,
  alpha_parameter,
  b_pop_sizes_param,
  b_pop_sizes_parameter,
  bd_tree_prior,
  beautier_folder,
  cbs_tree_prior,
  beast2_version,
  beauti_options,
  beta_parameter,
  ccp_tree_prior,
  cep_tree_prior,
  chain_length,
  clock_model,
  clock_model_name,
  clock_model_names,
  clock_models,
  clock_prior_distr_id,
  clock_rate_param,
  crown_age,
  crown_ages,
  distr_id,
  fasta_filename,
  fasta_filenames,
  filename,
  fixed_crown_age,
  fixed_crown_ages,
  freq_param,
  gamma_distr,
  gamma_site_model,
  group_sizes_dimension,
  gtr_site_model,
  has_non_strict_clock_model,
  has_tip_dating,
  hky_site_model,
  id,
  ids,
  inference_model,
  inference_models,
  initial_phylogenies,
  input_filename,
  input_filenames,
  is_monophyletic,
  jc69_site_model,
  kappa_param,
  log_every,
  m_param,
  mcmc,
  mode,
  mrca_prior,
  mrca_priors,
  mrca_prior_name,
  n_init_attempts,
  output_filename,
  param,
  param_id,
  phylogeny,
  pop_sizes_scaler_scale_factor,
  pre_burnin,
  rate_scaler_factor,
  rename_fun,
  rln_clock_model,
  sample_from_prior,
  sanitise_headers,
  screenlog,
  sequence_length,
  site_model,
  site_model_name,
  site_model_names,
  site_models,
  sort,
  store_every,
  strict_clock_model,
  taxa_names,
  tipdates_filename,
  tn93_site_model,
  tracelog,
  treelog,
  tree_prior,
  tree_prior_name,
  tree_prior_names,
  tree_priors,
  verbose,
  yule_tree_prior
)

Arguments