| alpha_parameter_to_xml | Internal function |
| are_clock_models | Determine if x consists out of clock_models objects |
| are_equal_mcmcs | Determine if two MCMCs are equal. |
| are_equal_screenlogs | Determine if two screenlogs are equal. |
| are_equal_tracelogs | Determine if two tracelogs are equal. |
| are_equal_treelogs | Determine if two treelogs are equal. |
| are_equal_xml_files | Determine if XML files result in equal trees |
| are_equal_xml_lines | Determine if XML lines result in equal trees |
| are_equivalent_xml_files | Internal function |
| are_equivalent_xml_lines | Determine if XML lines result in equivalent trees |
| are_equivalent_xml_lines_all | Determine if XML lines result in equivalent trees |
| are_equivalent_xml_lines_loggers | Determine if XML operator lines result in equivalent trees |
| are_equivalent_xml_lines_operators | Determine if XML operator lines result in equivalent trees |
| are_equivalent_xml_lines_section | Determine if XML lines result in equivalent trees |
| are_fasta_filenames | Checks if all filenames have a FASTA filename extension |
| are_ids | Determine if x consists out of IDs |
| are_init_clock_models | Determine if x consists out of initialized clock_models... |
| are_init_mrca_priors | Determine if x consists out of initialized MRCA priors |
| are_init_site_models | Determine if x consists out of initialized site_models... |
| are_init_tree_priors | Determine if x consists out of initialized tree_priors... |
| are_mrca_align_ids_in_fasta | Determine if the MRCA priors' alignment IDs are present in... |
| are_mrca_priors | Determine if x consists out of MRCA priors |
| are_mrca_taxon_names_in_fasta | Determine if the MRCA priors' taxa names are present in the... |
| are_rln_clock_models | Are the clock models Relaxed Log-Normal clock models? |
| are_site_models | Determine if x consists out of site_models objects |
| are_tree_priors | Determine if x consists out of tree_priors objects |
| bd_tree_prior_to_xml_prior_distr | Creates the tree prior section in the prior section of the... |
| beautier-package | 'beautier': A package to create a 'BEAST2' input file. |
| beta_parameter_to_xml | Internal function |
| b_pop_sizes_parameter_to_xml | Internal function |
| b_pop_sizes_param_to_xml | Internal function |
| cbs_tree_prior_to_xml_prior_distr | Creates the tree prior section in the prior section of the... |
| ccp_tree_prior_to_xml_prior_distr | Creates the tree prior section in the prior section of the... |
| ccp_tree_prior_to_xml_state | Convert a CCP tree prior to the XML as part of the 'state'... |
| cep_tree_prior_to_xml_prior_distr | Creates the tree prior section in the prior section of the... |
| check_alignment_id | Check if the 'alignment_id' is valid. |
| check_beauti_options | Check if the 'beauti_options' is a valid 'beauti_options'... |
| check_clock_model | Check if the clock model is a valid clock model. |
| check_clock_models | Check if the object is a list of one or more clock models. |
| check_empty_beautier_folder | Internal function |
| check_file_and_model_agree | Checks if the input FASTA file and the inference model agree. |
| check_file_exists | Function to check if a file exists. Calls 'stop' if the file... |
| check_filename | Check if the 'filename' is valid |
| check_gamma_site_model | Checks if the parameter is a valid gamma site model |
| check_gamma_site_model_names | Checks if the gamma site model has the right list elements'... |
| check_gtr_site_model | Check if the 'gtr_site_model' is a valid GTR nucleotide... |
| check_gtr_site_model_names | Check if the 'gtr_site_model' has the list elements of a... |
| check_inference_model | Check if the supplied object is a valid Bayesian phylogenetic... |
| check_inference_models | Check if the 'inference_model' is a valid BEAUti inference... |
| check_is_monophyletic | Check if 'is_monophyletic' has a valid value. |
| check_log_mode | Check if the supplied 'mode' is a valid logging mode. |
| check_log_sort | Check if the supplied 'sort' is a valid logging sorting... |
| check_mcmc | Check if the MCMC is a valid MCMC object. |
| check_mcmc_list_element_names | Check if the MCMC has the list elements of a valid MCMC... |
| check_mcmc_values | Check if the MCMC has the list elements with valid values for... |
| check_mrca_prior | Check if the MRCA prior is a valid MRCA prior. |
| check_mrca_prior_name | Check if 'mrca_prior_name' is a valid MRCA prior name. |
| check_mrca_prior_names | Check if the MRCA prior, which is a list, has all the named... |
| check_mrca_prior_taxa_names | Check the MRCA prior's taxon names are valid. |
| check_ns_mcmc | Check if this an MCMC that uses Nested Sampling to estimate a... |
| check_param | Check if the parameter is a valid parameter |
| check_param_names | Check if the 'param' has the list elements of a valid 'param'... |
| check_param_types | Check if the 'param' has the list elements of the right type... |
| check_phylogeny | Check if the phylogeny is a valid phylogeny object. |
| check_rename_fun | Check if the rename function is a valid filename rename... |
| check_rln_clock_model | Check if the clock model is a valid clock model. |
| check_screenlog | Check if a 'screenlog' is valid. |
| check_screenlog_names | Check if the 'screenlog' has the list elements of a valid... |
| check_screenlog_values | Check if the screenlog has the list elements with valid... |
| check_site_model | Check if the site model is a valid site model |
| check_site_model_names | Check if the 'site_model' has the list elements of a valid... |
| check_site_models | Check if the object is a list of one or more site models. |
| check_site_model_types | Check if the 'site_model' has the list elements of the right... |
| check_store_every | Check if 'store_every' holds a valid value |
| check_strict_clock_model | Check if the clock model is a valid clock model. |
| check_tn93_site_model | Check if the 'tn93_site_model' is a valid TN93 nucleotide... |
| check_tn93_site_model_names | Check if the 'tn93_site_model' has the list elements of a... |
| check_tracelog | Check if a 'tracelog' is valid. |
| check_tracelog_names | Check if the 'tracelog' has the list elements of a valid... |
| check_tracelog_values | Check if the tracelog has the list elements with valid values... |
| check_treelog | Check if a 'treelog' is valid. |
| check_treelog_names | Check if the 'treelog' has the list elements of a valid... |
| check_treelog_values | Check if the treelog has the list elements with valid values... |
| check_tree_prior | Check if the tree prior is a valid tree prior |
| check_tree_priors | Check if the object is a list of one or more tree priors. |
| clock_model_to_xml_operators | Internal function |
| clock_model_to_xml_prior_distr | Internal function |
| clock_model_to_xml_state | Internal function |
| clock_model_to_xml_tracelog | Internal function |
| clock_model_to_xml_treelogger | Convert a clock model to the XML of the 'TreeLogger' |
| clock_rate_param_to_xml | Internal function |
| compare_lines | Internal function |
| count_trailing_spaces | Count the number of spaces before the first character |
| create_alpha_param | Create a parameter called alpha |
| create_bd_tree_prior | Create a Birth-Death tree prior |
| create_beast2_beast_xml | Create the '<beast ...>' XML |
| create_beast2_input | Create a BEAST2 XML input text |
| create_beast2_input_beast | Creates the XML text for the 'beast' tag of a BEAST2... |
| create_beast2_input_data | Creates the 'data' section of a BEAST2 XML parameter file |
| create_beast2_input_data_sequences | Creates the data section of a BEAST2 XML parameter file |
| create_beast2_input_distr | Creates the distribution section of a BEAST2 XML parameter... |
| create_beast2_input_distr_lh | Creates the XML text for the 'distribution' tag with the... |
| create_beast2_input_distr_prior | Creates the prior section in the distribution section of a... |
| create_beast2_input_file | Create a BEAST2 input file |
| create_beast2_input_file_from_model | Create a BEAST2 input file from an inference model |
| create_beast2_input_from_model | Create a BEAST2 XML input text from an inference model |
| create_beast2_input_init | Creates the 'init' section of a BEAST2 XML parameter file |
| create_beast2_input_map | Creates the map section of a BEAST2 XML parameter file |
| create_beast2_input_operators | Creates the operators section of a BEAST2 XML parameter file |
| create_beast2_input_run | Creates the "run" section of a BEAST2 XML parameter file |
| create_beast2_input_state | Creates the "state" section of a BEAST2 XML parameter file |
| create_beautier_tempfolder | Create the default 'beautier' temporary folder |
| create_beauti_options | Function to create a set of 'BEAUti' options. |
| create_beauti_options_v2_4 | Function to create the BEAUti options for version 2.4. |
| create_beauti_options_v2_6 | Function to create the BEAUti options for version 2.6. |
| create_beta_distr | Create a beta distribution |
| create_beta_param | Create a parameter called beta |
| create_b_pop_sizes_param | Create a parameter called 'b_pop_sizes'. |
| create_branch_rate_model_xml | Internal function to create the 'branchRateModel' section of... |
| create_cbs_tree_prior | Create a Coalescent Bayesian Skyline tree prior |
| create_ccp_tree_prior | Create a Coalescent Constant Population tree prior |
| create_cep_tree_prior | Create a Coalescent Exponential Population tree prior |
| create_clock_model | General function to create a clock model |
| create_clock_model_from_name | Create a clock model from name |
| create_clock_models | Creates all supported clock models, which is a list of the... |
| create_clock_models_from_names | Create clock models from their names |
| create_clock_rate_param | Create a parameter called 'clock_rate', as needed by... |
| create_clock_rate_state_node_parameter_xml | Internal function |
| create_data_xml | Create the '<data ..>' XML |
| create_distr | General function to create a distribution. |
| create_exp_distr | Create an exponential distribution |
| create_freq_param | Create a parameter called freq |
| create_gamma_distr | Create a gamma distribution |
| create_gamma_site_model | Create a gamma site model, part of a site model |
| create_gtr_site_model | Create a GTR site model |
| create_gtr_subst_model_xml | Converts a GTR site model to XML, used in the 'substModel'... |
| create_hky_site_model | Create an HKY site model |
| create_hky_subst_model_xml | Converts a site model to XML, used in the 'substModel'... |
| create_inference_model | Create a Bayesian phylogenetic inference model. |
| create_inv_gamma_distr | Create an inverse-gamma distribution |
| create_jc69_site_model | Create a JC69 site model |
| create_jc69_subst_model_xml | Converts a JC69 site model to XML, used in the 'substModel'... |
| create_kappa_1_param | Create a parameter called kappa 1 |
| create_kappa_2_param | Create a parameter called kappa 2 |
| create_kappa_param | Create a parameter called kappa |
| create_lambda_param | Create a parameter called lambda |
| create_laplace_distr | Create a Laplace distribution |
| create_loggers_xml | Creates the three logger sections of a BEAST2 XML parameter... |
| create_log_normal_distr | Create a log-normal distribution |
| create_mcmc | Create an MCMC configuration. |
| create_mean_param | Create a parameter called mean |
| create_m_param | Create a parameter called m |
| create_mrca_prior | Create a Most Recent Common Ancestor prior |
| create_mu_param | Create a parameter called mu |
| create_normal_distr | Create an normal distribution |
| create_ns_inference_model | Create an inference model to measure the evidence of. |
| create_ns_mcmc | Create an MCMC object to estimate the marginal likelihood... |
| create_one_div_x_distr | Create a 1/x distribution |
| create_param | General function to create a parameter. |
| create_poisson_distr | Create a Poisson distribution |
| create_rate_ac_param | Create a parameter called 'rate AC' |
| create_rate_ag_param | Create a parameter called 'rate AG' |
| create_rate_at_param | Create a parameter called 'rate AT' |
| create_rate_categories_state_node_xml | Internal function |
| create_rate_cg_param | Create a parameter called 'rate CG' |
| create_rate_ct_param | Create a parameter called 'rate CT' |
| create_rate_gt_param | Create a parameter called 'rate GT' |
| create_rln_clock_branch_rate_model_xml | Internal function |
| create_rln_clock_model | Create a relaxed log-normal clock model |
| create_scale_param | Create a parameter called scale |
| create_screenlog | Create a 'screenlog' object |
| create_screenlog_xml | Creates the 'screenlog' section of the 'logger' section of a... |
| create_sigma_param | Create a parameter called sigma |
| create_site_model | General function to create a site model. |
| create_site_model_from_name | Create a site model from name |
| create_site_model_parameters_xml | Internal function to creates the XML text for the... |
| create_site_models | Creates all supported site models which is a list of the... |
| create_site_models_from_names | Create site models from their names |
| create_site_model_xml | Internal function to creates the XML text for the 'siteModel'... |
| create_s_param | Create a parameter called s |
| create_strict_clock_branch_rate_model_xml | Internal function. |
| create_strict_clock_model | Create a strict clock model |
| create_strict_clock_rate_scaler_operator_xml | Internal function |
| create_subst_model_xml | Internal function to create the 'substModel' section |
| create_temp_screenlog_filename | Create a filename for a temporary 'screenlog' file |
| create_temp_tracelog_filename | Create a filename for a temporary 'tracelog' file |
| create_temp_treelog_filename | Create a filename for a temporary 'treelog' file |
| create_test_inference_model | Create a testing inference model. |
| create_test_mcmc | Create an MCMC configuration for testing. |
| create_test_ns_inference_model | Create an inference model to be tested by Nested Sampling |
| create_test_ns_mcmc | Create an NS MCMC object for testing |
| create_test_screenlog | Create a 'screenlog' object, to be used in testing |
| create_test_tracelog | Create a 'tracelog' object, as used for testing |
| create_test_treelog | Create a 'treelog' object to be used in testing |
| create_tn93_site_model | Create a TN93 site model |
| create_tn93_subst_model_xml | Converts a TN93 site model to XML, used in the 'substModel'... |
| create_tracelog | Create a 'tracelog' object |
| create_tracelog_xml | Internal function |
| create_trait_set_string | Create a trait set string. |
| create_tree_likelihood_distr_xml | Creates the XML text for the 'distribution' tag with the... |
| create_treelog | Create a 'treelog' object |
| create_treelog_xml | Creates the XML text for the 'logger' tag with ID 'treelog'.... |
| create_tree_prior | Internal function to create a tree prior |
| create_tree_priors | Creates all supported tree priors, which is a list of the... |
| create_ucld_mean_state_node_param_xml | Internal function |
| create_ucld_stdev_state_node_param_xml | Internal function |
| create_uniform_distr | Create a uniform distribution |
| create_xml_declaration | Create the XML declaration of the BEAST2 XML input file |
| create_yule_tree_prior | Create a Yule tree prior |
| default_parameters_doc | Documentation of parameters (for example, 'create_param'.... |
| default_params_doc | Documentation of general function arguments. This function... |
| distr_to_xml | Internal function |
| distr_to_xml_beta | Internal function |
| distr_to_xml_exp | Internal function |
| distr_to_xml_inv_gamma | Internal function |
| distr_to_xml_laplace | Internal function |
| distr_to_xml_log_normal | Internal function |
| distr_to_xml_normal | Internal function |
| distr_to_xml_one_div_x | Internal function |
| distr_to_xml_poisson | Internal function |
| distr_to_xml_uniform | Internal function |
| extract_xml_loggers_from_lines | Extract everything between first loggers and last loggers... |
| extract_xml_operators_from_lines | Extract everything between first operators and last operators... |
| extract_xml_section_from_lines | Get the lines of an XML section, including the section tags |
| fasta_file_to_sequences | Convert a FASTA file to a table of sequences |
| find_clock_model | Finds a clock model with a certain ID |
| find_first_regex_line | Find the first line that satisfies a regex |
| find_first_xml_opening_tag_line | Find the line number of the first section's opening tag |
| find_last_regex_line | Find the index of the last line that matches a regex |
| find_last_xml_closing_tag_line | Find the highest line number of a section's closing tag |
| freq_equilibrium_to_xml | Creates the 'freq_equilibrium' as XML |
| freq_param_to_xml | Internal function |
| gamma_distr_to_xml | Internal function |
| gamma_site_models_to_xml_prior_distr | Deprecated function |
| gamma_site_model_to_xml_prior_distr | Internal function. |
| gamma_site_model_to_xml_state | Converts a gamma site model to XML, used in the 'state'... |
| get_alignment_id | Conclude the ID from a FASTA filename. |
| get_alignment_ids | Get the alignment IDs from one or more files. |
| get_alignment_ids_from_fasta_filenames | Get the alignment ID from one or more FASTA filenames. |
| get_beautier_folder | Get the path to the beautier temporary files folder |
| get_beautier_path | Get the full path of a file in the 'inst/extdata' folder |
| get_beautier_paths | Get the full paths of files in the 'inst/extdata' folder |
| get_beautier_tempfilename | Get a temporary filename |
| get_clock_model_name | Get the BEAUti name for a clock model |
| get_clock_model_names | Get the clock model names |
| get_clock_models_ids | Collect the IDs of the list of clock models |
| get_crown_age | Obtain the crown age of a phylogeny. |
| get_default_beast_namespace | Get the default 'namespace' element value of the 'beast' XML... |
| get_default_beast_namespace_v2_4 | Get the default 'namespace' element value of the 'beast' XML... |
| get_default_beast_namespace_v2_6 | Get the default 'namespace' element value of the 'beast' XML... |
| get_distr_names | Get the distribution names |
| get_distr_n_params | Get the number of parameters a distribution uses |
| get_fasta_filename | Get the path of a FASTA file used in testing |
| get_file_base_sans_ext | Get the base of the filename base without extension |
| get_freq_equilibrium_names | Returns valid values for the 'freq_equilibrium' argument |
| get_gamma_site_model_n_distrs | Get the number of distributions in a gamma site model |
| get_gamma_site_model_n_params | Get the number of distributions a site model has |
| get_has_non_strict_clock_model | Determines if there is at least one non-strict clock model in... |
| get_inference_model_filenames | Get the filenames stored in an inference model. |
| get_log_modes | Get the possible log modes |
| get_log_sorts | Get the possible log sorts |
| get_mcmc_filenames | Get the filenames stored in an MCMC. |
| get_n_taxa | Extract the number of taxa from a file |
| get_operator_id_pre | Get the prefix of operator IDs |
| get_param_names | Get the parameter names |
| get_remove_dir_fun | Get a function that, from a filename, returns the part... |
| get_remove_hex_fun | Get a function that removes the hex string from filenames. |
| get_replace_dir_fun | Get a function to replace the directory of a filename |
| get_site_model_names | Get the site models' names |
| get_site_model_n_distrs | Get the number of distributions a site model has |
| get_site_model_n_params | Get the number of distributions a site model has |
| get_site_models_n_distrs | Get the number of distributions a site model has |
| get_site_models_n_params | Get the number of distributions one or more site models have |
| get_taxa_names | Extract the names of taxa from a file |
| get_tree_prior_names | Get the tree prior names |
| get_tree_prior_n_distrs | Get the number of distributions a tree prior has |
| get_tree_prior_n_params | Get the number of parameters a tree prior has |
| get_tree_priors_n_distrs | Get the number of distributions a tree prior has |
| get_tree_priors_n_params | Get the number of parameters a list of tree priors has |
| get_xml_closing_tag | Get the XML closing tag |
| get_xml_opening_tag | Get the XML opening tag |
| gtr_site_model_to_xml_prior_distr | Internal function |
| gtr_site_model_to_xml_state | Converts a site model to XML, used in the 'state' section |
| has_mrca_prior | Determines if the inference model has an MRCA prior. |
| has_mrca_prior_with_distr | See if the inference model has one MRCA prior with a... |
| has_rln_clock_model | Determine if the 'inference_model' uses a relaxed log-normal... |
| has_strict_clock_model | Determine if the 'inference_model' uses a strict clock model. |
| has_tip_dating | Determine if the 'inference_model' uses tip dating. |
| has_xml_closing_tag | Is an XML closing tag with the value of 'section' present... |
| has_xml_opening_tag | Is an XML opening tag with value 'section' present among the... |
| has_xml_short_closing_tag | Is an XML closing tag with short closing text in one of the... |
| hky_site_model_to_xml_prior_distr | Internal function |
| hky_site_model_to_xml_state | Converts a site model to XML, used in the 'state' section |
| indent | Indent text for a certain number of spaces. If the text is... |
| init_bd_tree_prior | Initializes a Birth-Death tree prior |
| init_beta_distr | Initializes a beta distribution |
| init_ccp_tree_prior | Initializes a Coalescent Constant Population tree prior |
| init_cep_tree_prior | Initializes a Coalescent Exponential Population tree prior |
| init_clock_models | Initializes all clock models |
| init_distr | Initializes a distribution |
| init_exp_distr | Initializes an exponential distribution |
| init_gamma_distr | Initializes a gamma distribution |
| init_gamma_site_model | Initializes a gamma site model |
| init_gtr_site_model | Initializes a GTR site model |
| init_hky_site_model | Initializes an HKY site model |
| init_inference_model | Initialize an inference model |
| init_inv_gamma_distr | Initializes an inverse gamma distribution |
| init_jc69_site_model | Initializes a JC69 site model |
| init_laplace_distr | Initializes an Laplace distribution |
| init_log_normal_distr | Initializes an log-normal distribution |
| init_mrca_prior | Initialize the MRCA prior. |
| init_mrca_priors | Initializes all MRCA priors |
| init_normal_distr | Initializes an normal distribution |
| init_one_div_x_distr | Initializes an one-divided-by-x distribution |
| init_param | Initializes a parameter |
| init_poisson_distr | Initializes an Poisson distribution |
| init_rln_clock_model | Initializes a Relaxed Log-Normal clock model |
| init_site_models | Initializes all site models |
| init_strict_clock_model | Initializes a strict clock model |
| init_tn93_site_model | Initializes a TN93 site model |
| init_tree_priors | Initializes all tree priors |
| init_uniform_distr | Initializes a uniform distribution |
| init_yule_tree_prior | Initializes a Yule tree prior |
| interspace | Puts spaces in between the lines |
| is_alpha_param | Determine if the object is a valid alpha parameter |
| is_bd_tree_prior | Determine if the object is a valid Birth Death tree prior |
| is_beauti_options | Determine if the object is a valid 'beauti_options' |
| is_beta_distr | Determine if the object is a valid beta distribution, as... |
| is_beta_param | Determine if the object is a valid beta parameter |
| is_b_pop_sizes_param | Determine if the object is a valid b_pop_sizes parameter |
| is_cbs_tree_prior | Determine if the object is a valid constant coalescent... |
| is_ccp_tree_prior | Determine if the object is a valid constant coalescence... |
| is_cep_tree_prior | Determine if the object is a valid coalescent exponential... |
| is_clock_model | Determine if the object is a valid clock_model |
| is_clock_model_name | Determines if the name is a valid clock model name |
| is_clock_rate_param | Determine if the object is a valid clock_rate parameter |
| is_default_mcmc | Determine if the MCMC is a default MCMC |
| is_distr | Determine if the object is a valid distribution |
| is_distr_name | Determines if the name is a valid distribution name |
| is_exp_distr | Determine if the object is a valid exponential distribution... |
| is_freq_equilibrium_name | Checks if 'name' is a valid 'freq_equilibrium' argument value |
| is_freq_param | Determine if the object is a valid freq parameter |
| is_gamma_distr | Determine if the object is a valid gamma distribution, as... |
| is_gamma_site_model | Is object x a gamma site model? |
| is_gtr_site_model | Determine if the object is a valid GTR site model, as created... |
| is_hky_site_model | Determine if the object is a valid HKY site model, as created... |
| is_id | Determine if the object is a valid ID |
| is_inference_model | Determine if the input is an inference model |
| is_init_bd_tree_prior | Determine if x is an initialized Birth-Death tree_prior... |
| is_init_beta_distr | Determine if x is an initialized beta distribution object as... |
| is_init_cbs_tree_prior | Determine if x is an initialized Coalescent Bayesian Skyline... |
| is_init_ccp_tree_prior | Determine if x is an initialized Coalescent Constant... |
| is_init_cep_tree_prior | Determine if x is an initialized Coalescent Exponential... |
| is_init_clock_model | Determine if x is an initialized clock_model object, as... |
| is_init_distr | Determine if x is an initialized distribution object as... |
| is_init_exp_distr | Determine if x is an initialized exponential distribution... |
| is_init_gamma_distr | Determine if x is an initialized gamma distribution object |
| is_init_gamma_site_model | Determine if x is an initialized gamma site model, as created... |
| is_init_gtr_site_model | Determine if x is an initialized GTR site model as created by... |
| is_init_hky_site_model | Determine if x is an initialized HKY site model as created by... |
| is_init_inv_gamma_distr | Determine if x is an initialized inverse-gamma distribution... |
| is_init_jc69_site_model | Determine if x is an initialized JC69 site model as created... |
| is_init_laplace_distr | Determine if x is an initialized Laplace distribution as... |
| is_init_log_normal_distr | Determine if x is an initialized log_normal distribution... |
| is_init_mrca_prior | Determine if x is an initialized MRCA prior |
| is_init_normal_distr | Determine if x is an initialized normal distribution object... |
| is_init_one_div_x_distr | Determine if x is an initialized one_div_x distribution... |
| is_init_param | Determine if x is an initialized parameter, as created by... |
| is_init_poisson_distr | Determine if x is an initialized Poisson distribution object... |
| is_init_rln_clock_model | Determine if x is an initialized relaxed log-normal... |
| is_init_site_model | Determine if x is an initialized site model, as created by... |
| is_init_strict_clock_model | Determine if x is an initialized strict clock_model object |
| is_init_tn93_site_model | Determine if x is an initialized tn93 site model as created... |
| is_init_tree_prior | Determine if x is an initialized tree_prior objects |
| is_init_uniform_distr | Determine if x is an initialized uniform distribution object... |
| is_init_yule_tree_prior | Determine if x is an initialized Yule tree_prior object |
| is_in_patterns | Is there at least one regular expression having a match with... |
| is_inv_gamma_distr | Determine if the object is a valid inverse-gamma distribution... |
| is_jc69_site_model | Determine if the object is a valid JC69 site model |
| is_kappa_1_param | Determine if the object is a valid kappa 1 parameter |
| is_kappa_2_param | Determine if the object is a valid kappa 2 parameter |
| is_kappa_param | Determine if the object is a valid kappa parameter |
| is_lambda_param | Determine if the object is a valid lambda parameter |
| is_laplace_distr | Determine if the object is a valid Laplace distribution, as... |
| is_log_normal_distr | Determine if the object is a valid log-normal distribution,... |
| is_mcmc | Determine if the object is a valid MCMC |
| is_mcmc_nested_sampling | Determine if the object is a valid Nested-Sampling MCMC, as... |
| is_mean_param | Determine if the object is a valid mean parameter |
| is_m_param | Determine if the object is a valid m parameter |
| is_mrca_align_id_in_fasta | Determine if an MRCA prior's alignment IDs is present in the... |
| is_mrca_align_ids_in_fastas | Determine if an MRCA prior's alignment IDs are present in the... |
| is_mrca_prior | Determine of the object is an empty ('NA') or valid MRCA... |
| is_mrca_prior_with_distr | See if x is one MRCA prior with a distribution |
| is_mu_param | Determine if the object is a valid mu parameter |
| is_normal_distr | Determine if the object is a valid normal distribution as... |
| is_on_appveyor | Determines if the environment is AppVeyor |
| is_on_ci | Determines if the environment is a continuous integration... |
| is_one_bool | Check if the argument is one boolean |
| is_one_div_x_distr | Determine if the object is a valid 1/x distribution, as... |
| is_one_double | Determines if the argument is a double |
| is_one_empty_string | Determine if an object is one empty string |
| is_one_int | Determines if the argument is a whole number |
| is_one_na | Determines if x is one NA |
| is_one_string | Determines if the argument is one string |
| is_one_string_that_is_a_number | General function to create a distribution. |
| is_on_github_actions | Determines if the environment is GitHub Actions |
| is_on_travis | Determines if the environment is Travis CI |
| is_param | Determine if the object is a valid parameter |
| is_param_name | Determines if the name is a valid parameter name |
| is_phylo | Checks if the input is a phylogeny |
| is_poisson_distr | Determine if the object is a valid Poisson distribution as... |
| is_rate_ac_param | Determine if the object is a valid 'rate AC' parameter |
| is_rate_ag_param | Determine if the object is a valid 'rate AG' parameter |
| is_rate_at_param | Determine if the object is a valid 'rate AT' parameter |
| is_rate_cg_param | Determine if the object is a valid 'rate CG' parameter |
| is_rate_ct_param | Determine if the object is a valid 'rate CT' parameter |
| is_rate_gt_param | Determine if the object is a valid 'rate GT' parameter |
| is_rln_clock_model | Determine if the object is a valid relaxed log normal clock... |
| is_scale_param | Determine if the object is a valid scale parameter |
| is_sigma_param | Determine if the object is a valid sigma parameter |
| is_site_model | Determine if the object is a valid site_model |
| is_site_model_name | Determines if the name is a valid site_model name |
| is_s_param | Determine if the object is a valid s parameter |
| is_strict_clock_model | Determine if the object is a valid strict clock model, as... |
| is_tn93_site_model | Determine if the object is a valid TN93 site model, |
| is_tree_prior | Determine if an object is a valid tree prior |
| is_tree_prior_name | Determines if the name is a valid tree prior name |
| is_uniform_distr | Determine if the object is a valid uniform distribution as... |
| is_xml | Checks if the text is a valid XML node, that is, it has a... |
| is_yule_tree_prior | Determine if the object is a valid Yule tree prior, |
| jc69_site_model_to_xml_state | Converts a site model to XML, used in the 'state' section |
| kappa_param_to_xml | Internal function |
| mcmc_to_xml_run | Converts an MCMC object to the run section's XML |
| mcmc_to_xml_run_default | Converts an MCMC object to the run section's XML for a... |
| mcmc_to_xml_run_nested_sampling | Converts an MCMC object to the run section's XML for a... |
| m_param_to_xml | Internal function |
| mrca_priors_to_xml_prior_distr | Creates the the 'distribution"s prior section (which is part... |
| mrca_prior_to_xml_prior_distr | Creates the distribution section in the prior section of the... |
| mrca_prior_to_xml_state | Internal function to create the XML of an MRCA prior, as used... |
| mrca_prior_to_xml_taxonset | Creates the 'taxonset' section in the prior section of the... |
| mrca_prior_to_xml_tracelog | Internal function |
| no_taxa_to_xml_tree | Internal function |
| parameter_to_xml | Internal function |
| parameter_to_xml_kappa_1 | Internal function |
| parameter_to_xml_kappa_2 | Internal function |
| parameter_to_xml_lambda | Internal function |
| parameter_to_xml_mean | Internal function |
| parameter_to_xml_mu | Internal function |
| parameter_to_xml_rate_ac | Internal function |
| parameter_to_xml_rate_ag | Internal function |
| parameter_to_xml_rate_at | Internal function |
| parameter_to_xml_rate_cg | Internal function |
| parameter_to_xml_rate_ct | Internal function |
| parameter_to_xml_rate_gt | Internal function |
| parameter_to_xml_scale | Internal function |
| parameter_to_xml_sigma | Internal function |
| remove_beautier_folder | Check there are no files in the default beautier folder |
| remove_empty_lines | Remove all lines that are only whitespace |
| remove_multiline | Remove consecutive lines |
| rename_inference_model_filenames | Rename the filenames in an inference model |
| rename_mcmc_filenames | Rename the filenames within an MCMC |
| rln_clock_model_to_xml_mean_rate_prior | Internal function |
| rln_clock_model_to_xml_operators | Internal function |
| rln_clock_model_to_xml_prior_distr | Internal function |
| rln_clock_model_to_xml_state | Internal function |
| rln_clock_model_to_xml_tracelog | Internal function |
| rnd_phylo_to_xml_init | Creates the XML of a random phylogeny, as used in the 'init'... |
| site_models_to_xml_operators | Write the XML 'operators' section from the site models. |
| site_models_to_xml_prior_distr | Represent the site models as XML |
| site_models_to_xml_tracelog | Creates the site models' XML for the tracelog section |
| site_model_to_xml_operators | Converts a site model to XML, used in the 'operators' section |
| site_model_to_xml_prior_distr | Internal function |
| site_model_to_xml_state | Internal function to convert a site model to XML, used in the... |
| site_model_to_xml_tracelog | Creates the site model's XML for the tracelog section |
| s_parameter_to_xml | Internal function |
| strict_clock_model_to_xml_operators | Internal function |
| strict_clock_model_to_xml_prior_distr | Internal function |
| strict_clock_model_to_xml_state | Internal function |
| strict_clock_model_to_xml_tracelog | Internal function |
| taxa_to_xml_tree | Internal function |
| tipdate_taxa_to_xml_trait | Internal function |
| tipdate_taxa_to_xml_tree | Internal function |
| tn93_site_model_to_xml_prior_distr | Internal function |
| tn93_site_model_to_xml_state | Converts a site model to XML, used in the 'state' section |
| tree_model_to_tracelog_xml | Internal function |
| tree_priors_to_xml_prior_distr | Creates the distribution section in the prior section of the... |
| tree_priors_to_xml_tracelog | Creates the tree priors' XML for the tracelog section |
| tree_prior_to_xml_operators | Internal function |
| tree_prior_to_xml_prior_distr | Creates the distribution section in the prior section of the... |
| tree_prior_to_xml_state | Creates the XML of a tree prior, as used in the 'state'... |
| tree_prior_to_xml_tracelog | Creates the tree prior's XML for the tracelog section |
| unindent | Unindents text |
| yule_tree_prior_to_xml_operators | Internal function |
| yule_tree_prior_to_xml_prior_distr | Creates the 'prior' section in the prior section of the prior... |
