'BEAUti' from R

---

Documentation for package ‘beautier’ version 2.6.12

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

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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