are_clock_models        Determine if x consists out of clock_models
                        objects
are_equal_mcmcs         Determine if two MCMCs are equal.
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_site_models         Determine if x consists out of site_models
                        objects
are_tree_priors         Determine if x consists out of tree_priors
                        objects
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
beautier                'beautier': A package to create a 'BEAST2'
                        input file.
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
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_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_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_mcmc              Check if the MCMC is a valid MCMC object.
check_mrca_prior        Check if the MRCA prior is a valid MRCA prior.
check_phylogeny         Check if the phylogeny is a valid phylogeny
                        object.
check_rln_clock_model   Check if the clock model is a valid clock
                        model.
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_strict_clock_model
                        Check if the clock model is a valid clock
                        model.
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.
create_alpha_param      Create a parameter called alpha
create_bd_tree_prior    Create a Birth-Death tree prior
create_beast2_input     Create a BEAST2 XML input text
create_beast2_input_distr_lh
                        Creates the likelihood section in the
                        distribution section of a BEAST2 XML 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_screenlog
                        Creates the 'screenlog' section of the 'logger'
                        section of a BEAST2 XML parameter file
create_beast2_input_tracelog
                        Creates the 'tracelog' section of the 'logger'
                        section of a BEAST2 XML parameter file
create_beast2_input_treelogs
                        Creates the 'tracelog' section of the 'logger'
                        section of a BEAST2 XML parameter file
create_beauti_options   Function to create a set of BEAUti options.
create_beta_distr       Create a beta distribution
create_beta_param       Create a parameter called beta
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_distr            General function to create a distribution.
create_exp_distr        Create an exponential distribution
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_hky_site_model   Create an HKY site model
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_kappa_1_param    Create a parameter called kappa 1
create_kappa_2_param    Create a parameter called kappa 2
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_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_nested_sampling_mcmc
                        Create an MCMC object to estimate the marginal
                        likelihood using Nested Sampling.
create_normal_distr     Create an normal distribution
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_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_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_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_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_model
                        Create a strict clock model
create_tn93_site_model
                        Create a TN93 site model
create_tree_prior       Internal function to create a tree prior
create_tree_prior_from_name
                        Create a tree prior from name
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_priors_from_names
                        Create tree priors from their names
create_uniform_distr    Create a uniform distribution
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_beta       Converts a beta distribution to XML
distr_to_xml_exp        Converts an exponential distribution to XML
distr_to_xml_gamma      Converts a gamma distribution to XML
distr_to_xml_inv_gamma
                        Converts an inverse-gamma distribution to XML
distr_to_xml_laplace    Converts a Laplace distribution to XML
distr_to_xml_log_normal
                        Converts a log-normal distribution to XML
distr_to_xml_normal     Converts a normal distribution to XML
distr_to_xml_one_div_x
                        Converts a 1/x distribution to XML
distr_to_xml_poisson    Converts a Poisson distribution to XML
distr_to_xml_uniform    Converts a uniform distribution to XML
fasta_to_phylo          Create a random phylogeny, with the same taxa
                        names as the FASTA file and the desired crown
                        age
fastas_to_phylos        Create one or more random phylogenies.
get_alignment_id        Conclude the ID from a FASTA filename.
get_alignment_ids       Get the alignment ID from one or more FASTA
                        filenames.
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_clock_model_names   Get the clock model names
get_crown_age           Obtain the crown age of a phylogeny.
get_fasta_filename      Get the path of a FASTA file used in testing
get_gamma_site_model_n_distrs
                        Get the number of distributions in a gamma site
                        model
get_site_model_names    Get the site models' names
get_taxa_names          Extract the names of taxa from a file
get_tree_prior_names    Get the tree prior names
has_mrca_prior          Determines if the inference model has an MRCA
                        prior.
init_bd_tree_prior      Initializes a Birth-Death tree prior
init_ccp_tree_prior     Initializes a Coalescent Constant Population
                        tree prior
init_cep_tree_prior     Initializes a Coalescent Exponential Population
                        tree prior
init_gtr_site_model     Initializes a GTR site model
init_hky_site_model     Initializes an HKY site model
init_jc69_site_model    Initializes a JC69 site model
init_rln_clock_model    Initializes a Relaxed Log-Normal clock model
init_strict_clock_model
                        Initializes a strict clock model
init_tn93_site_model    Initializes a TN93 site model
init_yule_tree_prior    Initializes a Yule tree prior
is_bd_tree_prior        Determine if the object is a valid Birth Death
                        tree prior
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_init_beta_distr      Determine if x is an initialized beta
                        distribution object as created by
                        'create_beta_distr'
is_init_cep_tree_prior
                        Determine if x is an initialized Coalescent
                        Exponential Population tree_prior object
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_inv_gamma_distr
                        Determine if x is an initialized inverse-gamma
                        distribution as created by
                        'create_inv_gamma_distr'
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_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_poisson_distr   Determine if x is an initialized Poisson
                        distribution object as created by
                        'create_poisson_distr'
is_init_uniform_distr   Determine if x is an initialized uniform
                        distribution object as created by
                        'create_uniform_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_one_na               Determines if x is one NA
is_phylo                Checks if the input is a phylogeny
is_site_model           Determine if the object is a valid site_model
is_tree_prior           Determine if an object is a valid tree prior
is_yule_tree_prior      Determine if the object is a valid Yule tree
                        prior,
parameter_to_xml_alpha
                        Converts an alpha parameter to XML
parameter_to_xml_beta   Converts a beta parameter to XML
parameter_to_xml_clock_rate
                        Converts a 'clockRate' parameter to XML
parameter_to_xml_kappa_1
                        Converts a kappa 1 parameter to XML
parameter_to_xml_kappa_2
                        Converts a kappa 2 parameter to XML
parameter_to_xml_lambda
                        Converts a lambda parameter to XML
parameter_to_xml_m      Converts a m parameter to XML
parameter_to_xml_mean   Converts a mean parameter to XML
parameter_to_xml_mu     Converts a mu parameter to XML
parameter_to_xml_rate_ac
                        Converts a 'rate AC' parameter to XML
parameter_to_xml_rate_ag
                        Converts a 'rate AG' parameter to XML
parameter_to_xml_rate_at
                        Converts a 'rate AT' parameter to XML
parameter_to_xml_rate_cg
                        Converts a 'rate CG' parameter to XML
parameter_to_xml_rate_ct
                        Converts a 'rate CT' parameter to XML
parameter_to_xml_rate_gt
                        Converts a 'rate GT' parameter to XML
parameter_to_xml_s      Converts a s parameter to XML
parameter_to_xml_scale
                        Converts a scale parameter to XML
parameter_to_xml_sigma
                        Converts a sigma parameter to XML
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
