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prior.","topics":["check_mrca_prior"]},{"page":"check_mrca_prior_name","title":"Check if 'mrca_prior_name' is a valid MRCA prior name.","topics":["check_mrca_prior_name"]},{"page":"check_mrca_prior_names","title":"Check if the MRCA prior, which is a list, has all the named elements.","topics":["check_mrca_prior_names"]},{"page":"check_mrca_prior_taxa_names","title":"Check the MRCA prior's taxon names are valid.","topics":["check_mrca_prior_taxa_names"]},{"page":"check_ns_mcmc","title":"Check if this an MCMC that uses Nested Sampling to estimate a marginal likelihood.","topics":["check_mcmc_nested_sampling","check_nested_sampling_mcmc","check_ns_mcmc"]},{"page":"check_param","title":"Check if the parameter is a valid parameter","topics":["check_param"]},{"page":"check_param_names","title":"Check if the 'param' has the list elements of a valid 'param' object.","topics":["check_param_names"]},{"page":"check_param_types","title":"Check if the 'param' has the list elements of the right type for a valid 'param' object.","topics":["check_param_types"]},{"page":"check_phylogeny","title":"Check if the phylogeny is a valid phylogeny object.","topics":["check_phylogeny"]},{"page":"check_rename_fun","title":"Check if the rename function is a valid filename rename function","topics":["check_rename_fun"]},{"page":"check_rln_clock_model","title":"Check if the clock model is a valid clock model.","topics":["check_rln_clock_model"]},{"page":"check_screenlog","title":"Check if a 'screenlog' is valid.","topics":["check_screenlog"]},{"page":"check_screenlog_names","title":"Check if the 'screenlog' has the list elements of a valid 'screenlog' object.","topics":["check_screenlog_names"]},{"page":"check_screenlog_values","title":"Check if the screenlog has the list elements with valid values for being a valid screenlog object.","topics":["check_screenlog_values"]},{"page":"check_site_model","title":"Check if the site model is a valid site model","topics":["check_site_model"]},{"page":"check_site_model_names","title":"Check if the 'site_model' has the list elements of a valid 'site_model' object.","topics":["check_site_model_names"]},{"page":"check_site_model_types","title":"Check if the 'site_model' has the list elements of the right type for a valid 'site_model' object.","topics":["check_site_model_types"]},{"page":"check_site_models","title":"Check if the object is a list of one or more site models.","topics":["check_site_models"]},{"page":"check_store_every","title":"Check if 'store_every' holds a valid value","topics":["check_store_every"]},{"page":"check_strict_clock_model","title":"Check if the clock model is a valid clock model.","topics":["check_strict_clock_model"]},{"page":"check_tn93_site_model","title":"Check if the 'tn93_site_model' is a valid TN93 nucleotide substitution model.","topics":["check_tn93_site_model"]},{"page":"check_tn93_site_model_names","title":"Check if the 'tn93_site_model' has the list elements of a valid 'tn93_site_model' object.","topics":["check_tn93_site_model_names"]},{"page":"check_tracelog","title":"Check if a 'tracelog' is valid.","topics":["check_tracelog"]},{"page":"check_tracelog_names","title":"Check if the 'tracelog' has the list elements of a valid 'tracelog' object.","topics":["check_tracelog_names"]},{"page":"check_tracelog_values","title":"Check if the tracelog has the list elements with valid values for being a valid tracelog object.","topics":["check_tracelog_values"]},{"page":"check_tree_prior","title":"Check if the tree prior is a valid tree prior","topics":["check_tree_prior"]},{"page":"check_tree_priors","title":"Check if the object is a list of one or more tree priors.","topics":["check_tree_priors"]},{"page":"check_treelog","title":"Check if a 'treelog' is valid.","topics":["check_treelog"]},{"page":"check_treelog_names","title":"Check if the 'treelog' has the list elements of a valid 'treelog' object.","topics":["check_treelog_names"]},{"page":"check_treelog_values","title":"Check if the treelog has the list elements with valid values for being a valid treelog object.","topics":["check_treelog_values"]},{"page":"clock_model_to_xml_operators","title":"Internal function","topics":["clock_model_to_xml_operators"]},{"page":"clock_model_to_xml_prior_distr","title":"Internal function","topics":["clock_model_to_xml_prior_distr"]},{"page":"clock_model_to_xml_state","title":"Internal function","topics":["clock_model_to_xml_state"]},{"page":"clock_model_to_xml_tracelog","title":"Internal function","topics":["clock_model_to_xml_tracelog"]},{"page":"clock_model_to_xml_treelogger","title":"Convert a clock model to the XML of the 'TreeLogger'","topics":["clock_model_to_xml_treelogger"]},{"page":"clock_rate_param_to_xml","title":"Internal function","topics":["clock_rate_param_to_xml"]},{"page":"compare_lines","title":"Internal function","topics":["compare_lines"]},{"page":"count_trailing_spaces","title":"Count the number of spaces before the first character","topics":["count_trailing_spaces"]},{"page":"create_alpha_param","title":"Create a parameter called alpha","topics":["create_alpha_param","create_param_alpha"]},{"page":"create_b_pop_sizes_param","title":"Create a parameter called `b_pop_sizes`.","topics":["create_b_pop_sizes_param","create_param_b_pop_sizes"]},{"page":"create_bd_tree_prior","title":"Create a Birth-Death tree prior","topics":["create_bd_tree_prior","create_tree_prior_bd"]},{"page":"create_beast2_beast_xml","title":"Create the '' XML","topics":["create_beast2_beast_xml"]},{"page":"create_beast2_input","title":"Create a BEAST2 XML input text","topics":["create_beast2_input"]},{"page":"create_beast2_input_beast","title":"Creates the XML text for the 'beast' tag of a BEAST2 parameter file.","topics":["create_beast2_input_beast"]},{"page":"create_beast2_input_data","title":"Creates the 'data' section of a BEAST2 XML parameter file","topics":["create_beast2_input_data"]},{"page":"create_beast2_input_data_sequences","title":"Creates the data section of a BEAST2 XML parameter file","topics":["create_beast2_input_data_sequences"]},{"page":"create_beast2_input_distr","title":"Creates the distribution section of a BEAST2 XML parameter file.","topics":["create_beast2_input_distr"]},{"page":"create_beast2_input_distr_lh","title":"Creates the XML text for the 'distribution' tag with the 'likelihood' ID, of a BEAST2 parameter file.","topics":["create_beast2_input_distr_lh"]},{"page":"create_beast2_input_distr_prior","title":"Creates the prior section in the distribution section of a BEAST2 XML parameter file","topics":["create_beast2_input_distr_prior"]},{"page":"create_beast2_input_file","title":"Create a BEAST2 input file","topics":["create_beast2_input_file"]},{"page":"create_beast2_input_file_from_model","title":"Create a BEAST2 input file from an inference model","topics":["create_beast2_input_file_from_model"]},{"page":"create_beast2_input_from_model","title":"Create a BEAST2 XML input text from an inference model","topics":["create_beast2_input_from_model"]},{"page":"create_beast2_input_init","title":"Creates the 'init' section of a BEAST2 XML parameter file","topics":["create_beast2_input_init"]},{"page":"create_beast2_input_map","title":"Creates the map section of a BEAST2 XML parameter file","topics":["create_beast2_input_map"]},{"page":"create_beast2_input_operators","title":"Creates the operators section of a BEAST2 XML parameter file","topics":["create_beast2_input_operators"]},{"page":"create_beast2_input_run","title":"Creates the ''run'' section of a BEAST2 XML parameter file","topics":["create_beast2_input_run"]},{"page":"create_beast2_input_state","title":"Creates the ''state'' section of a BEAST2 XML parameter file","topics":["create_beast2_input_state"]},{"page":"create_beauti_options","title":"Function to create a set of `BEAUti` options.","topics":["create_beauti_options"]},{"page":"create_beauti_options_v2_4","title":"Function to create the BEAUti options for version 2.4.","topics":["create_beauti_options_v2_4"]},{"page":"create_beauti_options_v2_6","title":"Function to create the BEAUti options for version 2.6.","topics":["create_beauti_options_v2_6"]},{"page":"create_beautier_tempfolder","title":"Create the default `beautier` temporary folder","topics":["create_beautier_tempfolder"]},{"page":"create_beta_distr","title":"Create a beta distribution","topics":["create_beta_distr","create_distr_beta"]},{"page":"create_beta_param","title":"Create a parameter called beta","topics":["create_beta_param","create_param_beta"]},{"page":"create_branch_rate_model_xml","title":"Internal function to create the 'branchRateModel' section of the XML as text.","topics":["create_branch_rate_model_xml"]},{"page":"create_cbs_tree_prior","title":"Create a Coalescent Bayesian Skyline tree prior","topics":["create_cbs_tree_prior","create_tree_prior_cbs"]},{"page":"create_ccp_tree_prior","title":"Create a Coalescent Constant Population tree prior","topics":["create_ccp_tree_prior","create_tree_prior_ccp"]},{"page":"create_cep_tree_prior","title":"Create a Coalescent Exponential Population tree prior","topics":["create_cep_tree_prior","create_tree_prior_cep"]},{"page":"create_clock_model","title":"General function to create a clock model","topics":["create_clock_model"]},{"page":"create_clock_model_from_name","title":"Create a clock model from name","topics":["create_clock_model_from_name"]},{"page":"create_clock_models","title":"Creates all supported clock models, which is a list of the types returned by 'create_rln_clock_model', and 'create_strict_clock_model'","topics":["create_clock_models"]},{"page":"create_clock_models_from_names","title":"Create clock models from their names","topics":["create_clock_models_from_names"]},{"page":"create_clock_rate_param","title":"Create a parameter called 'clock_rate', as needed by 'create_strict_clock_model'","topics":["create_clock_rate_param","create_param_clock_rate"]},{"page":"create_clock_rate_state_node_parameter_xml","title":"Internal function","topics":["create_clock_rate_state_node_parameter_xml"]},{"page":"create_data_xml","title":"Create the '' XML","topics":["create_data_xml"]},{"page":"create_distr","title":"General function to create a distribution.","topics":["create_distr"]},{"page":"create_exp_distr","title":"Create an exponential distribution","topics":["create_distr_exp","create_exp_distr"]},{"page":"create_freq_param","title":"Create a parameter called freq","topics":["create_freq_param","create_param_freq"]},{"page":"create_gamma_distr","title":"Create a gamma distribution","topics":["create_distr_gamma","create_gamma_distr"]},{"page":"create_gamma_site_model","title":"Create a gamma site model, part of a site model","topics":["create_gamma_site_model"]},{"page":"create_gtr_site_model","title":"Create a GTR site model","topics":["create_gtr_site_model","create_site_model_gtr"]},{"page":"create_gtr_subst_model_xml","title":"Converts a GTR site model to XML, used in the 'substModel' section","topics":["create_gtr_subst_model_xml"]},{"page":"create_hky_site_model","title":"Create an HKY site model","topics":["create_hky_site_model","create_site_model_hky"]},{"page":"create_hky_subst_model_xml","title":"Converts a site model to XML, used in the 'substModel' section","topics":["create_hky_subst_model_xml"]},{"page":"create_inference_model","title":"Create a Bayesian phylogenetic inference model.","topics":["create_inference_model"]},{"page":"create_inv_gamma_distr","title":"Create an inverse-gamma distribution","topics":["create_distr_inv_gamma","create_inv_gamma_distr"]},{"page":"create_jc69_site_model","title":"Create a JC69 site model","topics":["create_jc69_site_model","create_site_model_jc69"]},{"page":"create_jc69_subst_model_xml","title":"Converts a JC69 site model to XML, used in the 'substModel' section","topics":["create_jc69_subst_model_xml"]},{"page":"create_kappa_1_param","title":"Create a parameter called kappa 1","topics":["create_kappa_1_param","create_param_kappa_1"]},{"page":"create_kappa_2_param","title":"Create a parameter called kappa 2","topics":["create_kappa_2_param","create_param_kappa_2"]},{"page":"create_kappa_param","title":"Create a parameter called kappa","topics":["create_kappa_param","create_param_kappa"]},{"page":"create_lambda_param","title":"Create a parameter called lambda","topics":["create_lambda_param","create_param_lambda"]},{"page":"create_laplace_distr","title":"Create a Laplace distribution","topics":["create_distr_laplace","create_laplace_distr"]},{"page":"create_log_normal_distr","title":"Create a log-normal distribution","topics":["create_distr_log_normal","create_log_normal_distr"]},{"page":"create_loggers_xml","title":"Creates the three logger sections of a BEAST2 XML parameter file","topics":["create_loggers_xml"]},{"page":"create_m_param","title":"Create a parameter called m","topics":["create_m_param","create_param_m"]},{"page":"create_mcmc","title":"Create an MCMC configuration.","topics":["create_mcmc"]},{"page":"create_mean_param","title":"Create a parameter called mean","topics":["create_mean_param","create_param_mean"]},{"page":"create_mrca_prior","title":"Create a Most Recent Common Ancestor prior","topics":["create_mrca_prior"]},{"page":"create_mu_param","title":"Create a parameter called mu","topics":["create_mu_param","create_param_mu"]},{"page":"create_normal_distr","title":"Create an normal distribution","topics":["create_distr_normal","create_normal_distr"]},{"page":"create_ns_inference_model","title":"Create an inference model to measure the evidence of.","topics":["create_ns_inference_model"]},{"page":"create_ns_mcmc","title":"Create an MCMC object to estimate the marginal likelihood using Nested Sampling.","topics":["create_mcmc_nested_sampling","create_ns_mcmc"]},{"page":"create_one_div_x_distr","title":"Create a 1/x distribution","topics":["create_distr_one_div_x","create_one_div_x_distr"]},{"page":"create_param","title":"General function to create a parameter.","topics":["create_param"]},{"page":"create_poisson_distr","title":"Create a Poisson distribution","topics":["create_distr_poisson","create_poisson_distr"]},{"page":"create_rate_ac_param","title":"Create a parameter called 'rate AC'","topics":["create_param_rate_ac","create_rate_ac_param"]},{"page":"create_rate_ag_param","title":"Create a parameter called 'rate AG'","topics":["create_param_rate_ag","create_rate_ag_param"]},{"page":"create_rate_at_param","title":"Create a parameter called 'rate AT'","topics":["create_param_rate_at","create_rate_at_param"]},{"page":"create_rate_categories_state_node_xml","title":"Internal function","topics":["create_rate_categories_state_node_xml"]},{"page":"create_rate_cg_param","title":"Create a parameter called 'rate CG'","topics":["create_param_rate_cg","create_rate_cg_param"]},{"page":"create_rate_ct_param","title":"Create a parameter called 'rate CT'","topics":["create_param_rate_ct","create_rate_ct_param"]},{"page":"create_rate_gt_param","title":"Create a parameter called 'rate GT'","topics":["create_param_rate_gt","create_rate_gt_param"]},{"page":"create_rln_clock_branch_rate_model_xml","title":"Internal function","topics":["create_rln_clock_branch_rate_model_xml"]},{"page":"create_rln_clock_model","title":"Create a relaxed log-normal clock model","topics":["create_clock_model_rln","create_rln_clock_model"]},{"page":"create_s_param","title":"Create a parameter called s","topics":["create_param_s","create_s_param"]},{"page":"create_scale_param","title":"Create a parameter called scale","topics":["create_param_scale","create_scale_param"]},{"page":"create_screenlog","title":"Create a 'screenlog' object","topics":["create_screenlog"]},{"page":"create_screenlog_xml","title":"Creates the 'screenlog' section of the 'logger' section of a BEAST2 XML parameter file","topics":["create_screenlog_xml"]},{"page":"create_sigma_param","title":"Create a parameter called sigma","topics":["create_param_sigma","create_sigma_param"]},{"page":"create_site_model","title":"General function to create a site model.","topics":["create_site_model"]},{"page":"create_site_model_from_name","title":"Create a site model from name","topics":["create_site_model_from_name"]},{"page":"create_site_model_parameters_xml","title":"Internal function to creates the XML text for the 'parameter's within the 'siteModel' section of a BEAST2 parameter file.","topics":["create_site_model_parameters_xml"]},{"page":"create_site_model_xml","title":"Internal function to creates the XML text for the 'siteModel' tag of a BEAST2 parameter file.","topics":["create_site_model_xml"]},{"page":"create_site_models","title":"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'","topics":["create_site_models"]},{"page":"create_site_models_from_names","title":"Create site models from their names","topics":["create_site_models_from_names"]},{"page":"create_strict_clock_branch_rate_model_xml","title":"Internal function.","topics":["create_strict_clock_branch_rate_model_xml"]},{"page":"create_strict_clock_model","title":"Create a strict clock model","topics":["create_clock_model_strict","create_strict_clock_model"]},{"page":"create_strict_clock_rate_scaler_operator_xml","title":"Internal function","topics":["create_strict_clock_rate_scaler_operator_xml"]},{"page":"create_subst_model_xml","title":"Internal function to create the 'substModel' section","topics":["create_subst_model_xml"]},{"page":"create_temp_screenlog_filename","title":"Create a filename for a temporary `screenlog` file","topics":["create_temp_screenlog_filename"]},{"page":"create_temp_tracelog_filename","title":"Create a filename for a temporary `tracelog` file","topics":["create_temp_tracelog_filename"]},{"page":"create_temp_treelog_filename","title":"Create a filename for a temporary `treelog` file","topics":["create_temp_treelog_filename"]},{"page":"create_test_inference_model","title":"Create a testing inference model.","topics":["create_test_inference_model"]},{"page":"create_test_mcmc","title":"Create an MCMC configuration for testing.","topics":["create_test_mcmc"]},{"page":"create_test_ns_inference_model","title":"Create an inference model to be tested by Nested Sampling","topics":["create_test_ns_inference_model"]},{"page":"create_test_ns_mcmc","title":"Create an NS MCMC object for testing","topics":["create_test_ns_mcmc"]},{"page":"create_test_screenlog","title":"Create a 'screenlog' object, to be used in testing","topics":["create_test_screenlog"]},{"page":"create_test_tracelog","title":"Create a 'tracelog' object, as used for testing","topics":["create_test_tracelog"]},{"page":"create_test_treelog","title":"Create a 'treelog' object to be used in testing","topics":["create_test_treelog"]},{"page":"create_tn93_site_model","title":"Create a TN93 site model","topics":["create_site_model_tn93","create_tn93_site_model"]},{"page":"create_tn93_subst_model_xml","title":"Converts a TN93 site model to XML, used in the 'substModel' section","topics":["create_tn93_subst_model_xml"]},{"page":"create_tracelog","title":"Create a 'tracelog' object","topics":["create_tracelog"]},{"page":"create_tracelog_xml","title":"Internal function","topics":["create_tracelog_xml"]},{"page":"create_trait_set_string","title":"Create a trait set string.","topics":["create_trait_set_string"]},{"page":"create_tree_likelihood_distr_xml","title":"Creates the XML text for the 'distribution' tag with the 'treeLikelihood' ID, of a BEAST2 parameter file.","topics":["create_tree_likelihood_distr_xml"]},{"page":"create_tree_prior","title":"Internal function to create a tree prior","topics":["create_tree_prior"]},{"page":"create_tree_priors","title":"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'","topics":["create_tree_priors"]},{"page":"create_treelog","title":"Create a 'treelog' object","topics":["create_treelog"]},{"page":"create_treelog_xml","title":"Creates the XML text for the `logger` tag with ID `treelog`. This section has these elements: ``` # nolint indeed long # nolint indeed long ```","topics":["create_treelog_xml"]},{"page":"create_ucld_mean_state_node_param_xml","title":"Internal function","topics":["create_ucld_mean_state_node_param_xml"]},{"page":"create_ucld_stdev_state_node_param_xml","title":"Internal function","topics":["create_ucld_stdev_state_node_param_xml"]},{"page":"create_uniform_distr","title":"Create a uniform distribution","topics":["create_distr_uniform","create_uniform_distr"]},{"page":"create_xml_declaration","title":"Create the XML declaration of the BEAST2 XML input file","topics":["create_xml_declaration"]},{"page":"create_yule_tree_prior","title":"Create a Yule tree prior","topics":["create_tree_prior_yule","create_yule_tree_prior"]},{"page":"default_parameters_doc","title":"Documentation of parameters (for example, 'create_param'. This function does nothing. It is intended to inherit documentation from.","topics":["default_parameters_doc"]},{"page":"default_params_doc","title":"Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.","topics":["default_params_doc"]},{"page":"distr_to_xml","title":"Internal function","topics":["distr_to_xml"]},{"page":"distr_to_xml_beta","title":"Internal function","topics":["distr_to_xml_beta"]},{"page":"distr_to_xml_exp","title":"Internal function","topics":["distr_to_xml_exp"]},{"page":"distr_to_xml_inv_gamma","title":"Internal function","topics":["distr_to_xml_inv_gamma"]},{"page":"distr_to_xml_laplace","title":"Internal function","topics":["distr_to_xml_laplace"]},{"page":"distr_to_xml_log_normal","title":"Internal function","topics":["distr_to_xml_log_normal"]},{"page":"distr_to_xml_normal","title":"Internal function","topics":["distr_to_xml_normal"]},{"page":"distr_to_xml_one_div_x","title":"Internal function","topics":["distr_to_xml_one_div_x"]},{"page":"distr_to_xml_poisson","title":"Internal function","topics":["distr_to_xml_poisson"]},{"page":"distr_to_xml_uniform","title":"Internal function","topics":["distr_to_xml_uniform"]},{"page":"extract_xml_loggers_from_lines","title":"Extract everything between first loggers and last loggers line","topics":["extract_xml_loggers_from_lines"]},{"page":"extract_xml_operators_from_lines","title":"Extract everything between first operators and last operators line","topics":["extract_xml_operators_from_lines"]},{"page":"extract_xml_section_from_lines","title":"Get the lines of an XML section, including the section tags","topics":["extract_xml_section_from_lines"]},{"page":"fasta_file_to_sequences","title":"Convert a FASTA file to a table of sequences","topics":["fasta_file_to_sequences"]},{"page":"find_clock_model","title":"Finds a clock model with a certain ID","topics":["find_clock_model"]},{"page":"find_first_regex_line","title":"Find the first line that satisfies a regex","topics":["find_first_regex_line"]},{"page":"find_first_xml_opening_tag_line","title":"Find the line number of the first section's opening tag","topics":["find_first_xml_opening_tag_line"]},{"page":"find_last_regex_line","title":"Find the index of the last line that matches a regex","topics":["find_last_regex_line"]},{"page":"find_last_xml_closing_tag_line","title":"Find the highest line number of a section's closing tag","topics":["find_last_xml_closing_tag_line"]},{"page":"freq_equilibrium_to_xml","title":"Creates the 'freq_equilibrium' as XML","topics":["freq_equilibrium_to_xml"]},{"page":"freq_param_to_xml","title":"Internal function","topics":["freq_param_to_xml"]},{"page":"gamma_distr_to_xml","title":"Internal function","topics":["gamma_distr_to_xml"]},{"page":"gamma_site_model_to_xml_prior_distr","title":"Internal function.","topics":["gamma_site_model_to_xml_prior_distr"]},{"page":"gamma_site_model_to_xml_state","title":"Converts a gamma site model to XML, used in the 'state' section","topics":["gamma_site_model_to_xml_state"]},{"page":"gamma_site_models_to_xml_prior_distr","title":"Deprecated 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name for a clock model","topics":["get_clock_model_name"]},{"page":"get_clock_model_names","title":"Get the clock model names","topics":["get_clock_model_names"]},{"page":"get_clock_models_ids","title":"Collect the IDs of the list of clock models","topics":["get_clock_models_ids"]},{"page":"get_crown_age","title":"Obtain the crown age of a phylogeny.","topics":["get_crown_age"]},{"page":"get_default_beast_namespace","title":"Get the default `namespace` element value of the `beast` XML tag.","topics":["get_default_beast_namespace"]},{"page":"get_default_beast_namespace_v2_4","title":"Get the default `namespace` element value of the `beast` XML tag for BEAST 2.4","topics":["get_default_beast_namespace_v2_4"]},{"page":"get_default_beast_namespace_v2_6","title":"Get the default `namespace` element value of the `beast` XML tag for BEAST 2.6","topics":["get_default_beast_namespace_v2_6"]},{"page":"get_distr_n_params","title":"Get the number of parameters a distribution uses","topics":["get_distr_n_params"]},{"page":"get_distr_names","title":"Get the distribution names","topics":["get_distr_names"]},{"page":"get_fasta_filename","title":"Get the path of a FASTA file used in testing","topics":["get_fasta_filename"]},{"page":"get_file_base_sans_ext","title":"Get the base of the filename base without extension","topics":["get_file_base_sans_ext"]},{"page":"get_freq_equilibrium_names","title":"Returns valid values for the 'freq_equilibrium' argument","topics":["get_freq_equilibrium_names"]},{"page":"get_gamma_site_model_n_distrs","title":"Get the number of distributions in a gamma site model","topics":["get_gamma_site_model_n_distrs"]},{"page":"get_gamma_site_model_n_params","title":"Get the number of distributions a site model has","topics":["get_gamma_site_model_n_params"]},{"page":"get_has_non_strict_clock_model","title":"Determines if there is at least one non-strict clock model in the list of one or more clock models","topics":["get_has_non_strict_clock_model"]},{"page":"get_inference_model_filenames","title":"Get the filenames stored in an inference model.","topics":["get_inference_model_filenames"]},{"page":"get_log_modes","title":"Get the possible log modes","topics":["get_log_modes"]},{"page":"get_log_sorts","title":"Get the possible log sorts","topics":["get_log_sorts"]},{"page":"get_mcmc_filenames","title":"Get the filenames stored in an MCMC.","topics":["get_mcmc_filenames"]},{"page":"get_n_taxa","title":"Extract the number of taxa from a file","topics":["get_n_taxa"]},{"page":"get_operator_id_pre","title":"Get the prefix of operator IDs","topics":["get_operator_id_pre"]},{"page":"get_param_names","title":"Get the parameter names","topics":["get_param_names"]},{"page":"get_remove_dir_fun","title":"Get a function that, from a filename, returns the part without the directory.","topics":["get_remove_dir_fun"]},{"page":"get_remove_hex_fun","title":"Get a function that removes the hex string from filenames.","topics":["get_remove_hex_fun"]},{"page":"get_replace_dir_fun","title":"Get a function to replace the directory of a filename","topics":["get_replace_dir_fun"]},{"page":"get_site_model_n_distrs","title":"Get the number of distributions a site model has","topics":["get_site_model_n_distrs"]},{"page":"get_site_model_n_params","title":"Get the number of distributions a site model has","topics":["get_site_model_n_params"]},{"page":"get_site_model_names","title":"Get the site models' names","topics":["get_site_model_names"]},{"page":"get_site_models_n_distrs","title":"Get the number of distributions a site model has","topics":["get_site_models_n_distrs"]},{"page":"get_site_models_n_params","title":"Get the number of distributions one or more site models have","topics":["get_site_models_n_params"]},{"page":"get_taxa_names","title":"Extract the names of taxa from a file","topics":["get_taxa_names"]},{"page":"get_tree_prior_n_distrs","title":"Get the number of distributions a tree prior has","topics":["get_tree_prior_n_distrs"]},{"page":"get_tree_prior_n_params","title":"Get the number of parameters a tree prior has","topics":["get_tree_prior_n_params"]},{"page":"get_tree_prior_names","title":"Get the tree prior names","topics":["get_tree_prior_names"]},{"page":"get_tree_priors_n_distrs","title":"Get the number of distributions a tree prior has","topics":["get_tree_priors_n_distrs"]},{"page":"get_tree_priors_n_params","title":"Get the number of parameters a list of tree priors has","topics":["get_tree_priors_n_params"]},{"page":"get_xml_closing_tag","title":"Get the XML closing tag","topics":["get_xml_closing_tag"]},{"page":"get_xml_opening_tag","title":"Get the XML opening tag","topics":["get_xml_opening_tag"]},{"page":"gtr_site_model_to_xml_prior_distr","title":"Internal function","topics":["gtr_site_model_to_xml_prior_distr"]},{"page":"gtr_site_model_to_xml_state","title":"Converts a site model to XML, used in the 'state' 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If the text is only whitespace, leave it as such","topics":["indent"]},{"page":"init_bd_tree_prior","title":"Initializes a Birth-Death tree prior","topics":["init_bd_tree_prior"]},{"page":"init_beta_distr","title":"Initializes a beta distribution","topics":["init_beta_distr"]},{"page":"init_ccp_tree_prior","title":"Initializes a Coalescent Constant Population tree prior","topics":["init_ccp_tree_prior"]},{"page":"init_cep_tree_prior","title":"Initializes a Coalescent Exponential Population tree prior","topics":["init_cep_tree_prior"]},{"page":"init_clock_models","title":"Initializes all clock models","topics":["init_clock_models"]},{"page":"init_distr","title":"Initializes a distribution","topics":["init_distr"]},{"page":"init_exp_distr","title":"Initializes an exponential distribution","topics":["init_exp_distr"]},{"page":"init_gamma_distr","title":"Initializes a gamma distribution","topics":["init_gamma_distr"]},{"page":"init_gamma_site_model","title":"Initializes a gamma site 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'create_beta_distr'","topics":["is_beta_distr"]},{"page":"is_beta_param","title":"Determine if the object is a valid beta parameter","topics":["is_beta_param"]},{"page":"is_cbs_tree_prior","title":"Determine if the object is a valid constant coalescent Bayesian skyline prior","topics":["is_cbs_tree_prior"]},{"page":"is_ccp_tree_prior","title":"Determine if the object is a valid constant coalescence population tree prior","topics":["is_ccp_tree_prior"]},{"page":"is_cep_tree_prior","title":"Determine if the object is a valid coalescent exponential population tree prior","topics":["is_cep_tree_prior"]},{"page":"is_clock_model","title":"Determine if the object is a valid clock_model","topics":["is_clock_model"]},{"page":"is_clock_model_name","title":"Determines if the name is a valid clock model name","topics":["is_clock_model_name"]},{"page":"is_clock_rate_param","title":"Determine if the object is a valid clock_rate 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'create_beta_distr'","topics":["is_init_beta_distr"]},{"page":"is_init_cbs_tree_prior","title":"Determine if x is an initialized Coalescent Bayesian Skyline tree_prior object","topics":["is_init_cbs_tree_prior"]},{"page":"is_init_ccp_tree_prior","title":"Determine if x is an initialized Coalescent Constant Population tree_prior object","topics":["is_init_ccp_tree_prior"]},{"page":"is_init_cep_tree_prior","title":"Determine if x is an initialized Coalescent Exponential Population tree_prior object","topics":["is_init_cep_tree_prior"]},{"page":"is_init_clock_model","title":"Determine if x is an initialized clock_model object, as created by 'create_clock_model'","topics":["is_init_clock_model"]},{"page":"is_init_distr","title":"Determine if x is an initialized distribution object as created by 'create_distr'","topics":["is_init_distr"]},{"page":"is_init_exp_distr","title":"Determine if x is an initialized exponential distribution object as created by 'create_exp_distr'","topics":["is_init_exp_distr"]},{"page":"is_init_gamma_distr","title":"Determine if x is an initialized gamma distribution object","topics":["is_init_gamma_distr"]},{"page":"is_init_gamma_site_model","title":"Determine if x is an initialized gamma site model, as created by 'create_gamma_site_model'","topics":["is_init_gamma_site_model"]},{"page":"is_init_gtr_site_model","title":"Determine if x is an initialized GTR site model as created by 'create_gtr_site_model'","topics":["is_init_gtr_site_model"]},{"page":"is_init_hky_site_model","title":"Determine if x is an initialized HKY site model as created by 'create_hky_site_model'","topics":["is_init_hky_site_model"]},{"page":"is_init_inv_gamma_distr","title":"Determine if x is an initialized inverse-gamma distribution as created by 'create_inv_gamma_distr'","topics":["is_init_inv_gamma_distr"]},{"page":"is_init_jc69_site_model","title":"Determine if x is an initialized JC69 site model as created by 'create_jc69_site_model'","topics":["is_init_jc69_site_model"]},{"page":"is_init_laplace_distr","title":"Determine if x is an initialized Laplace distribution as created by 'create_laplace_distr'","topics":["is_init_laplace_distr"]},{"page":"is_init_log_normal_distr","title":"Determine if x is an initialized log_normal distribution object as created by 'create_log_normal_distr'","topics":["is_init_log_normal_distr"]},{"page":"is_init_mrca_prior","title":"Determine if x is an initialized MRCA prior","topics":["is_init_mrca_prior"]},{"page":"is_init_normal_distr","title":"Determine if x is an initialized normal distribution object as created by 'create_normal_distr'","topics":["is_init_normal_distr"]},{"page":"is_init_one_div_x_distr","title":"Determine if x is an initialized one_div_x distribution object as created by 'create_one_div_x_distr'","topics":["is_init_one_div_x_distr"]},{"page":"is_init_param","title":"Determine if x is an initialized parameter, as created by create_param","topics":["is_init_param"]},{"page":"is_init_poisson_distr","title":"Determine if x is an initialized Poisson distribution object as created by 'create_poisson_distr'","topics":["is_init_poisson_distr"]},{"page":"is_init_rln_clock_model","title":"Determine if x is an initialized relaxed log-normal clock_model object","topics":["is_init_rln_clock_model"]},{"page":"is_init_site_model","title":"Determine if x is an initialized site model, as created by 'create_site_model'","topics":["is_init_site_model"]},{"page":"is_init_strict_clock_model","title":"Determine if x is an initialized strict clock_model object","topics":["is_init_strict_clock_model"]},{"page":"is_init_tn93_site_model","title":"Determine if x is an initialized tn93 site model as created by 'create_tn93_site_model'","topics":["is_init_tn93_site_model"]},{"page":"is_init_tree_prior","title":"Determine if x is an initialized tree_prior 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parameter","topics":["is_kappa_param"]},{"page":"is_lambda_param","title":"Determine if the object is a valid lambda parameter","topics":["is_lambda_param"]},{"page":"is_laplace_distr","title":"Determine if the object is a valid Laplace distribution, as created by 'create_laplace_distr'","topics":["is_laplace_distr"]},{"page":"is_log_normal_distr","title":"Determine if the object is a valid log-normal distribution, as created by 'create_log_normal_distr'","topics":["is_log_normal_distr"]},{"page":"is_m_param","title":"Determine if the object is a valid m parameter","topics":["is_m_param"]},{"page":"is_mcmc","title":"Determine if the object is a valid MCMC","topics":["is_mcmc"]},{"page":"is_mcmc_nested_sampling","title":"Determine if the object is a valid Nested-Sampling MCMC, as used in [1]","topics":["is_mcmc_nested_sampling","is_nested_sampling_mcmc"]},{"page":"is_mean_param","title":"Determine if the object is a valid mean parameter","topics":["is_mean_param"]},{"page":"is_mrca_align_id_in_fasta","title":"Determine if an MRCA prior's alignment IDs is present in the FASTA file","topics":["is_mrca_align_id_in_fasta"]},{"page":"is_mrca_align_ids_in_fastas","title":"Determine if an MRCA prior's alignment IDs are present in the FASTA files","topics":["is_mrca_align_ids_in_fastas"]},{"page":"is_mrca_prior","title":"Determine of the object is an empty ('NA') or valid MRCA prior.","topics":["is_mrca_prior"]},{"page":"is_mrca_prior_with_distr","title":"See if x is one MRCA prior with a distribution","topics":["is_mrca_prior_with_distr"]},{"page":"is_mu_param","title":"Determine if the object is a valid mu parameter","topics":["is_mu_param"]},{"page":"is_normal_distr","title":"Determine if the object is a valid normal distribution as created by 'create_normal_distr'","topics":["is_normal_distr"]},{"page":"is_on_appveyor","title":"Determines if the environment is 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number","topics":["is_one_int"]},{"page":"is_one_na","title":"Determines if x is one NA","topics":["is_one_na"]},{"page":"is_one_string","title":"Determines if the argument is one string","topics":["is_one_string"]},{"page":"is_one_string_that_is_a_number","title":"General function to create a distribution.","topics":["is_one_string_that_is_a_number"]},{"page":"is_param","title":"Determine if the object is a valid parameter","topics":["is_param"]},{"page":"is_param_name","title":"Determines if the name is a valid parameter name","topics":["is_param_name"]},{"page":"is_phylo","title":"Checks if the input is a phylogeny","topics":["is_phylo"]},{"page":"is_poisson_distr","title":"Determine if the object is a valid Poisson distribution as created by 'create_poisson_distr'","topics":["is_poisson_distr"]},{"page":"is_rate_ac_param","title":"Determine if the object is a valid 'rate AC' parameter","topics":["is_rate_ac_param"]},{"page":"is_rate_ag_param","title":"Determine if the object is a 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is installed properly.","topics":["check_beast2"]},{"page":"check_beast2_options","title":"Check if the 'beast2_options' is a valid BEAST2 options object.","topics":["check_beast2_options"]},{"page":"check_beast2_options_data_types","title":"Check if the 'beast2_options', which is a list, has all elements of the right data types","topics":["check_beast2_options_data_types"]},{"page":"check_beast2_options_do_not_overwrite_existing_files","title":"Internal function","topics":["check_beast2_options_do_not_overwrite_existing_files"]},{"page":"check_beast2_options_filenames_differ","title":"Check if the filenames in 'beast2_options' differ","topics":["check_beast2_options_filenames_differ"]},{"page":"check_beast2_options_names","title":"Check if the 'beast2_options', which is a list, has all the elements needed.","topics":["check_beast2_options_names"]},{"page":"check_beast2_optionses","title":"Check if the 'beast2_options' is a valid BEAST2 options 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Will stop if there is a problem with the BEAST2 '.jar' path.","topics":["check_beast2_path"]},{"page":"check_can_create_dir_for_state_output_file","title":"Internal function","topics":["check_can_create_dir_for_state_output_file"]},{"page":"check_can_create_file","title":"Internal function","topics":["check_can_create_file"]},{"page":"check_can_create_screenlog_file","title":"Internal function","topics":["check_can_create_screenlog_file"]},{"page":"check_can_create_state_output_file","title":"Internal function","topics":["check_can_create_state_output_file"]},{"page":"check_can_create_tracelog_file","title":"Internal function to check if the MCMC's tracelog file can be created.","topics":["check_can_create_tracelog_file"]},{"page":"check_can_create_treelog_file","title":"Internal function","topics":["check_can_create_treelog_file"]},{"page":"check_empty_beastier_folder","title":"Check there are no files in the default beastier folder","topics":["check_empty_beastier_folder"]},{"page":"check_empty_beaustier_folders","title":"Check there are no files in the default `beautier` and `beastier` folders","topics":["check_empty_beaustier_folders"]},{"page":"check_input_filename","title":"Checks the input filename. 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librdf_statement.","topics":["librdf_free_statement"]},{"page":"librdf_free_storage","title":"Destructor - destroy a librdf_storage object.","topics":["librdf_free_storage"]},{"page":"librdf_free_stream","title":"Destructor - destroy an libdf_stream object.","topics":["librdf_free_stream"]},{"page":"librdf_free_uri","title":"Destructor - destroy a librdf_uri object.","topics":["librdf_free_uri"]},{"page":"librdf_free_world","title":"Terminate the library and frees all allocated resources.","topics":["librdf_free_world"]},{"page":"librdf_hash_to_string","title":"Format the hash as a string, suitable for parsing by librdf_hash_from_string.","topics":["librdf_hash_to_string"]},{"page":"librdf_internal_test_error","title":"For internal testing, not part of public API","topics":["librdf_internal_test_error"]},{"page":"librdf_internal_test_warning","title":"For internal testing, not part of public API","topics":["librdf_internal_test_warning"]},{"page":"librdf_iterator_end","title":"Test if the iterator has finished.","topics":["librdf_iterator_end"]},{"page":"librdf_iterator_get_context","title":"Get the context of the current object on the iterator.","topics":["librdf_iterator_get_context"]},{"page":"librdf_iterator_get_object","title":"Get the current object from the iterator.","topics":["librdf_iterator_get_object"]},{"page":"librdf_iterator_next","title":"Move to the next iterator element.","topics":["librdf_iterator_next"]},{"page":"librdf_log_message_code","title":"Retrieve error code from log message.","topics":["librdf_log_message_code"]},{"page":"librdf_log_message_facility","title":"Retrieve facility that generated the message.","topics":["librdf_log_message_facility"]},{"page":"librdf_log_message_level","title":"Retrieve severity of log message.","topics":["librdf_log_message_level"]},{"page":"librdf_log_message_locator","title":"Retrieve locator of log entry.","topics":["librdf_log_message_locator"]},{"page":"librdf_log_message_message","title":"Retrieve text message from log entry.","topics":["librdf_log_message_message"]},{"page":"librdf_model_add","title":"Create and add a new statement about a resource to the model.","topics":["librdf_model_add"]},{"page":"librdf_model_add_statement","title":"Add a statement to the model.","topics":["librdf_model_add_statement"]},{"page":"librdf_model_add_statements","title":"Add a stream of statements to the model.","topics":["librdf_model_add_statements"]},{"page":"librdf_model_add_string_literal_statement","title":"Create and add a new statement about a literal to the model.","topics":["librdf_model_add_string_literal_statement"]},{"page":"librdf_model_add_typed_literal_statement","title":"Create and add a new statement about a typed literal to the model.","topics":["librdf_model_add_typed_literal_statement"]},{"page":"librdf_model_as_stream","title":"List the model contents as a stream of statements.","topics":["librdf_model_as_stream"]},{"page":"librdf_model_contains_context","title":"Check for a context in the model.","topics":["librdf_model_contains_context"]},{"page":"librdf_model_contains_statement","title":"Check for a statement in the model.","topics":["librdf_model_contains_statement"]},{"page":"librdf_model_context_add_statement","title":"Add a statement to a model with a context.","topics":["librdf_model_context_add_statement"]},{"page":"librdf_model_context_add_statements","title":"Add statements to a model with a context.","topics":["librdf_model_context_add_statements"]},{"page":"librdf_model_context_as_stream","title":"List all statements in a model context.","topics":["librdf_model_context_as_stream"]},{"page":"librdf_model_context_remove_statement","title":"Remove a statement from a model in a context.","topics":["librdf_model_context_remove_statement"]},{"page":"librdf_model_context_remove_statements","title":"Remove statements from a model with the given context.","topics":["librdf_model_context_remove_statements"]},{"page":"librdf_model_find_statements","title":"Find matching statements in the model.","topics":["librdf_model_find_statements"]},{"page":"librdf_model_find_statements_in_context","title":"Search the model for matching statements in a given context.","topics":["librdf_model_find_statements_in_context"]},{"page":"librdf_model_get_arc","title":"Return one arc (predicate) of an arc in an RDF graph given source (subject) and target (object).","topics":["librdf_model_get_arc"]},{"page":"librdf_model_get_arcs","title":"Return the arcs (predicates) of an arc in an RDF graph given source (subject) and target (object).","topics":["librdf_model_get_arcs"]},{"page":"librdf_model_get_arcs_in","title":"Return the properties pointing to the given resource.","topics":["librdf_model_get_arcs_in"]},{"page":"librdf_model_get_arcs_out","title":"Return the properties pointing from the given resource.","topics":["librdf_model_get_arcs_out"]},{"page":"librdf_model_get_contexts","title":"Return the list of contexts in the graph.","topics":["librdf_model_get_contexts"]},{"page":"librdf_model_get_feature","title":"Get the value of a graph feature .","topics":["librdf_model_get_feature"]},{"page":"librdf_model_get_source","title":"Return one source (subject) of arc in an RDF graph given arc (predicate) and target (object).","topics":["librdf_model_get_source"]},{"page":"librdf_model_get_sources","title":"Return the sources (subjects) of arc in an RDF graph given arc (predicate) and target (object).","topics":["librdf_model_get_sources"]},{"page":"librdf_model_get_target","title":"Return one target (object) of an arc in an RDF graph given source (subject) and arc (predicate).","topics":["librdf_model_get_target"]},{"page":"librdf_model_get_targets","title":"Return the targets (objects) of an arc in an RDF graph given source (subject) and arc (predicate).","topics":["librdf_model_get_targets"]},{"page":"librdf_model_has_arc_in","title":"Check if a node has a given property pointing to it.","topics":["librdf_model_has_arc_in"]},{"page":"librdf_model_has_arc_out","title":"Check if a node has a given property pointing from it.","topics":["librdf_model_has_arc_out"]},{"page":"librdf_model_load","title":"Load content from a URI into the model.","topics":["librdf_model_load"]},{"page":"librdf_model_query_execute","title":"Execute a query against the model.","topics":["librdf_model_query_execute"]},{"page":"librdf_model_remove_statement","title":"Remove a known statement from the model.","topics":["librdf_model_remove_statement"]},{"page":"librdf_model_set_feature","title":"Set the value of a graph feature.","topics":["librdf_model_set_feature"]},{"page":"librdf_model_size","title":"Get the number of statements in the model.","topics":["librdf_model_size"]},{"page":"librdf_model_sync","title":"Synchronise the model to the model implementation.","topics":["librdf_model_sync"]},{"page":"librdf_model_to_string","title":"Write serialized model to a string.","topics":["librdf_model_to_string"]},{"page":"librdf_model_transaction_commit","title":"Commit a transaction.","topics":["librdf_model_transaction_commit"]},{"page":"librdf_model_transaction_rollback","title":"Rollback a transaction.","topics":["librdf_model_transaction_rollback"]},{"page":"librdf_model_transaction_start","title":"Start a transaction","topics":["librdf_model_transaction_start"]},{"page":"librdf_new_digest","title":"Constructor - create a new librdf_digest object.","topics":["librdf_new_digest"]},{"page":"librdf_new_hash","title":"Constructor - create a new librdf_hash object.","topics":["librdf_new_hash"]},{"page":"librdf_new_hash_from_array_of_strings","title":"Constructor - create a new librdf_hash object from an array of strings.","topics":["librdf_new_hash_from_array_of_strings"]},{"page":"librdf_new_hash_from_string","title":"Constructor - create a new librdf_hash object from a string.","topics":["librdf_new_hash_from_string"]},{"page":"librdf_new_model","title":"Constructor - create a new storage librdf_model object.","topics":["librdf_new_model"]},{"page":"librdf_new_model_from_model","title":"Copy constructor - create a new librdf_model from an existing one.","topics":["librdf_new_model_from_model"]},{"page":"librdf_new_model_with_options","title":"Constructor - Create a new librdf_model with storage.","topics":["librdf_new_model_with_options"]},{"page":"librdf_new_node","title":"Constructor - create a new librdf_node object with a private identifier.","topics":["librdf_new_node"]},{"page":"librdf_new_node_from_blank_identifier","title":"Constructor - create a new blank node librdf_node object from a blank node identifier.","topics":["librdf_new_node_from_blank_identifier"]},{"page":"librdf_new_node_from_literal","title":"Constructor - create a new literal librdf_node object.","topics":["librdf_new_node_from_literal"]},{"page":"librdf_new_node_from_node","title":"Copy constructor - create a new librdf_node object from an existing librdf_node object.","topics":["librdf_new_node_from_node"]},{"page":"librdf_new_node_from_normalised_uri_string","title":"Constructor - create a new librdf_node object from a UTF-8 encoded URI string normalised to a new base URI.","topics":["librdf_new_node_from_normalised_uri_string"]},{"page":"librdf_new_node_from_typed_literal","title":"Constructor - create a new typed literal librdf_node object.","topics":["librdf_new_node_from_typed_literal"]},{"page":"librdf_new_node_from_uri","title":"Constructor - create a new resource librdf_node object with a given URI.","topics":["librdf_new_node_from_uri"]},{"page":"librdf_new_node_from_uri_local_name","title":"Constructor - create a new resource librdf_node object with a given URI and local name.","topics":["librdf_new_node_from_uri_local_name"]},{"page":"librdf_new_node_from_uri_string","title":"Constructor - create a new librdf_node object from a URI string.","topics":["librdf_new_node_from_uri_string"]},{"page":"librdf_new_parser","title":"Constructor - create a new librdf_parser object.","topics":["librdf_new_parser"]},{"page":"librdf_new_query","title":"Constructor - create a new librdf_query object.","topics":["librdf_new_query"]},{"page":"librdf_new_query_from_query","title":"Copy constructor - create a new librdf_query object from an existing one","topics":["librdf_new_query_from_query"]},{"page":"librdf_new_serializer","title":"Constructor - create a new librdf_serializer object.","topics":["librdf_new_serializer"]},{"page":"librdf_new_statement","title":"Constructor - create a new empty librdf_statement.","topics":["librdf_new_statement"]},{"page":"librdf_new_statement_from_nodes","title":"Constructor - create a new librdf_statement from existing librdf_node objects.","topics":["librdf_new_statement_from_nodes"]},{"page":"librdf_new_statement_from_statement","title":"Copy constructor - create a new librdf_statement from an existing librdf_statement. Creates a deep copy - changes to original statement nodes are not reflected in the copy.","topics":["librdf_new_statement_from_statement"]},{"page":"librdf_new_storage","title":"Constructor - create a new librdf_storage object.","topics":["librdf_new_storage"]},{"page":"librdf_new_storage_from_storage","title":"Copy constructor - create a new librdf_storage object from an existing one","topics":["librdf_new_storage_from_storage"]},{"page":"librdf_new_uri","title":"Constructor - create a new librdf_uri object from a URI string.","topics":["librdf_new_uri"]},{"page":"librdf_new_uri_from_filename","title":"Constructor - create a new librdf_uri object from a filename.","topics":["librdf_new_uri_from_filename"]},{"page":"librdf_new_uri_from_uri","title":"Copy constructor - create a new librdf_uri object from an existing librdf_uri object.","topics":["librdf_new_uri_from_uri"]},{"page":"librdf_new_world","title":"Create a new Redland execution environment.","topics":["librdf_new_world"]},{"page":"librdf_node_equals","title":"Compare two librdf_node objects for equality.","topics":["librdf_node_equals"]},{"page":"librdf_node_get_blank_identifier","title":"Get the blank node identifier as a UTF-8 encoded string.","topics":["librdf_node_get_blank_identifier"]},{"page":"librdf_node_get_li_ordinal","title":"Get the node li object ordinal value.","topics":["librdf_node_get_li_ordinal"]},{"page":"librdf_node_get_literal_value","title":"Get the literal value of the node as a UTF-8 encoded string.","topics":["librdf_node_get_literal_value"]},{"page":"librdf_node_get_literal_value_as_latin1","title":"Get the string literal value of the node as ISO Latin-1.","topics":["librdf_node_get_literal_value_as_latin1"]},{"page":"librdf_node_get_literal_value_datatype_uri","title":"Get the typed literal datatype URI of the literal node.","topics":["librdf_node_get_literal_value_datatype_uri"]},{"page":"librdf_node_get_literal_value_is_wf_xml","title":"Get the XML well-formness property of the node.","topics":["librdf_node_get_literal_value_is_wf_xml"]},{"page":"librdf_node_get_literal_value_language","title":"Get the XML language of the node.","topics":["librdf_node_get_literal_value_language"]},{"page":"librdf_node_get_type","title":"Get the type of the node.","topics":["librdf_node_get_type"]},{"page":"librdf_node_get_uri","title":"Get the URI for a node object.","topics":["librdf_node_get_uri"]},{"page":"librdf_node_is_blank","title":"Check node is a blank nodeID.","topics":["librdf_node_is_blank"]},{"page":"librdf_node_is_literal","title":"Check node is a literal.","topics":["librdf_node_is_literal"]},{"page":"librdf_node_is_resource","title":"Check node is a resource.","topics":["librdf_node_is_resource"]},{"page":"librdf_parser_check_name","title":"Check if a parser name is known","topics":["librdf_parser_check_name"]},{"page":"librdf_parser_get_accept_header","title":"Get an HTTP Accept value for the parser.","topics":["librdf_parser_get_accept_header"]},{"page":"librdf_parser_get_feature","title":"Get the value of a parser feature.","topics":["librdf_parser_get_feature"]},{"page":"librdf_parser_get_namespaces_seen_count","title":"Get the number of namespaces seen during parsing","topics":["librdf_parser_get_namespaces_seen_count"]},{"page":"librdf_parser_get_namespaces_seen_prefix","title":"Get the prefix of namespaces seen during parsing","topics":["librdf_parser_get_namespaces_seen_prefix"]},{"page":"librdf_parser_get_namespaces_seen_uri","title":"Get the uri of namespaces seen during parsing","topics":["librdf_parser_get_namespaces_seen_uri"]},{"page":"librdf_parser_guess_name2","title":"Get a parser name for content with type or identifier","topics":["librdf_parser_guess_name2"]},{"page":"librdf_parser_parse_as_stream","title":"Parse a URI to a librdf_stream of statements.","topics":["librdf_parser_parse_as_stream"]},{"page":"librdf_parser_parse_counted_string_as_stream","title":"Parse a counted string of content to a librdf_stream of statements.","topics":["librdf_parser_parse_counted_string_as_stream"]},{"page":"librdf_parser_parse_counted_string_into_model","title":"Parse a counted string of content into an librdf_model.","topics":["librdf_parser_parse_counted_string_into_model"]},{"page":"librdf_parser_parse_into_model","title":"Parse a URI of content into an librdf_model.","topics":["librdf_parser_parse_into_model"]},{"page":"librdf_parser_parse_string_as_stream","title":"Parse a string of content to a librdf_stream of statements.","topics":["librdf_parser_parse_string_as_stream"]},{"page":"librdf_parser_parse_string_into_model","title":"Parse a string of content into an librdf_model.","topics":["librdf_parser_parse_string_into_model"]},{"page":"librdf_parser_set_feature","title":"Set the value of a parser feature.","topics":["librdf_parser_set_feature"]},{"page":"librdf_query_execute","title":"Run the query on a model.","topics":["librdf_query_execute"]},{"page":"librdf_query_get_limit","title":"Get the query-specified limit on results.","topics":["librdf_query_get_limit"]},{"page":"librdf_query_get_offset","title":"Get the query-specified offset on results.","topics":["librdf_query_get_offset"]},{"page":"librdf_query_results_as_stream","title":"Get a query result as an RDF graph in librdf_stream form","topics":["librdf_query_results_as_stream"]},{"page":"librdf_query_results_finished","title":"Find out if binding results are exhausted.","topics":["librdf_query_results_finished"]},{"page":"librdf_query_results_get_binding_name","title":"Get binding name for the current result.","topics":["librdf_query_results_get_binding_name"]},{"page":"librdf_query_results_get_binding_value","title":"Get one binding value for the current result.","topics":["librdf_query_results_get_binding_value"]},{"page":"librdf_query_results_get_binding_value_by_name","title":"Get one binding value for a given name in the current result.","topics":["librdf_query_results_get_binding_value_by_name"]},{"page":"librdf_query_results_get_bindings_count","title":"Get the number of bound variables in the result.","topics":["librdf_query_results_get_bindings_count"]},{"page":"librdf_query_results_get_boolean","title":"Get boolean query result.","topics":["librdf_query_results_get_boolean"]},{"page":"librdf_query_results_get_count","title":"Get number of bindings so far.","topics":["librdf_query_results_get_count"]},{"page":"librdf_query_results_is_bindings","title":"Test if librdf_query_results is variable bindings format.","topics":["librdf_query_results_is_bindings"]},{"page":"librdf_query_results_is_boolean","title":"Test if librdf_query_results is boolean format.","topics":["librdf_query_results_is_boolean"]},{"page":"librdf_query_results_is_graph","title":"Test if librdf_query_results is RDF graph format.","topics":["librdf_query_results_is_graph"]},{"page":"librdf_query_results_is_syntax","title":"Test if librdf_query_results is a syntax.","topics":["librdf_query_results_is_syntax"]},{"page":"librdf_query_results_next","title":"Move to the next result.","topics":["librdf_query_results_next"]},{"page":"librdf_query_results_to_file2","title":"Write a query results to a file.","topics":["librdf_query_results_to_file2"]},{"page":"librdf_query_results_to_string2","title":"Turn a query results into a string.","topics":["librdf_query_results_to_string2"]},{"page":"librdf_query_set_limit","title":"Set the query-specified limit on results.","topics":["librdf_query_set_limit"]},{"page":"librdf_query_set_offset","title":"Set the query-specified offset on results.","topics":["librdf_query_set_offset"]},{"page":"librdf_serializer_check_name","title":"Check if a serializer name is known","topics":["librdf_serializer_check_name"]},{"page":"librdf_serializer_get_feature","title":"Get the value of a serializer feature.","topics":["librdf_serializer_get_feature"]},{"page":"librdf_serializer_serialize_model_to_file","title":"Write a serialized librdf_model to a file.","topics":["librdf_serializer_serialize_model_to_file"]},{"page":"librdf_serializer_serialize_model_to_string","title":"Write a serialized librdf_model to a string. The returned string must be freed by the caller using librdf_free_memory().","topics":["librdf_serializer_serialize_model_to_string"]},{"page":"librdf_serializer_serialize_stream_to_file","title":"Write a librdf_stream to a file.","topics":["librdf_serializer_serialize_stream_to_file"]},{"page":"librdf_serializer_serialize_stream_to_string","title":"Write a librdf_stream to a string.","topics":["librdf_serializer_serialize_stream_to_string"]},{"page":"librdf_serializer_set_feature","title":"Set the value of a serializer feature.","topics":["librdf_serializer_set_feature"]},{"page":"librdf_serializer_set_namespace","title":"Set a namespace URI/prefix mapping.","topics":["librdf_serializer_set_namespace"]},{"page":"librdf_short_copyright_string","title":"Short copyright string (one line).","topics":["librdf_short_copyright_string"]},{"page":"librdf_short_copyright_string_get","title":"Return Redland librdf copyright string","topics":["librdf_short_copyright_string_get"]},{"page":"librdf_statement_equals","title":"Check if two statements are equal.","topics":["librdf_statement_equals"]},{"page":"librdf_statement_get_object","title":"Get the statement object.","topics":["librdf_statement_get_object"]},{"page":"librdf_statement_get_predicate","title":"Get the statement predicate.","topics":["librdf_statement_get_predicate"]},{"page":"librdf_statement_get_subject","title":"Get the statement subject.","topics":["librdf_statement_get_subject"]},{"page":"librdf_statement_is_complete","title":"Check if statement is a complete and legal RDF triple.","topics":["librdf_statement_is_complete"]},{"page":"librdf_statement_match","title":"Match a statement against a 'partial' statement.","topics":["librdf_statement_match"]},{"page":"librdf_statement_set_object","title":"Set the statement object.","topics":["librdf_statement_set_object"]},{"page":"librdf_statement_set_predicate","title":"Set the statement predicate.","topics":["librdf_statement_set_predicate"]},{"page":"librdf_statement_set_subject","title":"Set the statement subject.","topics":["librdf_statement_set_subject"]},{"page":"librdf_stream_end","title":"Test if the stream has ended.","topics":["librdf_stream_end"]},{"page":"librdf_stream_get_object","title":"Get the current librdf_statement in the stream.","topics":["librdf_stream_get_object"]},{"page":"librdf_stream_next","title":"Move to the next librdf_statement in the stream.","topics":["librdf_stream_next"]},{"page":"librdf_uri_compare","title":"Compare two librdf_uri objects lexicographically.","topics":["librdf_uri_compare"]},{"page":"librdf_uri_equals","title":"Compare two librdf_uri objects for equality.","topics":["librdf_uri_equals"]},{"page":"librdf_uri_to_string","title":"Format the URI as a string.","topics":["librdf_uri_to_string"]},{"page":"librdf_version_decimal","title":"Library full version as a decimal integer.","topics":["librdf_version_decimal"]},{"page":"librdf_version_decimal_get","title":"Return Redland librdf copyright","topics":["librdf_version_decimal_get"]},{"page":"librdf_version_major","title":"Library major version number as a decimal integer.","topics":["librdf_version_major"]},{"page":"librdf_version_major_get","title":"Return the Redland librdf major version number","topics":["librdf_version_major_get"]},{"page":"librdf_version_minor","title":"Library minor version number as a decimal integer.","topics":["librdf_version_minor"]},{"page":"librdf_version_minor_get","title":"Return the Redland librdf minor version number","topics":["librdf_version_minor_get"]},{"page":"librdf_version_release","title":"Library release version number as a decimal integer.","topics":["librdf_version_release"]},{"page":"librdf_version_release_get","title":"Return the Redland librdf release version 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