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It is intended to inherit is parameters' documentation.","topics":["default_params_doc"]},{"page":"do_minimal_run","title":"Do a minimal BEAST2 run","topics":["do_minimal_run"]},{"page":"extract_screenlog_filename_from_beast2_input_file","title":"Internal function to extract the screenlog filename for a BEAST2 input file","topics":["extract_screenlog_filename_from_beast2_input_file"]},{"page":"extract_tracelog_filename_from_beast2_input_file","title":"Internal function to extract the tracelog filename for a BEAST2 input file","topics":["extract_tracelog_filename_from_beast2_input_file"]},{"page":"extract_treelog_filename_from_beast2_input_file","title":"Internal function to extract the treelog filename for a BEAST2 input file","topics":["extract_treelog_filename_from_beast2_input_file"]},{"page":"get_alignment_ids_from_xml_filename","title":"Get the alignment ID from a file with one alignment","topics":["get_alignment_ids_from_xml_filename"]},{"page":"get_beast2_example_filename","title":"Get the full path of a BEAST2 example file","topics":["get_beast2_example_filename"]},{"page":"get_beast2_example_filenames","title":"Get a list with the full paths of all BEAST2 example filenames","topics":["get_beast2_example_filenames"]},{"page":"get_beast2_main_class_name","title":"Get the BEAST2 main class name.","topics":["get_beast2_main_class_name"]},{"page":"get_beast2_options_filenames","title":"Extract the filenames from a `beast2_options`","topics":["get_beast2_options_filenames"]},{"page":"get_beast2_version","title":"Get the BEAST2 version","topics":["get_beast2_version"]},{"page":"get_beastier_folder","title":"Get the path to the beastier temporary files folder","topics":["get_beastier_folder"]},{"page":"get_beastier_path","title":"Get the full path of a file in the 'inst/extdata' folder","topics":["get_beastier_path"]},{"page":"get_beastier_paths","title":"Get the full paths of files in the 'inst/extdata' folder","topics":["get_beastier_paths"]},{"page":"get_beastier_tempfilename","title":"Get a temporary filename","topics":["get_beastier_tempfilename"]},{"page":"get_default_beast2_bin_path","title":"Get the default BEAST2 binary file ('beast', that is) path","topics":["get_default_beast2_bin_path"]},{"page":"get_default_beast2_download_url","title":"Get the default BEAST2 download URL, which depends on the operating system","topics":["get_default_beast2_download_url"]},{"page":"get_default_beast2_download_url_linux","title":"Get the BEAST2 download URL for Linux","topics":["get_default_beast2_download_url_linux"]},{"page":"get_default_beast2_download_url_win","title":"Get the BEAST2 download URL for Windows","topics":["get_default_beast2_download_url_win"]},{"page":"get_default_beast2_folder","title":"Get the path to the folder where this package installs BEAST2 by default","topics":["get_default_beast2_folder"]},{"page":"get_default_beast2_jar_path","title":"Get the default BEAST2 jar file's path","topics":["get_default_beast2_jar_path"]},{"page":"get_default_beast2_path","title":"Get the default BEAST2 path","topics":["get_default_beast2_path"]},{"page":"get_default_beast2_version","title":"Get the default BEAST2 version that is used by beastier","topics":["get_default_beast2_version"]},{"page":"get_default_java_path","title":"Obtains the default path to the Java executable","topics":["get_default_java_path"]},{"page":"get_duplicate_param_ids","title":"Find duplicate 'RealParameter' IDs","topics":["get_duplicate_param_ids"]},{"page":"get_java_version","title":"Get the Java version","topics":["get_java_version"]},{"page":"get_trees_filenames","title":"Get the .trees filenames that BEAST2 will produce","topics":["get_trees_filenames"]},{"page":"gives_beast2_warning","title":"Determines if BEAST2 issues a warning when using the BEAST2 XML input file","topics":["gives_beast2_warning"]},{"page":"has_unique_ids","title":"Determine if the XML text has unique parameter IDs","topics":["has_unique_ids"]},{"page":"install_beast2","title":"Deprecated function to install BEAST2","topics":["install_beast2"]},{"page":"is_alignment","title":"Determines if the input is an alignment of type DNAbin","topics":["is_alignment"]},{"page":"is_beast2_input_file","title":"Is a file a valid BEAST2 input file?","topics":["is_beast2_input_file"]},{"page":"is_beast2_installed","title":"Checks if BEAST2 is installed","topics":["is_beast2_installed"]},{"page":"is_bin_path","title":"Is the path a path to the BEAST2 binary file? Does not check if the file at that path is present","topics":["is_bin_path"]},{"page":"is_jar_path","title":"Is the path a path to the BEAST2 jar file? Does not check if the file at that path is present","topics":["is_jar_path"]},{"page":"is_on_appveyor","title":"Deprecated function, use is_on_appveyor","topics":["is_on_appveyor"]},{"page":"is_on_ci","title":"Deprecated function, use is_on_ci","topics":["is_on_ci"]},{"page":"is_on_travis","title":"Deprecated function, use is_on_travis","topics":["is_on_travis"]},{"page":"is_win_bin_path","title":"Is the path a path to the BEAST2 binary file? 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Although we envisioned git2rdata with a git\nworkflow in mind, you can use it in combination with other\nversion control systems like subversion or mercurial. 3)\ngit2rdata is a useful tool in a reproducible and traceable\nworkflow. vignette(\"workflow\", package = \"git2rdata\") gives a\ntoy example. 4) vignette(\"efficiency\", package = \"git2rdata\")\nprovides some insight into the efficiency of file storage, git\nrepository size and speed for writing and reading.","License":"GPL-3","URL":"https://ropensci.github.io/git2rdata/,\nhttps://github.com/ropensci/git2rdata/,\nhttps://doi.org/10.5281/zenodo.1485309","BugReports":"https://github.com/ropensci/git2rdata/issues","VignetteBuilder":"knitr","Config/checklist/communities":"inbo","Config/checklist/keywords":"git; version control; plain text data","Encoding":"UTF-8","Language":"en-GB","Roxygen":"list(markdown = TRUE)","RoxygenNote":"7.3.2","Collate":"'clean_data_path.R' 'datahash.R' 'display_metadata.R'\n'git2rdata_package.R' 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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 function","topics":["gamma_site_models_to_xml_prior_distr"]},{"page":"get_alignment_id","title":"Conclude the ID from a FASTA filename.","topics":["get_alignment_id"]},{"page":"get_alignment_ids","title":"Get the alignment IDs from one or more files.","topics":["get_alignment_ids"]},{"page":"get_alignment_ids_from_fasta_filenames","title":"Get the alignment ID from one or more FASTA filenames.","topics":["get_alignment_ids_from_fasta_filenames"]},{"page":"get_beautier_folder","title":"Get the path to the beautier temporary files folder","topics":["get_beautier_folder"]},{"page":"get_beautier_path","title":"Get the full path of a file in the 'inst/extdata' folder","topics":["get_beautier_path"]},{"page":"get_beautier_paths","title":"Get the full paths of files in the 'inst/extdata' folder","topics":["get_beautier_paths"]},{"page":"get_beautier_tempfilename","title":"Get a temporary filename","topics":["get_beautier_tempfilename"]},{"page":"get_clock_model_name","title":"Get the BEAUti 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' section","topics":["gtr_site_model_to_xml_state"]},{"page":"has_mrca_prior","title":"Determines if the inference model has an MRCA prior.","topics":["has_mrca_prior"]},{"page":"has_mrca_prior_with_distr","title":"See if the inference model has one MRCA prior with a distribution","topics":["has_mrca_prior_with_distr"]},{"page":"has_rln_clock_model","title":"Determine if the 'inference_model' uses a relaxed log-normal clock model.","topics":["has_rln_clock_model"]},{"page":"has_strict_clock_model","title":"Determine if the 'inference_model' uses a strict clock model.","topics":["has_strict_clock_model"]},{"page":"has_tip_dating","title":"Determine if the 'inference_model' uses tip dating.","topics":["has_tip_dating"]},{"page":"has_xml_closing_tag","title":"Is an XML closing tag with the value of 'section' present among the lines of the text?","topics":["has_xml_closing_tag"]},{"page":"has_xml_opening_tag","title":"Is an XML opening tag with value 'section' present among the lines of the text?","topics":["has_xml_opening_tag"]},{"page":"has_xml_short_closing_tag","title":"Is an XML closing tag with short closing text in one of the lines of the text?","topics":["has_xml_short_closing_tag"]},{"page":"hky_site_model_to_xml_prior_distr","title":"Internal function","topics":["hky_site_model_to_xml_prior_distr"]},{"page":"hky_site_model_to_xml_state","title":"Converts a site model to XML, used in the 'state' section","topics":["hky_site_model_to_xml_state"]},{"page":"indent","title":"Indent text for a certain number of spaces. 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 parameter","topics":["is_clock_rate_param"]},{"page":"is_default_mcmc","title":"Determine if the MCMC is a default MCMC","topics":["is_default_mcmc"]},{"page":"is_distr","title":"Determine if the object is a valid distribution","topics":["is_distr"]},{"page":"is_distr_name","title":"Determines if the name is a valid distribution name","topics":["is_distr_name"]},{"page":"is_exp_distr","title":"Determine if the object is a valid exponential distribution as created by 'create_exp_distr'","topics":["is_exp_distr"]},{"page":"is_freq_equilibrium_name","title":"Checks if 'name' is a valid 'freq_equilibrium' argument value","topics":["is_freq_equilibrium_name"]},{"page":"is_freq_param","title":"Determine if the object is a valid freq parameter","topics":["is_freq_param"]},{"page":"is_gamma_distr","title":"Determine if the object is a valid gamma distribution, as created by 'create_gamma_distr'","topics":["is_gamma_distr"]},{"page":"is_gamma_site_model","title":"Is object x a gamma site model?","topics":["is_gamma_site_model"]},{"page":"is_gtr_site_model","title":"Determine if the object is a valid GTR site model, as created by 'create_gtr_site_model'","topics":["is_gtr_site_model"]},{"page":"is_hky_site_model","title":"Determine if the object is a valid HKY site model, as created by 'create_hky_site_model'","topics":["is_hky_site_model"]},{"page":"is_id","title":"Determine if the object is a valid ID","topics":["is_id"]},{"page":"is_in_patterns","title":"Is there at least one regular expression having a match with the line?","topics":["is_in_patterns"]},{"page":"is_inference_model","title":"Determine if the input is an inference model","topics":["is_inference_model"]},{"page":"is_init_bd_tree_prior","title":"Determine if x is an initialized Birth-Death tree_prior object","topics":["is_init_bd_tree_prior"]},{"page":"is_init_beta_distr","title":"Determine if x is an initialized beta distribution object as created by '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 objects","topics":["is_init_tree_prior"]},{"page":"is_init_uniform_distr","title":"Determine if x is an initialized uniform distribution object as created by 'create_uniform_distr'","topics":["is_init_uniform_distr"]},{"page":"is_init_yule_tree_prior","title":"Determine if x is an initialized Yule tree_prior object","topics":["is_init_yule_tree_prior"]},{"page":"is_inv_gamma_distr","title":"Determine if the object is a valid inverse-gamma distribution as created by 'create_inv_gamma_distr'","topics":["is_inv_gamma_distr"]},{"page":"is_jc69_site_model","title":"Determine if the object is a valid JC69 site model","topics":["is_jc69_site_model"]},{"page":"is_kappa_1_param","title":"Determine if the object is a valid kappa 1 parameter","topics":["is_kappa_1_param"]},{"page":"is_kappa_2_param","title":"Determine if the object is a valid kappa 2 parameter","topics":["is_kappa_2_param"]},{"page":"is_kappa_param","title":"Determine if the object is a valid kappa 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 AppVeyor","topics":["is_on_appveyor"]},{"page":"is_on_ci","title":"Determines if the environment is a continuous integration service","topics":["is_on_ci"]},{"page":"is_on_github_actions","title":"Determines if the environment is GitHub Actions","topics":["is_on_github_actions"]},{"page":"is_on_travis","title":"Determines if the environment is Travis CI","topics":["is_on_travis"]},{"page":"is_one_bool","title":"Check if the argument is one boolean","topics":["is_one_bool"]},{"page":"is_one_div_x_distr","title":"Determine if the object is a valid 1/x distribution, as created by 'create_one_div_x_distr'","topics":["is_one_div_x_distr"]},{"page":"is_one_double","title":"Determines if the argument is a double","topics":["is_one_double"]},{"page":"is_one_empty_string","title":"Determine if an object is one empty string","topics":["is_one_empty_string"]},{"page":"is_one_int","title":"Determines if the argument is a whole 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 valid 'rate AG' parameter","topics":["is_rate_ag_param"]},{"page":"is_rate_at_param","title":"Determine if the object is a valid 'rate AT' parameter","topics":["is_rate_at_param"]},{"page":"is_rate_cg_param","title":"Determine if the object is a valid 'rate CG' parameter","topics":["is_rate_cg_param"]},{"page":"is_rate_ct_param","title":"Determine if the object is a valid 'rate CT' parameter","topics":["is_rate_ct_param"]},{"page":"is_rate_gt_param","title":"Determine if the object is a valid 'rate GT' parameter","topics":["is_rate_gt_param"]},{"page":"is_rln_clock_model","title":"Determine if the object is a valid relaxed log normal clock model","topics":["is_rln_clock_model"]},{"page":"is_s_param","title":"Determine if the object is a valid s parameter","topics":["is_s_param"]},{"page":"is_scale_param","title":"Determine if the object is a valid scale parameter","topics":["is_scale_param"]},{"page":"is_sigma_param","title":"Determine if the object is a valid sigma parameter","topics":["is_sigma_param"]},{"page":"is_site_model","title":"Determine if the object is a valid site_model","topics":["is_site_model"]},{"page":"is_site_model_name","title":"Determines if the name is a valid site_model name","topics":["is_site_model_name"]},{"page":"is_strict_clock_model","title":"Determine if the object is a valid strict clock model, as returned by 'create_strict_clock_model'","topics":["is_strict_clock_model"]},{"page":"is_tn93_site_model","title":"Determine if the object is a valid TN93 site model,","topics":["is_tn93_site_model"]},{"page":"is_tree_prior","title":"Determine if an object is a valid tree prior","topics":["is_tree_prior"]},{"page":"is_tree_prior_name","title":"Determines if the name is a valid tree prior name","topics":["is_tree_prior_name"]},{"page":"is_uniform_distr","title":"Determine if the object is a valid uniform distribution as created by 'create_uniform_distr'","topics":["is_uniform_distr"]},{"page":"is_xml","title":"Checks if the text is a valid XML node, that is, it has a opening and matching closing tag","topics":["is_xml"]},{"page":"is_yule_tree_prior","title":"Determine if the object is a valid Yule tree prior,","topics":["is_yule_tree_prior"]},{"page":"jc69_site_model_to_xml_state","title":"Converts a site model to XML, used in the 'state' section","topics":["jc69_site_model_to_xml_state"]},{"page":"kappa_param_to_xml","title":"Internal function","topics":["kappa_param_to_xml"]},{"page":"m_param_to_xml","title":"Internal function","topics":["m_param_to_xml"]},{"page":"mcmc_to_xml_run","title":"Converts an MCMC object to the run section's XML","topics":["mcmc_to_xml_run"]},{"page":"mcmc_to_xml_run_default","title":"Converts an MCMC object to the run section's XML for a default MCMC","topics":["mcmc_to_xml_run_default"]},{"page":"mcmc_to_xml_run_nested_sampling","title":"Converts an MCMC object to the run section's XML for a Nested-Sampling 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file.","topics":["mrca_priors_to_xml_prior_distr"]},{"page":"no_taxa_to_xml_tree","title":"Internal function","topics":["no_taxa_to_xml_tree"]},{"page":"parameter_to_xml","title":"Internal function","topics":["parameter_to_xml"]},{"page":"parameter_to_xml_kappa_1","title":"Internal function","topics":["parameter_to_xml_kappa_1"]},{"page":"parameter_to_xml_kappa_2","title":"Internal function","topics":["parameter_to_xml_kappa_2"]},{"page":"parameter_to_xml_lambda","title":"Internal function","topics":["parameter_to_xml_lambda"]},{"page":"parameter_to_xml_mean","title":"Internal function","topics":["parameter_to_xml_mean"]},{"page":"parameter_to_xml_mu","title":"Internal function","topics":["parameter_to_xml_mu"]},{"page":"parameter_to_xml_rate_ac","title":"Internal function","topics":["parameter_to_xml_rate_ac"]},{"page":"parameter_to_xml_rate_ag","title":"Internal function","topics":["parameter_to_xml_rate_ag"]},{"page":"parameter_to_xml_rate_at","title":"Internal function","topics":["parameter_to_xml_rate_at"]},{"page":"parameter_to_xml_rate_cg","title":"Internal function","topics":["parameter_to_xml_rate_cg"]},{"page":"parameter_to_xml_rate_ct","title":"Internal function","topics":["parameter_to_xml_rate_ct"]},{"page":"parameter_to_xml_rate_gt","title":"Internal function","topics":["parameter_to_xml_rate_gt"]},{"page":"parameter_to_xml_scale","title":"Internal function","topics":["parameter_to_xml_scale"]},{"page":"parameter_to_xml_sigma","title":"Internal function","topics":["parameter_to_xml_sigma"]},{"page":"remove_beautier_folder","title":"Check there are no files in the default beautier folder","topics":["remove_beautier_folder"]},{"page":"remove_empty_lines","title":"Remove all lines that are only whitespace","topics":["remove_empty_lines"]},{"page":"remove_multiline","title":"Remove consecutive lines","topics":["remove_multiline"]},{"page":"rename_inference_model_filenames","title":"Rename the filenames in an inference model","topics":["rename_inference_model_filenames"]},{"page":"rename_mcmc_filenames","title":"Rename the filenames within an MCMC","topics":["rename_mcmc_filenames"]},{"page":"rln_clock_model_to_xml_mean_rate_prior","title":"Internal function","topics":["rln_clock_model_to_xml_mean_rate_prior"]},{"page":"rln_clock_model_to_xml_operators","title":"Internal function","topics":["rln_clock_model_to_xml_operators"]},{"page":"rln_clock_model_to_xml_prior_distr","title":"Internal function","topics":["rln_clock_model_to_xml_prior_distr"]},{"page":"rln_clock_model_to_xml_state","title":"Internal function","topics":["rln_clock_model_to_xml_state"]},{"page":"rln_clock_model_to_xml_tracelog","title":"Internal function","topics":["rln_clock_model_to_xml_tracelog"]},{"page":"rnd_phylo_to_xml_init","title":"Creates the XML of a random phylogeny, as used in the 'init' section","topics":["rnd_phylo_to_xml_init"]},{"page":"s_parameter_to_xml","title":"Internal function","topics":["s_parameter_to_xml"]},{"page":"site_model_to_xml_operators","title":"Converts a site model to XML, used in the 'operators' section","topics":["site_model_to_xml_operators"]},{"page":"site_model_to_xml_prior_distr","title":"Internal function","topics":["site_model_to_xml_prior_distr"]},{"page":"site_model_to_xml_state","title":"Internal function to convert a site model to XML, used in the `state` section","topics":["site_model_to_xml_state"]},{"page":"site_model_to_xml_tracelog","title":"Creates the site model's XML for the tracelog section","topics":["site_model_to_xml_tracelog"]},{"page":"site_models_to_xml_operators","title":"Write the XML 'operators' section from the site models.","topics":["site_models_to_xml_operators"]},{"page":"site_models_to_xml_prior_distr","title":"Represent the site models as XML","topics":["site_models_to_xml_prior_distr"]},{"page":"site_models_to_xml_tracelog","title":"Creates the site models' XML for the tracelog 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\"rev\"),\nperson(\"Christopher T.\", \"Kenny\", role = \"rev\")\n)","Description":"Based on individual market shares of all participants in a\nmarket or space, the package offers a set of different\nstructural and concentration measures frequently - and not so\nfrequently - used in research and in practice. Measures can be\ncalculated in groups or individually. The calculated measure or\nthe resulting vector in table format should help practitioners\nmake more informed decisions. Methods used in this package are\nfrom: 1. Chang, E. J., Guerra, S. M., de Souza Penaloza, R. A.\n& Tabak, B. M. (2005) \"Banking concentration: the Brazilian\ncase\". 2. Cobham, A. and A. Summer (2013). \"Is It All About\nthe Tails? The Palma Measure of Income Inequality\". 3. Garcia\nAlba Idunate, P. (1994). \"Un Indice de dominancia para el\nanalisis de la estructura de los mercados\". 4. Ginevicius, R.\nand S. Cirba (2009). \"Additive measurement of market\nconcentration\" . 5.\nHerfindahl, O. C. (1950), \"Concentration in the steel industry\"\n(PhD thesis). 6. Hirschmann, A. O. (1945), \"National power and\nstructure of foreign trade\". 7. Melnik, A., O. Shy, and R.\nStenbacka (2008), \"Assessing market dominance\"\n. 8. Palma, J. G. (2006).\n\"Globalizing Inequality: 'Centrifugal' and 'Centripetal' Forces\nat Work\". 9. Shannon, C. E. (1948). \"A Mathematical Theory of\nCommunication\". 10. Simpson, E. H. (1949). \"Measurement of\nDiversity\" .","License":"GPL (>= 3)","URL":"https://github.com/ropensci/concstats/,\nhttps://docs.ropensci.org/concstats/(website)","BugReports":"https://github.com/ropensci/concstats/issues/","VignetteBuilder":"knitr, rmarkdown","Encoding":"UTF-8","Language":"en-US","LazyData":"true","Roxygen":"list(markdown = TRUE)","RoxygenNote":"7.3.1","Config/testthat/edition":"3","Repository":"https://ropensci.r-universe.dev","RemoteUrl":"https://github.com/ropensci/concstats","RemoteRef":"master","RemoteSha":"c450c9e1713c2ce7b9ca44323e462112f6feefd8","NeedsCompilation":"no","Packaged":{"Date":"2024-11-30 08:36:49 UTC","User":"root"},"Author":"Andreas Schneider [aut, cre] (),\nSebastian Wojcik [rev],\nChristopher T. 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RDF is\ndescribed at . This package\nsupports RDF by implementing an R interface to the Redland RDF\nC library, described at\n. 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object.","topics":["librdf_free_hash"]},{"page":"librdf_free_iterator","title":"Destructor - destroy a librdf_iterator object.","topics":["librdf_free_iterator"]},{"page":"librdf_free_model","title":"Destructor - Destroy a librdf_model object.","topics":["librdf_free_model"]},{"page":"librdf_free_node","title":"Destructor - destroy an librdf_node object.","topics":["librdf_free_node"]},{"page":"librdf_free_parser","title":"Destructor - destroys a librdf_parser object.","topics":["librdf_free_parser"]},{"page":"librdf_free_query","title":"Destructor - destroy a librdf_query object.","topics":["librdf_free_query"]},{"page":"librdf_free_query_results","title":"Destructor - destroy a librdf_query_results object.","topics":["librdf_free_query_results"]},{"page":"librdf_free_serializer","title":"Destructor - destroys a librdf_serializer object.","topics":["librdf_free_serializer"]},{"page":"librdf_free_statement","title":"Destructor - destroy a 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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 number","topics":["librdf_version_release_get"]},{"page":"librdf_version_string","title":"Library full version as a string.","topics":["librdf_version_string"]},{"page":"librdf_version_string_get","title":"Return the Redland librdf version as a string.","topics":["librdf_version_string_get"]},{"page":"librdf_world_get_feature","title":"Get the value of a world feature.","topics":["librdf_world_get_feature"]},{"page":"librdf_world_open","title":"Open a created redland world environment.","topics":["librdf_world_open"]},{"page":"librdf_world_set_feature","title":"Set the value of a world feature.","topics":["librdf_world_set_feature"]},{"page":"librdf_world_set_logger","title":"Set the world log handling function.","topics":["librdf_world_set_logger"]},{"page":"mergeNamespace_roclet","title":"A custom Roxygen roclet that adds Redland RDF functions to NAMESPACE file generated by Roxygen.","topics":["mergeNamespace_roclet"]},{"page":"Model-class","title":"A Redland Model 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We\nprovide functions to remove artifacts, standardize tunnel\nposition and tunnel axes, select a region of interest, isolate\nspecific trajectories, fill gaps in trajectory data, and\ncalculate 3D and per-axis velocity. For experiments of visual\nguidance, we also provide functions that use subject position\nto estimate perception of visual stimuli.","Maintainer":"Vikram B. Baliga ","License":"GPL-3","Encoding":"UTF-8","Roxygen":"list(markdown = TRUE)","RoxygenNote":"7.2.3","VignetteBuilder":"knitr","URL":"https://github.com/ropensci/pathviewr/,\nhttps://docs.ropensci.org/pathviewr/","BugReports":"https://github.com/ropensci/pathviewr/issues/","Config/pak/sysreqs":"libicu-dev","Repository":"https://ropensci.r-universe.dev","RemoteUrl":"https://github.com/ropensci/pathviewr","RemoteRef":"master","RemoteSha":"e591cb88815bc706e6415472d2c6846cf639ad8c","NeedsCompilation":"no","Packaged":{"Date":"2024-11-27 03:57:03 UTC","User":"root"},"Author":"Vikram B. Baliga [aut, cre] (),\nMelissa S. 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height","topics":["relabel_viewr_axes"]},{"page":"remove_duplicate_frames","title":"Remove any duplicates or aliased frames within trajectories","topics":["remove_duplicate_frames"]},{"page":"remove_vel_anomalies","title":"Remove any rows which show sharp shifts in velocity that are likely due to tracking errors","topics":["remove_vel_anomalies"]},{"page":"rename_viewr_characters","title":"Rename subjects in the data via pattern detection","topics":["rename_viewr_characters"]},{"page":"rescale_tunnel_data","title":"Rescale position data within a 'viewr' object","topics":["rescale_tunnel_data"]},{"page":"rm_by_trajnum","title":"Remove subjects by trajectory number","topics":["rm_by_trajnum"]},{"page":"rotate_tunnel","title":"Rotate a tunnel so that perches are approximately aligned","topics":["rotate_tunnel"]},{"page":"section_tunnel_by","title":"Bin data along a specified axis","topics":["section_tunnel_by"]},{"page":"select_x_percent","title":"Select a region of interest within the 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