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_pop_sizes_param_to_xml
                        Internal function
b_pop_sizes_parameter_to_xml
                        Internal function
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
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_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_filename          Check if the 'filename' is valid
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_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_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_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_site_models       Check if the object is a list of one or more
                        site models.
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_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.
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.
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_b_pop_sizes_param
                        Create a parameter called 'b_pop_sizes'.
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_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_beautier_tempfolder
                        Create the default 'beautier' temporary folder
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_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_model_from_name
                        Create a clock model from name
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_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_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_log_normal_distr
                        Create a log-normal distribution
create_loggers_xml      Creates the three logger sections of a BEAST2
                        XML parameter file
create_m_param          Create a parameter called m
create_mcmc             Create an MCMC configuration.
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_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_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_s_param          Create a parameter called s
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_model_from_name
                        Create a site model from name
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_xml   Internal function to creates the XML text for
                        the 'siteModel' tag of a BEAST2 parameter file.
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_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_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_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_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_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
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
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
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
gamma_distr_to_xml      Internal 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
gamma_site_models_to_xml_prior_distr
                        Deprecated function
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_model_name    Get the BEAUti name for a clock model
get_clock_model_names   Get the clock model names
get_clock_models_ids    Collect the IDs of the list of clock models
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_n_params      Get the number of parameters a distribution
                        uses
get_distr_names         Get the distribution names
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_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_site_model_names    Get the site models' names
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_taxa_names          Extract the names of taxa from a file
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_tree_prior_names    Get the tree prior names
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_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
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
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_b_pop_sizes_param    Determine if the object is a valid b_pop_sizes
                        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_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_in_patterns          Is there at least one regular expression having
                        a match with the line?
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_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_m_param              Determine if the object is a valid m parameter
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_id_in_fasta
                        Determine if an MRCA prior's alignment IDs is
                        present in the FASTA file
is_mrca_align_ids_in_fastas
                        Determine if an MRCA prior's alignment IDs are
                        present in the FASTA files
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_normal_distr         Determine if the object is a valid normal
                        distribution as created by
                        'create_normal_distr'
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_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_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_s_param              Determine if the object is a valid s parameter
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_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,
jc69_site_model_to_xml_state
                        Converts a site model to XML, used in the
                        'state' section
kappa_param_to_xml      Internal function
m_param_to_xml          Internal function
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_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
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.
no_taxa_to_xml_tree     Internal function
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
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_parameter_to_xml      Internal function
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
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
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
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_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
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
unindent                Unindents text
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
