# 'BEAUti' from R

## Documentation for package ‘beautier’ version 2.6.12

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G H I J K M N P R S T U Y

## -- A --

alpha_parameter_to_xml | Internal function
are_clock_models | Determine if x consists out of clock_models objects
are_equal_mcmcs | Determine if two MCMCs are equal.
are_equal_screenlogs | Determine if two screenlogs are equal.
are_equal_tracelogs | Determine if two tracelogs are equal.
are_equal_treelogs | Determine if two treelogs are equal.
are_equal_xml_files | Determine if XML files result in equal trees
are_equal_xml_lines | Determine if XML lines result in equal trees
are_equivalent_xml_files | Internal function
are_equivalent_xml_lines | Determine if XML lines result in equivalent trees
are_equivalent_xml_lines_all | Determine if XML lines result in equivalent trees
are_equivalent_xml_lines_loggers | Determine if XML operator lines result in equivalent trees
are_equivalent_xml_lines_operators | Determine if XML operator lines result in equivalent trees
are_equivalent_xml_lines_section | Determine if XML lines result in equivalent trees
are_fasta_filenames | Checks if all filenames have a FASTA filename extension
are_ids | Determine if x consists out of IDs
are_init_clock_models | Determine if x consists out of initialized clock_models objects
are_init_mrca_priors | Determine if x consists out of initialized MRCA priors
are_init_site_models | Determine if x consists out of initialized site_models objects
are_init_tree_priors | Determine if x consists out of initialized tree_priors objects
are_mrca_align_ids_in_fasta | Determine if the MRCA priors' alignment IDs are present in the FASTA files
are_mrca_priors | Determine if x consists out of MRCA priors
are_mrca_taxon_names_in_fasta | Determine if the MRCA priors' taxa names are present in the FASTA files
are_rln_clock_models | Are the clock models Relaxed Log-Normal clock models?
are_site_models | Determine if x consists out of site_models objects
are_tree_priors | Determine if x consists out of tree_priors objects

## -- B --

bd_tree_prior_to_xml_prior_distr | 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
beta_parameter_to_xml | Internal function
b_pop_sizes_parameter_to_xml | Internal function
b_pop_sizes_param_to_xml | Internal function

## -- C --

cbs_tree_prior_to_xml_prior_distr | 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
ccp_tree_prior_to_xml_prior_distr | 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
ccp_tree_prior_to_xml_state | Convert a CCP tree prior to the XML as part of the 'state' section
cep_tree_prior_to_xml_prior_distr | 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
check_alignment_id | Check if the 'alignment_id' is valid.
check_beauti_options | Check if the 'beauti_options' is a valid 'beauti_options' object.
check_clock_model | Check if the clock model is a valid clock model.
check_clock_models | Check if the object is a list of one or more clock models.
check_empty_beautier_folder | Internal function
check_filename | Check if the 'filename' is valid
check_file_and_model_agree | Checks if the input FASTA file and the inference model agree.
check_file_exists | Function to check if a file exists. Calls 'stop' if the file is absent
check_gamma_site_model | Checks if the parameter is a valid gamma site model
check_gamma_site_model_names | Checks if the gamma site model has the right list elements' names
check_gtr_site_model | Check if the 'gtr_site_model' is a valid GTR nucleotide substitution model.
check_gtr_site_model_names | Check if the 'gtr_site_model' has the list elements of a valid 'gtr_site_model' object.
check_inference_model | Check if the supplied object is a valid Bayesian phylogenetic inference model.
check_inference_models | Check if the 'inference_model' is a valid BEAUti inference model.
check_is_monophyletic | Check if 'is_monophyletic' has a valid value.
check_log_mode | Check if the supplied 'mode' is a valid logging mode.
check_log_sort | Check if the supplied 'sort' is a valid logging sorting option.
check_mcmc | Check if the MCMC is a valid MCMC object.
check_mcmc_list_element_names | Check if the MCMC has the list elements of a valid MCMC object.
check_mcmc_nested_sampling | Check if this an MCMC that uses Nested Sampling to estimate a marginal likelihood.
check_mcmc_values | Check if the MCMC has the list elements with valid values for being a valid MCMC object.
check_mrca_prior | Check if the MRCA prior is a valid MRCA prior.
check_mrca_prior_name | Check if 'mrca_prior_name' is a valid MRCA prior name.
check_mrca_prior_names | Check if the MRCA prior, which is a list, has all the named elements.
check_mrca_prior_taxa_names | Check the MRCA prior's taxon names are valid.
check_nested_sampling_mcmc | Check if this an MCMC that uses Nested Sampling to estimate a marginal likelihood.
check_ns_mcmc | Check if this an MCMC that uses Nested Sampling to estimate a marginal likelihood.
check_param | Check if the parameter is a valid parameter
check_param_names | Check if the 'param' has the list elements of a valid 'param' object.
check_param_types | Check if the 'param' has the list elements of the right type for a valid 'param' object.
check_phylogeny | Check if the phylogeny is a valid phylogeny object.
check_rename_fun | Check if the rename function is a valid filename rename function
check_rln_clock_model | Check if the clock model is a valid clock model.
check_screenlog | Check if a 'screenlog' is valid.
check_screenlog_names | Check if the 'screenlog' has the list elements of a valid 'screenlog' object.
check_screenlog_values | Check if the screenlog has the list elements with valid values for being a valid screenlog object.
check_site_model | Check if the site model is a valid site model
check_site_models | Check if the object is a list of one or more site models.
check_site_model_names | Check if the 'site_model' has the list elements of a valid 'site_model' object.
check_site_model_types | Check if the 'site_model' has the list elements of the right type for a valid 'site_model' object.
check_store_every | Check if 'store_every' holds a valid value
check_strict_clock_model | Check if the clock model is a valid clock model.
check_tn93_site_model | Check if the 'tn93_site_model' is a valid TN93 nucleotide substitution model.
check_tn93_site_model_names | Check if the 'tn93_site_model' has the list elements of a valid 'tn93_site_model' object.
check_tracelog | Check if a 'tracelog' is valid.
check_tracelog_names | Check if the 'tracelog' has the list elements of a valid 'tracelog' object.
check_tracelog_values | Check if the tracelog has the list elements with valid values for being a valid tracelog object.
check_treelog | Check if a 'treelog' is valid.
check_treelog_names | Check if the 'treelog' has the list elements of a valid 'treelog' object.
check_treelog_values | Check if the treelog has the list elements with valid values for being a valid treelog object.
check_tree_prior | Check if the tree prior is a valid tree prior
check_tree_priors | Check if the object is a list of one or more tree priors.
clock_model_to_xml_operators | Internal function
clock_model_to_xml_prior_distr | Internal function
clock_model_to_xml_state | Internal function
clock_model_to_xml_tracelog | Internal function
clock_model_to_xml_treelogger | Convert a clock model to the XML of the 'TreeLogger'
clock_rate_param_to_xml | Internal function
compare_lines | Internal function
count_trailing_spaces | Count the number of spaces before the first character
create_alpha_param | Create a parameter called alpha
create_bd_tree_prior | Create a Birth-Death tree prior
create_beast2_beast_xml | Create the '<beast ...>' XML
create_beast2_input | Create a BEAST2 XML input text
create_beast2_input_beast | Creates the XML text for the 'beast' tag of a BEAST2 parameter file.
create_beast2_input_data | Creates the 'data' section of a BEAST2 XML parameter file
create_beast2_input_data_sequences | Creates the data section of a BEAST2 XML parameter file
create_beast2_input_distr | Creates the distribution section of a BEAST2 XML parameter file.
create_beast2_input_distr_lh | Creates the XML text for the 'distribution' tag with the 'likelihood' ID, of a BEAST2 parameter file.
create_beast2_input_distr_prior | Creates the prior section in the distribution section of a BEAST2 XML parameter file
create_beast2_input_file | Create a BEAST2 input file
create_beast2_input_file_from_model | Create a BEAST2 input file from an inference model
create_beast2_input_from_model | Create a BEAST2 XML input text from an inference model
create_beast2_input_init | Creates the 'init' section of a BEAST2 XML parameter file
create_beast2_input_map | Creates the map section of a BEAST2 XML parameter file
create_beast2_input_operators | Creates the operators section of a BEAST2 XML parameter file
create_beast2_input_run | Creates the "run" section of a BEAST2 XML parameter file
create_beast2_input_state | Creates the "state" section of a BEAST2 XML parameter file
create_beautier_tempfolder | Create the default 'beautier' temporary folder
create_beauti_options | Function to create a set of 'BEAUti' options.
create_beauti_options_v2_4 | Function to create the BEAUti options for version 2.4.
create_beauti_options_v2_6 | Function to create the BEAUti options for version 2.6.
create_beta_distr | Create a beta distribution
create_beta_param | Create a parameter called beta
create_branch_rate_model_xml | Internal function to create the 'branchRateModel' section of the XML as text.
create_b_pop_sizes_param | Create a parameter called 'b_pop_sizes'.
create_cbs_tree_prior | Create a Coalescent Bayesian Skyline tree prior
create_ccp_tree_prior | Create a Coalescent Constant Population tree prior
create_cep_tree_prior | Create a Coalescent Exponential Population tree prior
create_clock_model | General function to create a clock model
create_clock_models | Creates all supported clock models, which is a list of the types returned by 'create_rln_clock_model', and 'create_strict_clock_model'
create_clock_models_from_names | Create clock models from their names
create_clock_model_from_name | Create a clock model from name
create_clock_model_rln | Create a relaxed log-normal clock model
create_clock_model_strict | Create a strict clock model
create_clock_rate_param | Create a parameter called 'clock_rate', as needed by 'create_strict_clock_model'
create_clock_rate_state_node_parameter_xml | Internal function
create_data_xml | Create the '<data ..>' XML
create_distr | General function to create a distribution.
create_distr_beta | Create a beta distribution
create_distr_exp | Create an exponential distribution
create_distr_gamma | Create a gamma distribution
create_distr_inv_gamma | Create an inverse-gamma distribution
create_distr_laplace | Create a Laplace distribution
create_distr_log_normal | Create a log-normal distribution
create_distr_normal | Create an normal distribution
create_distr_one_div_x | Create a 1/x distribution
create_distr_poisson | Create a Poisson distribution
create_distr_uniform | Create a uniform distribution
create_exp_distr | Create an exponential distribution
create_freq_param | Create a parameter called freq
create_gamma_distr | Create a gamma distribution
create_gamma_site_model | Create a gamma site model, part of a site model
create_gtr_site_model | Create a GTR site model
create_gtr_subst_model_xml | Converts a GTR site model to XML, used in the 'substModel' section
create_hky_site_model | Create an HKY site model
create_hky_subst_model_xml | Converts a site model to XML, used in the 'substModel' section
create_inference_model | Create a Bayesian phylogenetic inference model.
create_inv_gamma_distr | Create an inverse-gamma distribution
create_jc69_site_model | Create a JC69 site model
create_jc69_subst_model_xml | Converts a JC69 site model to XML, used in the 'substModel' section
create_kappa_1_param | Create a parameter called kappa 1
create_kappa_2_param | Create a parameter called kappa 2
create_kappa_param | Create a parameter called kappa
create_lambda_param | Create a parameter called lambda
create_laplace_distr | Create a Laplace distribution
create_loggers_xml | Creates the three logger sections of a BEAST2 XML parameter file
create_log_normal_distr | Create a log-normal distribution
create_mcmc | Create an MCMC configuration.
create_mcmc_nested_sampling | Create an MCMC object to estimate the marginal likelihood using Nested Sampling.
create_mean_param | Create a parameter called mean
create_mrca_prior | Create a Most Recent Common Ancestor prior
create_mu_param | Create a parameter called mu
create_m_param | Create a parameter called m
create_normal_distr | Create an normal distribution
create_ns_inference_model | Create an inference model to measure the evidence of.
create_ns_mcmc | Create an MCMC object to estimate the marginal likelihood using Nested Sampling.
create_one_div_x_distr | Create a 1/x distribution
create_param | General function to create a parameter.
create_param_alpha | Create a parameter called alpha
create_param_beta | Create a parameter called beta
create_param_b_pop_sizes | Create a parameter called 'b_pop_sizes'.
create_param_clock_rate | Create a parameter called 'clock_rate', as needed by 'create_strict_clock_model'
create_param_freq | Create a parameter called freq
create_param_kappa | Create a parameter called kappa
create_param_kappa_1 | Create a parameter called kappa 1
create_param_kappa_2 | Create a parameter called kappa 2
create_param_lambda | Create a parameter called lambda
create_param_m | Create a parameter called m
create_param_mean | Create a parameter called mean
create_param_mu | Create a parameter called mu
create_param_rate_ac | Create a parameter called 'rate AC'
create_param_rate_ag | Create a parameter called 'rate AG'
create_param_rate_at | Create a parameter called 'rate AT'
create_param_rate_cg | Create a parameter called 'rate CG'
create_param_rate_ct | Create a parameter called 'rate CT'
create_param_rate_gt | Create a parameter called 'rate GT'
create_param_s | Create a parameter called s
create_param_scale | Create a parameter called scale
create_param_sigma | Create a parameter called sigma
create_poisson_distr | Create a Poisson distribution
create_rate_ac_param | Create a parameter called 'rate AC'
create_rate_ag_param | Create a parameter called 'rate AG'
create_rate_at_param | Create a parameter called 'rate AT'
create_rate_categories_state_node_xml | Internal function
create_rate_cg_param | Create a parameter called 'rate CG'
create_rate_ct_param | Create a parameter called 'rate CT'
create_rate_gt_param | Create a parameter called 'rate GT'
create_rln_clock_branch_rate_model_xml | Internal function
create_rln_clock_model | Create a relaxed log-normal clock model
create_scale_param | Create a parameter called scale
create_screenlog | Create a 'screenlog' object
create_screenlog_xml | Creates the 'screenlog' section of the 'logger' section of a BEAST2 XML parameter file
create_sigma_param | Create a parameter called sigma
create_site_model | General function to create a site model.
create_site_models | 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'
create_site_models_from_names | Create site models from their names
create_site_model_from_name | Create a site model from name
create_site_model_gtr | Create a GTR site model
create_site_model_hky | Create an HKY site model
create_site_model_jc69 | Create a JC69 site model
create_site_model_parameters_xml | Internal function to creates the XML text for the 'parameter's within the 'siteModel' section of a BEAST2 parameter file.
create_site_model_tn93 | Create a TN93 site model
create_site_model_xml | Internal function to creates the XML text for the 'siteModel' tag of a BEAST2 parameter file.
create_strict_clock_branch_rate_model_xml | Internal function.
create_strict_clock_model | Create a strict clock model
create_strict_clock_rate_scaler_operator_xml | Internal function
create_subst_model_xml | Internal function to create the 'substModel' section
create_s_param | Create a parameter called s
create_temp_screenlog_filename | Create a filename for a temporary 'screenlog' file
create_temp_tracelog_filename | Create a filename for a temporary 'tracelog' file
create_temp_treelog_filename | Create a filename for a temporary 'treelog' file
create_test_inference_model | Create a testing inference model.
create_test_mcmc | Create an MCMC configuration for testing.
create_test_ns_inference_model | Create an inference model to be tested by Nested Sampling
create_test_ns_mcmc | Create an NS MCMC object for testing
create_test_screenlog | Create a 'screenlog' object, to be used in testing
create_test_tracelog | Create a 'tracelog' object, as used for testing
create_test_treelog | Create a 'treelog' object to be used in testing
create_tn93_site_model | Create a TN93 site model
create_tn93_subst_model_xml | Converts a TN93 site model to XML, used in the 'substModel' section
create_tracelog | Create a 'tracelog' object
create_tracelog_xml | Internal function
create_trait_set_string | Create a trait set string.
create_treelog | Create a 'treelog' object

create_treelog_xml

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> "'

create_tree_likelihood_distr_xml | Creates the XML text for the 'distribution' tag with the 'treeLikelihood' ID, of a BEAST2 parameter file.
create_tree_prior | Internal function to create a tree prior
create_tree_priors | 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'
create_tree_prior_bd | Create a Birth-Death tree prior
create_tree_prior_cbs | Create a Coalescent Bayesian Skyline tree prior
create_tree_prior_ccp | Create a Coalescent Constant Population tree prior
create_tree_prior_cep | Create a Coalescent Exponential Population tree prior
create_tree_prior_yule | Create a Yule tree prior
create_ucld_mean_state_node_param_xml | Internal function
create_ucld_stdev_state_node_param_xml | Internal function
create_uniform_distr | Create a uniform distribution
create_xml_declaration | Create the XML declaration of the BEAST2 XML input file
create_yule_tree_prior | Create a Yule tree prior

## -- D --

default_parameters_doc | Documentation of parameters (for example, 'create_param'. This function does nothing. It is intended to inherit documentation from.
default_params_doc | Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.
distr_to_xml | Internal function
distr_to_xml_beta | Internal function
distr_to_xml_exp | Internal function
distr_to_xml_inv_gamma | Internal function
distr_to_xml_laplace | Internal function
distr_to_xml_log_normal | Internal function
distr_to_xml_normal | Internal function
distr_to_xml_one_div_x | Internal function
distr_to_xml_poisson | Internal function
distr_to_xml_uniform | Internal function

## -- E --

extract_xml_loggers_from_lines | Extract everything between first loggers and last loggers line
extract_xml_operators_from_lines | Extract everything between first operators and last operators line
extract_xml_section_from_lines | Get the lines of an XML section, including the section tags

## -- F --

fasta_file_to_sequences | Convert a FASTA file to a table of sequences
find_clock_model | Finds a clock model with a certain ID
find_first_regex_line | Find the first line that satisfies a regex
find_first_xml_opening_tag_line | Find the line number of the first section's opening tag
find_last_regex_line | Find the index of the last line that matches a regex
find_last_xml_closing_tag_line | Find the highest line number of a section's closing tag
freq_equilibrium_to_xml | Creates the 'freq_equilibrium' as XML
freq_param_to_xml | Internal function

## -- G --

gamma_distr_to_xml | Internal function
gamma_site_models_to_xml_prior_distr | Deprecated function
gamma_site_model_to_xml_prior_distr | Internal function.
gamma_site_model_to_xml_state | Converts a gamma site model to XML, used in the 'state' section
get_alignment_id | Conclude the ID from a FASTA filename.
get_alignment_ids | Get the alignment IDs from one or more files.
get_alignment_ids_from_fasta_filenames | Get the alignment ID from one or more FASTA filenames.
get_beautier_folder | Get the path to the beautier temporary files folder
get_beautier_path | Get the full path of a file in the 'inst/extdata' folder
get_beautier_paths | Get the full paths of files in the 'inst/extdata' folder
get_beautier_tempfilename | Get a temporary filename
get_clock_models_ids | Collect the IDs of the list of clock models
get_clock_model_name | Get the BEAUti name for a clock model
get_clock_model_names | Get the clock model names
get_crown_age | Obtain the crown age of a phylogeny.
get_default_beast_namespace | Get the default 'namespace' element value of the 'beast' XML tag.
get_default_beast_namespace_v2_4 | Get the default 'namespace' element value of the 'beast' XML tag for BEAST 2.4
get_default_beast_namespace_v2_6 | Get the default 'namespace' element value of the 'beast' XML tag for BEAST 2.6
get_distr_names | Get the distribution names
get_distr_n_params | Get the number of parameters a distribution uses
get_fasta_filename | Get the path of a FASTA file used in testing
get_file_base_sans_ext | Get the base of the filename base without extension
get_freq_equilibrium_names | Returns valid values for the 'freq_equilibrium' argument
get_gamma_site_model_n_distrs | Get the number of distributions in a gamma site model
get_gamma_site_model_n_params | Get the number of distributions a site model has
get_has_non_strict_clock_model | Determines if there is at least one non-strict clock model in the list of one or more clock models
get_inference_model_filenames | Get the filenames stored in an inference model.
get_log_modes | Get the possible log modes
get_log_sorts | Get the possible log sorts
get_mcmc_filenames | Get the filenames stored in an MCMC.
get_n_taxa | Extract the number of taxa from a file
get_operator_id_pre | Get the prefix of operator IDs
get_param_names | Get the parameter names
get_remove_dir_fun | Get a function that, from a filename, returns the part without the directory.
get_remove_hex_fun | Get a function that removes the hex string from filenames.
get_replace_dir_fun | Get a function to replace the directory of a filename
get_site_models_n_distrs | Get the number of distributions a site model has
get_site_models_n_params | Get the number of distributions one or more site models have
get_site_model_names | Get the site models' names
get_site_model_n_distrs | Get the number of distributions a site model has
get_site_model_n_params | Get the number of distributions a site model has
get_taxa_names | Extract the names of taxa from a file
get_tree_priors_n_distrs | Get the number of distributions a tree prior has
get_tree_priors_n_params | Get the number of parameters a list of tree priors has
get_tree_prior_names | Get the tree prior names
get_tree_prior_n_distrs | Get the number of distributions a tree prior has
get_tree_prior_n_params | Get the number of parameters a tree prior has
get_xml_closing_tag | Get the XML closing tag
get_xml_opening_tag | Get the XML opening tag
gtr_site_model_to_xml_prior_distr | Internal function
gtr_site_model_to_xml_state | Converts a site model to XML, used in the 'state' section

## -- H --

has_mrca_prior | Determines if the inference model has an MRCA prior.
has_mrca_prior_with_distr | See if the inference model has one MRCA prior with a distribution
has_rln_clock_model | Determine if the 'inference_model' uses a relaxed log-normal clock model.
has_strict_clock_model | Determine if the 'inference_model' uses a strict clock model.
has_tip_dating | Determine if the 'inference_model' uses tip dating.
has_xml_closing_tag | Is an XML closing tag with the value of 'section' present among the lines of the text?
has_xml_opening_tag | Is an XML opening tag with value 'section' present among the lines of the text?
has_xml_short_closing_tag | Is an XML closing tag with short closing text in one of the lines of the text?
hky_site_model_to_xml_prior_distr | Internal function
hky_site_model_to_xml_state | Converts a site model to XML, used in the 'state' section

## -- I --

indent | Indent text for a certain number of spaces. If the text is only whitespace, leave it as such
init_bd_tree_prior | Initializes a Birth-Death tree prior
init_beta_distr | Initializes a beta distribution
init_ccp_tree_prior | Initializes a Coalescent Constant Population tree prior
init_cep_tree_prior | Initializes a Coalescent Exponential Population tree prior
init_clock_models | Initializes all clock models
init_distr | Initializes a distribution
init_exp_distr | Initializes an exponential distribution
init_gamma_distr | Initializes a gamma distribution
init_gamma_site_model | Initializes a gamma site model
init_gtr_site_model | Initializes a GTR site model
init_hky_site_model | Initializes an HKY site model
init_inference_model | Initialize an inference model
init_inv_gamma_distr | Initializes an inverse gamma distribution
init_jc69_site_model | Initializes a JC69 site model
init_laplace_distr | Initializes an Laplace distribution
init_log_normal_distr | Initializes an log-normal distribution
init_mrca_prior | Initialize the MRCA prior.
init_mrca_priors | Initializes all MRCA priors
init_normal_distr | Initializes an normal distribution
init_one_div_x_distr | Initializes an one-divided-by-x distribution
init_param | Initializes a parameter
init_poisson_distr | Initializes an Poisson distribution
init_rln_clock_model | Initializes a Relaxed Log-Normal clock model
init_site_models | Initializes all site models
init_strict_clock_model | Initializes a strict clock model
init_tn93_site_model | Initializes a TN93 site model
init_tree_priors | Initializes all tree priors
init_uniform_distr | Initializes a uniform distribution
init_yule_tree_prior | Initializes a Yule tree prior
interspace | Puts spaces in between the lines
is_alpha_param | Determine if the object is a valid alpha parameter
is_bd_tree_prior | Determine if the object is a valid Birth Death tree prior
is_beauti_options | Determine if the object is a valid 'beauti_options'
is_beta_distr | Determine if the object is a valid beta distribution, as created by 'create_beta_distr'
is_beta_param | Determine if the object is a valid beta parameter
is_b_pop_sizes_param | Determine if the object is a valid b_pop_sizes parameter
is_cbs_tree_prior | Determine if the object is a valid constant coalescent Bayesian skyline prior
is_ccp_tree_prior | Determine if the object is a valid constant coalescence population tree prior
is_cep_tree_prior | Determine if the object is a valid coalescent exponential population tree prior
is_clock_model | Determine if the object is a valid clock_model
is_clock_model_name | Determines if the name is a valid clock model name
is_clock_rate_param | Determine if the object is a valid clock_rate parameter
is_default_mcmc | Determine if the MCMC is a default MCMC
is_distr | Determine if the object is a valid distribution
is_distr_name | Determines if the name is a valid distribution name
is_exp_distr | Determine if the object is a valid exponential distribution as created by 'create_exp_distr'
is_freq_equilibrium_name | Checks if 'name' is a valid 'freq_equilibrium' argument value
is_freq_param | Determine if the object is a valid freq parameter
is_gamma_distr | Determine if the object is a valid gamma distribution, as created by 'create_gamma_distr'
is_gamma_site_model | Is object x a gamma site model?
is_gtr_site_model | Determine if the object is a valid GTR site model, as created by 'create_gtr_site_model'
is_hky_site_model | Determine if the object is a valid HKY site model, as created by 'create_hky_site_model'
is_id | Determine if the object is a valid ID
is_inference_model | Determine if the input is an inference model
is_init_bd_tree_prior | Determine if x is an initialized Birth-Death tree_prior object
is_init_beta_distr | Determine if x is an initialized beta distribution object as created by 'create_beta_distr'
is_init_cbs_tree_prior | Determine if x is an initialized Coalescent Bayesian Skyline tree_prior object
is_init_ccp_tree_prior | Determine if x is an initialized Coalescent Constant Population tree_prior object
is_init_cep_tree_prior | Determine if x is an initialized Coalescent Exponential Population tree_prior object
is_init_clock_model | Determine if x is an initialized clock_model object, as created by 'create_clock_model'
is_init_distr | Determine if x is an initialized distribution object as created by 'create_distr'
is_init_exp_distr | Determine if x is an initialized exponential distribution object as created by 'create_exp_distr'
is_init_gamma_distr | Determine if x is an initialized gamma distribution object
is_init_gamma_site_model | Determine if x is an initialized gamma site model, as created by 'create_gamma_site_model'
is_init_gtr_site_model | Determine if x is an initialized GTR site model as created by 'create_gtr_site_model'
is_init_hky_site_model | Determine if x is an initialized HKY site model as created by 'create_hky_site_model'
is_init_inv_gamma_distr | Determine if x is an initialized inverse-gamma distribution as created by 'create_inv_gamma_distr'
is_init_jc69_site_model | Determine if x is an initialized JC69 site model as created by 'create_jc69_site_model'
is_init_laplace_distr | Determine if x is an initialized Laplace distribution as created by 'create_laplace_distr'
is_init_log_normal_distr | Determine if x is an initialized log_normal distribution object as created by 'create_log_normal_distr'
is_init_mrca_prior | Determine if x is an initialized MRCA prior
is_init_normal_distr | Determine if x is an initialized normal distribution object as created by 'create_normal_distr'
is_init_one_div_x_distr | Determine if x is an initialized one_div_x distribution object as created by 'create_one_div_x_distr'
is_init_param | Determine if x is an initialized parameter, as created by create_param
is_init_poisson_distr | Determine if x is an initialized Poisson distribution object as created by 'create_poisson_distr'
is_init_rln_clock_model | Determine if x is an initialized relaxed log-normal clock_model object
is_init_site_model | Determine if x is an initialized site model, as created by 'create_site_model'
is_init_strict_clock_model | Determine if x is an initialized strict clock_model object
is_init_tn93_site_model | Determine if x is an initialized tn93 site model as created by 'create_tn93_site_model'
is_init_tree_prior | Determine if x is an initialized tree_prior objects
is_init_uniform_distr | Determine if x is an initialized uniform distribution object as created by 'create_uniform_distr'
is_init_yule_tree_prior | Determine if x is an initialized Yule tree_prior object
is_inv_gamma_distr | Determine if the object is a valid inverse-gamma distribution as created by 'create_inv_gamma_distr'
is_in_patterns | Is there at least one regular expression having a match with the line?
is_jc69_site_model | Determine if the object is a valid JC69 site model
is_kappa_1_param | Determine if the object is a valid kappa 1 parameter
is_kappa_2_param | Determine if the object is a valid kappa 2 parameter
is_kappa_param | Determine if the object is a valid kappa parameter
is_lambda_param | Determine if the object is a valid lambda parameter
is_laplace_distr | Determine if the object is a valid Laplace distribution, as created by 'create_laplace_distr'
is_log_normal_distr | Determine if the object is a valid log-normal distribution, as created by 'create_log_normal_distr'
is_mcmc | Determine if the object is a valid MCMC
is_mcmc_nested_sampling | Determine if the object is a valid Nested-Sampling MCMC, as used in [1]
is_mean_param | Determine if the object is a valid mean parameter
is_mrca_align_ids_in_fastas | Determine if an MRCA prior's alignment IDs are present in the FASTA files
is_mrca_align_id_in_fasta | Determine if an MRCA prior's alignment IDs is present in the FASTA file
is_mrca_prior | Determine of the object is an empty ('NA') or valid MRCA prior.
is_mrca_prior_with_distr | See if x is one MRCA prior with a distribution
is_mu_param | Determine if the object is a valid mu parameter
is_m_param | Determine if the object is a valid m parameter
is_nested_sampling_mcmc | Determine if the object is a valid Nested-Sampling MCMC, as used in [1]
is_normal_distr | Determine if the object is a valid normal distribution as created by 'create_normal_distr'
is_one_bool | Check if the argument is one boolean
is_one_div_x_distr | Determine if the object is a valid 1/x distribution, as created by 'create_one_div_x_distr'
is_one_double | Determines if the argument is a double
is_one_empty_string | Determine if an object is one empty string
is_one_int | Determines if the argument is a whole number
is_one_na | Determines if x is one NA
is_one_string | Determines if the argument is one string
is_one_string_that_is_a_number | General function to create a distribution.
is_on_appveyor | Determines if the environment is AppVeyor
is_on_ci | Determines if the environment is a continuous integration service
is_on_github_actions | Determines if the environment is GitHub Actions
is_on_travis | Determines if the environment is Travis CI
is_param | Determine if the object is a valid parameter
is_param_name | Determines if the name is a valid parameter name
is_phylo | Checks if the input is a phylogeny
is_poisson_distr | Determine if the object is a valid Poisson distribution as created by 'create_poisson_distr'
is_rate_ac_param | Determine if the object is a valid 'rate AC' parameter
is_rate_ag_param | Determine if the object is a valid 'rate AG' parameter
is_rate_at_param | Determine if the object is a valid 'rate AT' parameter
is_rate_cg_param | Determine if the object is a valid 'rate CG' parameter
is_rate_ct_param | Determine if the object is a valid 'rate CT' parameter
is_rate_gt_param | Determine if the object is a valid 'rate GT' parameter
is_rln_clock_model | Determine if the object is a valid relaxed log normal clock model
is_scale_param | Determine if the object is a valid scale parameter
is_sigma_param | Determine if the object is a valid sigma parameter
is_site_model | Determine if the object is a valid site_model
is_site_model_name | Determines if the name is a valid site_model name
is_strict_clock_model | Determine if the object is a valid strict clock model, as returned by 'create_strict_clock_model'
is_s_param | Determine if the object is a valid s parameter
is_tn93_site_model | Determine if the object is a valid TN93 site model,
is_tree_prior | Determine if an object is a valid tree prior
is_tree_prior_name | Determines if the name is a valid tree prior name
is_uniform_distr | Determine if the object is a valid uniform distribution as created by 'create_uniform_distr'
is_xml | Checks if the text is a valid XML node, that is, it has a opening and matching closing tag
is_yule_tree_prior | Determine if the object is a valid Yule tree prior,

## -- J --

jc69_site_model_to_xml_state | Converts a site model to XML, used in the 'state' section

## -- K --

kappa_param_to_xml | Internal function

## -- M --

mcmc_to_xml_run | Converts an MCMC object to the run section's XML
mcmc_to_xml_run_default | Converts an MCMC object to the run section's XML for a default MCMC
mcmc_to_xml_run_nested_sampling | Converts an MCMC object to the run section's XML for a Nested-Sampling MCMC
mrca_priors_to_xml_prior_distr | Creates the the 'distribution"s prior section (which is part of a posterior distribution section) of a BEAST2 XML parameter file.
mrca_prior_to_xml_prior_distr | Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file.
mrca_prior_to_xml_state | Internal function to create the XML of an MRCA prior, as used in the 'state' section
mrca_prior_to_xml_taxonset | Creates the 'taxonset' section in the prior section of the distribution section of a BEAST2 XML parameter file.
mrca_prior_to_xml_tracelog | Internal function
m_param_to_xml | Internal function

## -- N --

no_taxa_to_xml_tree | Internal function

## -- P --

parameter_to_xml | Internal function
parameter_to_xml_kappa_1 | Internal function
parameter_to_xml_kappa_2 | Internal function
parameter_to_xml_lambda | Internal function
parameter_to_xml_mean | Internal function
parameter_to_xml_mu | Internal function
parameter_to_xml_rate_ac | Internal function
parameter_to_xml_rate_ag | Internal function
parameter_to_xml_rate_at | Internal function
parameter_to_xml_rate_cg | Internal function
parameter_to_xml_rate_ct | Internal function
parameter_to_xml_rate_gt | Internal function
parameter_to_xml_scale | Internal function
parameter_to_xml_sigma | Internal function

## -- R --

remove_beautier_folder | Check there are no files in the default beautier folder
remove_empty_lines | Remove all lines that are only whitespace
remove_multiline | Remove consecutive lines
rename_inference_model_filenames | Rename the filenames in an inference model
rename_mcmc_filenames | Rename the filenames within an MCMC
rln_clock_model_to_xml_mean_rate_prior | Internal function
rln_clock_model_to_xml_operators | Internal function
rln_clock_model_to_xml_prior_distr | Internal function
rln_clock_model_to_xml_state | Internal function
rln_clock_model_to_xml_tracelog | Internal function
rnd_phylo_to_xml_init | Creates the XML of a random phylogeny, as used in the 'init' section

## -- S --

site_models_to_xml_operators | Write the XML 'operators' section from the site models.
site_models_to_xml_prior_distr | Represent the site models as XML
site_models_to_xml_tracelog | Creates the site models' XML for the tracelog section
site_model_to_xml_operators | Converts a site model to XML, used in the 'operators' section
site_model_to_xml_prior_distr | Internal function
site_model_to_xml_state | Internal function to convert a site model to XML, used in the 'state' section
site_model_to_xml_tracelog | Creates the site model's XML for the tracelog section
strict_clock_model_to_xml_operators | Internal function
strict_clock_model_to_xml_prior_distr | Internal function
strict_clock_model_to_xml_state | Internal function
strict_clock_model_to_xml_tracelog | Internal function
s_parameter_to_xml | Internal function

## -- T --

taxa_to_xml_tree | Internal function
tipdate_taxa_to_xml_trait | Internal function
tipdate_taxa_to_xml_tree | Internal function
tn93_site_model_to_xml_prior_distr | Internal function
tn93_site_model_to_xml_state | Converts a site model to XML, used in the 'state' section
tree_model_to_tracelog_xml | Internal function
tree_priors_to_xml_prior_distr | Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file.
tree_priors_to_xml_tracelog | Creates the tree priors' XML for the tracelog section
tree_prior_to_xml_operators | Internal function
tree_prior_to_xml_prior_distr | Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file.
tree_prior_to_xml_state | Creates the XML of a tree prior, as used in the 'state' section
tree_prior_to_xml_tracelog | Creates the tree prior's XML for the tracelog section

## -- U --

unindent | Unindents text

## -- Y --

yule_tree_prior_to_xml_operators | Internal function
yule_tree_prior_to_xml_prior_distr | Creates the 'prior' section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Yule tree prior