'BEAUti' from R


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Documentation for package ‘beautier’ version 2.6.2

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A B C D E F G H I 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
beautier 'beautier': A package to create a 'BEAST2' input file.
beta_parameter_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 Check there are no files in the default beautier folder
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_models_to_xml_operators Deprecated
clock_models_to_xml_prior_distr Deprecated function
clock_models_to_xml_state Deprecated internal function
clock_models_to_xml_tracelog Deprecated internal function
clock_model_to_xml_operators Converts a clock model to the 'operators' section of the XML as text
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_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_rln_xml Internal function
create_branch_rate_model_sc_xml Internal function to call create_branch_rate_model_xml for a strict clock.
create_branch_rate_model_stuff_xml Internal function called by create_branch_rate_model_xml
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_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_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_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_clock_rate Create a parameter called 'clock_rate', as needed by 'create_strict_clock_model'
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_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_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
create_test_tracelog Create a 'tracelog' object
create_test_treelog Create a 'treelog' object
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

-- G --

gamma_distr_to_xml Internal function
gamma_site_models_to_xml_prior_distr Creates the gamma site models section in the distribution section of a BEAST2 XML parameter file
gamma_site_model_to_xml_prior_distr Creates the gamma site models section in the distribution section of a BEAST2 XML parameter file
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_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

-- 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?

-- 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_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_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_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_int Determines if the argument is a whole number
is_one_na Determines if x is one NA
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,

-- 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_priors_to_xml_tracelog Creates the MRCA priors' XML for the tracelog section
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_s Internal function
parameter_to_xml_scale Internal function
parameter_to_xml_sigma Internal function

-- R --

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 Used by 'clock_models_to_xml_prior_distr'
rln_clock_model_to_xml_prior_distr 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 Converts a site model to XML, used in the 'prior' section
site_model_to_xml_state Converts 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

-- T --

taxa_to_xml_tree Internal function
tipdate_taxa_to_xml_trait Internal function
tipdate_taxa_to_xml_tree Internal function
tree_models_to_xml_tracelog Creates the tree models' XML for the tracelog section
tree_model_to_tracelog_xml Internal function
tree_priors_to_xml_operators Deprecated
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