| Internal function | alpha_parameter_to_xml |
| Determine if x consists out of clock_models objects | are_clock_models |
| Determine if two MCMCs are equal. | are_equal_mcmcs |
| Determine if two screenlogs are equal. | are_equal_screenlogs |
| Determine if two tracelogs are equal. | are_equal_tracelogs |
| Determine if two treelogs are equal. | are_equal_treelogs |
| Determine if XML files result in equal trees | are_equal_xml_files |
| Determine if XML lines result in equal trees | are_equal_xml_lines |
| Internal function | are_equivalent_xml_files |
| Determine if XML lines result in equivalent trees | are_equivalent_xml_lines |
| Determine if XML lines result in equivalent trees | are_equivalent_xml_lines_all |
| Determine if XML operator 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 lines result in equivalent trees | are_equivalent_xml_lines_section |
| Checks if all filenames have a FASTA filename extension | are_fasta_filenames |
| Determine if x consists out of IDs | are_ids |
| Determine if x consists out of initialized clock_models objects | are_init_clock_models |
| Determine if x consists out of initialized MRCA priors | are_init_mrca_priors |
| Determine if x consists out of initialized site_models objects | are_init_site_models |
| Determine if x consists out of initialized tree_priors objects | are_init_tree_priors |
| Determine if the MRCA priors' alignment IDs are present in the FASTA files | are_mrca_align_ids_in_fasta |
| Determine if x consists out of MRCA priors | are_mrca_priors |
| Determine if the MRCA priors' taxa names are present in the FASTA files | are_mrca_taxon_names_in_fasta |
| Are the clock models Relaxed Log-Normal clock models? | are_rln_clock_models |
| Determine if x consists out of site_models objects | are_site_models |
| Determine if x consists out of tree_priors objects | are_tree_priors |
| Internal function | b_pop_sizes_param_to_xml |
| Internal function | b_pop_sizes_parameter_to_xml |
| Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Birth-Death tree prior | bd_tree_prior_to_xml_prior_distr |
| Internal function | beta_parameter_to_xml |
| Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Birth-Death tree prior | cbs_tree_prior_to_xml_prior_distr |
| Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Coalescent Constant Population tree prior | ccp_tree_prior_to_xml_prior_distr |
| Convert a CCP tree prior to the XML as part of the 'state' section | ccp_tree_prior_to_xml_state |
| Creates the tree prior section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Coalescent Exponential Population tree prior | cep_tree_prior_to_xml_prior_distr |
| Check if the 'alignment_id' is valid. | check_alignment_id |
| Check if the 'beauti_options' is a valid 'beauti_options' object. | check_beauti_options |
| Check if the clock model is a valid clock model. | check_clock_model |
| Check if the object is a list of one or more clock models. | check_clock_models |
| Internal function | check_empty_beautier_folder |
| Checks if the input FASTA file and the inference model agree. | check_file_and_model_agree |
| Function to check if a file exists. Calls 'stop' if the file is absent | check_file_exists |
| Check if the `filename` is valid | check_filename |
| Checks if the parameter is a valid gamma site model | check_gamma_site_model |
| Checks if the gamma site model has the right list elements' names | check_gamma_site_model_names |
| Check if the 'gtr_site_model' is a valid GTR nucleotide substitution model. | check_gtr_site_model |
| Check if the 'gtr_site_model' has the list elements of a valid 'gtr_site_model' object. | check_gtr_site_model_names |
| Check if the supplied object is a valid Bayesian phylogenetic inference model. | check_inference_model |
| Check if the 'inference_model' is a valid BEAUti inference model. | check_inference_models |
| Check if 'is_monophyletic' has a valid value. | check_is_monophyletic |
| Check if the supplied 'mode' is a valid logging mode. | check_log_mode |
| Check if the supplied 'sort' is a valid logging sorting option. | check_log_sort |
| Check if the MCMC is a valid MCMC object. | check_mcmc |
| Check if the MCMC has the list elements of a valid MCMC object. | check_mcmc_list_element_names |
| Check if the MCMC has the list elements with valid values for being a valid MCMC object. | check_mcmc_values |
| Check if the MRCA prior is a valid MRCA prior. | check_mrca_prior |
| Check if 'mrca_prior_name' is a valid MRCA prior name. | check_mrca_prior_name |
| Check if the MRCA prior, which is a list, has all the named elements. | check_mrca_prior_names |
| Check the MRCA prior's taxon names are valid. | check_mrca_prior_taxa_names |
| Check if this an MCMC that uses Nested Sampling to estimate a marginal likelihood. | check_mcmc_nested_sampling check_nested_sampling_mcmc check_ns_mcmc |
| Check if the parameter is a valid parameter | check_param |
| Check if the 'param' has the list elements of a valid 'param' object. | check_param_names |
| Check if the 'param' has the list elements of the right type for a valid 'param' object. | check_param_types |
| Check if the phylogeny is a valid phylogeny object. | check_phylogeny |
| Check if the rename function is a valid filename rename function | check_rename_fun |
| Check if the clock model is a valid clock model. | check_rln_clock_model |
| Check if a 'screenlog' is valid. | check_screenlog |
| Check if the 'screenlog' has the list elements of a valid 'screenlog' object. | check_screenlog_names |
| Check if the screenlog has the list elements with valid values for being a valid screenlog object. | check_screenlog_values |
| Check if the site model is a valid site model | check_site_model |
| Check if the 'site_model' has the list elements of a valid 'site_model' object. | check_site_model_names |
| Check if the 'site_model' has the list elements of the right type for a valid 'site_model' object. | check_site_model_types |
| Check if the object is a list of one or more site models. | check_site_models |
| Check if 'store_every' holds a valid value | check_store_every |
| Check if the clock model is a valid clock model. | check_strict_clock_model |
| Check if the 'tn93_site_model' is a valid TN93 nucleotide substitution model. | check_tn93_site_model |
| Check if the 'tn93_site_model' has the list elements of a valid 'tn93_site_model' object. | check_tn93_site_model_names |
| Check if a 'tracelog' is valid. | check_tracelog |
| Check if the 'tracelog' has the list elements of a valid 'tracelog' object. | check_tracelog_names |
| Check if the tracelog has the list elements with valid values for being a valid tracelog object. | check_tracelog_values |
| Check if the tree prior is a valid tree prior | check_tree_prior |
| Check if the object is a list of one or more tree priors. | check_tree_priors |
| Check if a 'treelog' is valid. | check_treelog |
| Check if the 'treelog' has the list elements of a valid 'treelog' object. | check_treelog_names |
| Check if the treelog has the list elements with valid values for being a valid treelog object. | check_treelog_values |
| Internal function | 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 |
| Convert a clock model to the XML of the 'TreeLogger' | clock_model_to_xml_treelogger |
| Internal function | clock_rate_param_to_xml |
| Internal function | compare_lines |
| Count the number of spaces before the first character | count_trailing_spaces |
| Create a parameter called alpha | create_alpha_param create_param_alpha |
| Create a parameter called `b_pop_sizes`. | create_b_pop_sizes_param create_param_b_pop_sizes |
| Create a Birth-Death tree prior | create_bd_tree_prior create_tree_prior_bd |
| Create the '<beast ...>' XML | create_beast2_beast_xml |
| Create a BEAST2 XML input text | create_beast2_input |
| Creates the XML text for the 'beast' tag of a BEAST2 parameter file. | create_beast2_input_beast |
| Creates the 'data' section of a BEAST2 XML parameter file | create_beast2_input_data |
| Creates the data section of a BEAST2 XML parameter file | create_beast2_input_data_sequences |
| Creates the distribution section of a BEAST2 XML parameter file. | create_beast2_input_distr |
| Creates the XML text for the 'distribution' tag with the 'likelihood' ID, of a BEAST2 parameter file. | create_beast2_input_distr_lh |
| Creates the prior section in the distribution section of a BEAST2 XML parameter file | create_beast2_input_distr_prior |
| Create a BEAST2 input file | create_beast2_input_file |
| Create a BEAST2 input file from an inference model | create_beast2_input_file_from_model |
| Create a BEAST2 XML input text from an inference model | create_beast2_input_from_model |
| Creates the 'init' section of a BEAST2 XML parameter file | create_beast2_input_init |
| Creates the map section of a BEAST2 XML parameter file | create_beast2_input_map |
| Creates the operators section of a BEAST2 XML parameter file | create_beast2_input_operators |
| Creates the ''run'' section of a BEAST2 XML parameter file | create_beast2_input_run |
| Creates the ''state'' section of a BEAST2 XML parameter file | create_beast2_input_state |
| Function to create a set of `BEAUti` options. | create_beauti_options |
| Function to create the BEAUti options for version 2.4. | create_beauti_options_v2_4 |
| Function to create the BEAUti options for version 2.6. | create_beauti_options_v2_6 |
| Create the default `beautier` temporary folder | create_beautier_tempfolder |
| Create a beta distribution | create_beta_distr create_distr_beta |
| Create a parameter called beta | create_beta_param create_param_beta |
| Internal function to create the 'branchRateModel' section of the XML as text. | create_branch_rate_model_xml |
| Create a Coalescent Bayesian Skyline tree prior | create_cbs_tree_prior create_tree_prior_cbs |
| Create a Coalescent Constant Population tree prior | create_ccp_tree_prior create_tree_prior_ccp |
| Create a Coalescent Exponential Population tree prior | create_cep_tree_prior create_tree_prior_cep |
| General function to create a clock model | create_clock_model |
| Create a clock model from name | create_clock_model_from_name |
| Creates all supported clock models, which is a list of the types returned by 'create_rln_clock_model', and 'create_strict_clock_model' | create_clock_models |
| Create clock models from their names | create_clock_models_from_names |
| Create a parameter called 'clock_rate', as needed by 'create_strict_clock_model' | create_clock_rate_param create_param_clock_rate |
| Internal function | create_clock_rate_state_node_parameter_xml |
| Create the '<data ..>' XML | create_data_xml |
| General function to create a distribution. | create_distr |
| Create an exponential distribution | create_distr_exp create_exp_distr |
| Create a parameter called freq | create_freq_param create_param_freq |
| Create a gamma distribution | create_distr_gamma create_gamma_distr |
| Create a gamma site model, part of a site model | create_gamma_site_model |
| Create a GTR site model | create_gtr_site_model create_site_model_gtr |
| Converts a GTR site model to XML, used in the 'substModel' section | create_gtr_subst_model_xml |
| Create an HKY site model | create_hky_site_model create_site_model_hky |
| Converts a site model to XML, used in the 'substModel' section | create_hky_subst_model_xml |
| Create a Bayesian phylogenetic inference model. | create_inference_model |
| Create an inverse-gamma distribution | create_distr_inv_gamma create_inv_gamma_distr |
| Create a JC69 site model | create_jc69_site_model create_site_model_jc69 |
| Converts a JC69 site model to XML, used in the 'substModel' section | create_jc69_subst_model_xml |
| Create a parameter called kappa 1 | create_kappa_1_param create_param_kappa_1 |
| Create a parameter called kappa 2 | create_kappa_2_param create_param_kappa_2 |
| Create a parameter called kappa | create_kappa_param create_param_kappa |
| Create a parameter called lambda | create_lambda_param create_param_lambda |
| Create a Laplace distribution | create_distr_laplace create_laplace_distr |
| Create a log-normal distribution | create_distr_log_normal create_log_normal_distr |
| Creates the three logger sections of a BEAST2 XML parameter file | create_loggers_xml |
| Create a parameter called m | create_m_param create_param_m |
| Create an MCMC configuration. | create_mcmc |
| Create a parameter called mean | create_mean_param create_param_mean |
| Create a Most Recent Common Ancestor prior | create_mrca_prior |
| Create a parameter called mu | create_mu_param create_param_mu |
| Create an normal distribution | create_distr_normal create_normal_distr |
| Create an inference model to measure the evidence of. | create_ns_inference_model |
| Create an MCMC object to estimate the marginal likelihood using Nested Sampling. | create_mcmc_nested_sampling create_ns_mcmc |
| Create a 1/x distribution | create_distr_one_div_x create_one_div_x_distr |
| General function to create a parameter. | create_param |
| Create a Poisson distribution | create_distr_poisson create_poisson_distr |
| Create a parameter called 'rate AC' | create_param_rate_ac create_rate_ac_param |
| Create a parameter called 'rate AG' | create_param_rate_ag create_rate_ag_param |
| Create a parameter called 'rate AT' | create_param_rate_at create_rate_at_param |
| Internal function | create_rate_categories_state_node_xml |
| Create a parameter called 'rate CG' | create_param_rate_cg create_rate_cg_param |
| Create a parameter called 'rate CT' | create_param_rate_ct create_rate_ct_param |
| Create a parameter called 'rate GT' | create_param_rate_gt create_rate_gt_param |
| Internal function | create_rln_clock_branch_rate_model_xml |
| Create a relaxed log-normal clock model | create_clock_model_rln create_rln_clock_model |
| Create a parameter called s | create_param_s create_s_param |
| Create a parameter called scale | create_param_scale create_scale_param |
| Create a 'screenlog' object | create_screenlog |
| Creates the 'screenlog' section of the 'logger' section of a BEAST2 XML parameter file | create_screenlog_xml |
| Create a parameter called sigma | create_param_sigma create_sigma_param |
| General function to create a site model. | create_site_model |
| Create a site model from name | create_site_model_from_name |
| Internal function to creates the XML text for the 'parameter's within the 'siteModel' section of a BEAST2 parameter file. | create_site_model_parameters_xml |
| Internal function to creates the XML text for the 'siteModel' tag of a BEAST2 parameter file. | create_site_model_xml |
| Creates all supported site models which is a list of the types returned by 'create_gtr_site_model', 'create_hky_site_model', 'create_jc69_site_model' and 'create_tn93_site_model' | create_site_models |
| Create site models from their names | create_site_models_from_names |
| Internal function. | create_strict_clock_branch_rate_model_xml |
| Create a strict clock model | create_clock_model_strict create_strict_clock_model |
| Internal function | create_strict_clock_rate_scaler_operator_xml |
| Internal function to create the 'substModel' section | create_subst_model_xml |
| Create a filename for a temporary `screenlog` file | create_temp_screenlog_filename |
| Create a filename for a temporary `tracelog` file | create_temp_tracelog_filename |
| Create a filename for a temporary `treelog` file | create_temp_treelog_filename |
| Create a testing inference model. | create_test_inference_model |
| Create an MCMC configuration for testing. | create_test_mcmc |
| Create an inference model to be tested by Nested Sampling | create_test_ns_inference_model |
| Create an NS MCMC object for testing | create_test_ns_mcmc |
| Create a 'screenlog' object, to be used in testing | create_test_screenlog |
| Create a 'tracelog' object, as used for testing | create_test_tracelog |
| Create a 'treelog' object to be used in testing | create_test_treelog |
| Create a TN93 site model | create_site_model_tn93 create_tn93_site_model |
| Converts a TN93 site model to XML, used in the 'substModel' section | create_tn93_subst_model_xml |
| Create a 'tracelog' object | create_tracelog |
| Internal function | create_tracelog_xml |
| Create a trait set string. | create_trait_set_string |
| Creates the XML text for the 'distribution' tag with the 'treeLikelihood' ID, of a BEAST2 parameter file. | create_tree_likelihood_distr_xml |
| Internal function to create a tree prior | create_tree_prior |
| Creates all supported tree priors, which is a list of the types returned by 'create_bd_tree_prior', 'create_cbs_tree_prior', 'create_ccp_tree_prior', 'create_cep_tree_prior' and 'create_yule_tree_prior' | create_tree_priors |
| Create a 'treelog' object | create_treelog |
| Creates the XML text for the `logger` tag with ID `treelog`. This section has these elements: ``` <logger id="treelog.t:test_output_0" spec="Logger" fileName="my_treelog.trees" logEvery="345000" mode="tree" sanitiseHeaders="true" sort="smart"> # nolint indeed long <log id="TreeWithMetaDataLogger.t:test_output_0" spec="beast.evolution.tree.TreeWithMetaDataLogger" tree="@Tree.t:test_output_0"/> # nolint indeed long </logger> ``` | create_treelog_xml |
| Internal function | create_ucld_mean_state_node_param_xml |
| Internal function | create_ucld_stdev_state_node_param_xml |
| Create a uniform distribution | create_distr_uniform create_uniform_distr |
| Create the XML declaration of the BEAST2 XML input file | create_xml_declaration |
| Create a Yule tree prior | create_tree_prior_yule create_yule_tree_prior |
| Documentation of parameters (for example, 'create_param'. This function does nothing. It is intended to inherit documentation from. | default_parameters_doc |
| Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation. | default_params_doc |
| Internal 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 |
| Extract everything between first loggers and last loggers line | extract_xml_loggers_from_lines |
| Extract everything between first operators and last operators line | extract_xml_operators_from_lines |
| Get the lines of an XML section, including the section tags | extract_xml_section_from_lines |
| Convert a FASTA file to a table of sequences | fasta_file_to_sequences |
| Finds a clock model with a certain ID | find_clock_model |
| Find the first line that satisfies a regex | find_first_regex_line |
| Find the line number of the first section's opening tag | find_first_xml_opening_tag_line |
| Find the index of the last line that matches a regex | find_last_regex_line |
| Find the highest line number of a section's closing tag | find_last_xml_closing_tag_line |
| Creates the 'freq_equilibrium' as XML | freq_equilibrium_to_xml |
| Internal function | freq_param_to_xml |
| Internal function | gamma_distr_to_xml |
| Internal function. | gamma_site_model_to_xml_prior_distr |
| Converts a gamma site model to XML, used in the 'state' section | gamma_site_model_to_xml_state |
| Deprecated function | gamma_site_models_to_xml_prior_distr |
| Conclude the ID from a FASTA filename. | get_alignment_id |
| Get the alignment IDs from one or more files. | get_alignment_ids |
| Get the alignment ID from one or more FASTA filenames. | get_alignment_ids_from_fasta_filenames |
| Get the path to the beautier temporary files folder | get_beautier_folder |
| Get the full path of a file in the 'inst/extdata' folder | get_beautier_path |
| Get the full paths of files in the 'inst/extdata' folder | get_beautier_paths |
| Get a temporary filename | get_beautier_tempfilename |
| Get the BEAUti name for a clock model | get_clock_model_name |
| Get the clock model names | get_clock_model_names |
| Collect the IDs of the list of clock models | get_clock_models_ids |
| Obtain the crown age of a phylogeny. | get_crown_age |
| Get the default `namespace` element value of the `beast` XML tag. | get_default_beast_namespace |
| Get the default `namespace` element value of the `beast` XML tag for BEAST 2.4 | get_default_beast_namespace_v2_4 |
| Get the default `namespace` element value of the `beast` XML tag for BEAST 2.6 | get_default_beast_namespace_v2_6 |
| Get the number of parameters a distribution uses | get_distr_n_params |
| Get the distribution names | get_distr_names |
| Get the path of a FASTA file used in testing | get_fasta_filename |
| Get the base of the filename base without extension | get_file_base_sans_ext |
| Returns valid values for the 'freq_equilibrium' argument | get_freq_equilibrium_names |
| Get the number of distributions in a gamma site model | get_gamma_site_model_n_distrs |
| Get the number of distributions a site model has | get_gamma_site_model_n_params |
| Determines if there is at least one non-strict clock model in the list of one or more clock models | get_has_non_strict_clock_model |
| Get the filenames stored in an inference model. | get_inference_model_filenames |
| Get the possible log modes | get_log_modes |
| Get the possible log sorts | get_log_sorts |
| Get the filenames stored in an MCMC. | get_mcmc_filenames |
| Extract the number of taxa from a file | get_n_taxa |
| Get the prefix of operator IDs | get_operator_id_pre |
| Get the parameter names | get_param_names |
| Get a function that, from a filename, returns the part without the directory. | get_remove_dir_fun |
| Get a function that removes the hex string from filenames. | get_remove_hex_fun |
| Get a function to replace the directory of a filename | get_replace_dir_fun |
| Get the number of distributions a site model has | get_site_model_n_distrs |
| Get the number of distributions a site model has | get_site_model_n_params |
| Get the site models' names | get_site_model_names |
| Get the number of distributions a site model has | get_site_models_n_distrs |
| Get the number of distributions one or more site models have | get_site_models_n_params |
| Extract the names of taxa from a file | get_taxa_names |
| Get the number of distributions a tree prior has | get_tree_prior_n_distrs |
| Get the number of parameters a tree prior has | get_tree_prior_n_params |
| Get the tree prior names | get_tree_prior_names |
| Get the number of distributions a tree prior has | get_tree_priors_n_distrs |
| Get the number of parameters a list of tree priors has | get_tree_priors_n_params |
| Get the XML closing tag | get_xml_closing_tag |
| Get the XML opening tag | get_xml_opening_tag |
| Internal function | gtr_site_model_to_xml_prior_distr |
| Converts a site model to XML, used in the 'state' section | gtr_site_model_to_xml_state |
| Determines if the inference model has an MRCA prior. | has_mrca_prior |
| See if the inference model has one MRCA prior with a distribution | has_mrca_prior_with_distr |
| Determine if the 'inference_model' uses a relaxed log-normal clock model. | has_rln_clock_model |
| Determine if the 'inference_model' uses a strict clock model. | has_strict_clock_model |
| Determine if the 'inference_model' uses tip dating. | has_tip_dating |
| Is an XML closing tag with the value of 'section' present among the lines of the text? | has_xml_closing_tag |
| Is an XML opening tag with value 'section' present among the lines of the text? | has_xml_opening_tag |
| Is an XML closing tag with short closing text in one of the lines of the text? | has_xml_short_closing_tag |
| Internal function | hky_site_model_to_xml_prior_distr |
| Converts a site model to XML, used in the 'state' section | hky_site_model_to_xml_state |
| Indent text for a certain number of spaces. If the text is only whitespace, leave it as such | indent |
| Initializes a Birth-Death tree prior | init_bd_tree_prior |
| Initializes a beta distribution | init_beta_distr |
| Initializes a Coalescent Constant Population tree prior | init_ccp_tree_prior |
| Initializes a Coalescent Exponential Population tree prior | init_cep_tree_prior |
| Initializes all clock models | init_clock_models |
| Initializes a distribution | init_distr |
| Initializes an exponential distribution | init_exp_distr |
| Initializes a gamma distribution | init_gamma_distr |
| Initializes a gamma site model | init_gamma_site_model |
| Initializes a GTR site model | init_gtr_site_model |
| Initializes an HKY site model | init_hky_site_model |
| Initialize an inference model | init_inference_model |
| Initializes an inverse gamma distribution | init_inv_gamma_distr |
| Initializes a JC69 site model | init_jc69_site_model |
| Initializes an Laplace distribution | init_laplace_distr |
| Initializes an log-normal distribution | init_log_normal_distr |
| Initialize the MRCA prior. | init_mrca_prior |
| Initializes all MRCA priors | init_mrca_priors |
| Initializes an normal distribution | init_normal_distr |
| Initializes an one-divided-by-x distribution | init_one_div_x_distr |
| Initializes a parameter | init_param |
| Initializes an Poisson distribution | init_poisson_distr |
| Initializes a Relaxed Log-Normal clock model | init_rln_clock_model |
| Initializes all site models | init_site_models |
| Initializes a strict clock model | init_strict_clock_model |
| Initializes a TN93 site model | init_tn93_site_model |
| Initializes all tree priors | init_tree_priors |
| Initializes a uniform distribution | init_uniform_distr |
| Initializes a Yule tree prior | init_yule_tree_prior |
| Puts spaces in between the lines | interspace |
| Determine if the object is a valid alpha parameter | is_alpha_param |
| Determine if the object is a valid b_pop_sizes parameter | is_b_pop_sizes_param |
| Determine if the object is a valid Birth Death tree prior | is_bd_tree_prior |
| Determine if the object is a valid 'beauti_options' | is_beauti_options |
| Determine if the object is a valid beta distribution, as created by 'create_beta_distr' | is_beta_distr |
| Determine if the object is a valid beta parameter | is_beta_param |
| Determine if the object is a valid constant coalescent Bayesian skyline prior | is_cbs_tree_prior |
| Determine if the object is a valid constant coalescence population tree prior | is_ccp_tree_prior |
| Determine if the object is a valid coalescent exponential population tree prior | is_cep_tree_prior |
| Determine if the object is a valid clock_model | is_clock_model |
| Determines if the name is a valid clock model name | is_clock_model_name |
| Determine if the object is a valid clock_rate parameter | is_clock_rate_param |
| Determine if the MCMC is a default MCMC | is_default_mcmc |
| Determine if the object is a valid distribution | is_distr |
| Determines if the name is a valid distribution name | is_distr_name |
| Determine if the object is a valid exponential distribution as created by 'create_exp_distr' | is_exp_distr |
| Checks if 'name' is a valid 'freq_equilibrium' argument value | is_freq_equilibrium_name |
| Determine if the object is a valid freq parameter | is_freq_param |
| Determine if the object is a valid gamma distribution, as created by 'create_gamma_distr' | is_gamma_distr |
| Is object x a gamma site model? | is_gamma_site_model |
| Determine if the object is a valid GTR site model, as created by 'create_gtr_site_model' | is_gtr_site_model |
| Determine if the object is a valid HKY site model, as created by 'create_hky_site_model' | is_hky_site_model |
| Determine if the object is a valid ID | is_id |
| Is there at least one regular expression having a match with the line? | is_in_patterns |
| Determine if the input is an inference model | is_inference_model |
| Determine if x is an initialized Birth-Death tree_prior object | is_init_bd_tree_prior |
| Determine if x is an initialized beta distribution object as created by 'create_beta_distr' | is_init_beta_distr |
| Determine if x is an initialized Coalescent Bayesian Skyline tree_prior object | is_init_cbs_tree_prior |
| Determine if x is an initialized Coalescent Constant Population tree_prior object | is_init_ccp_tree_prior |
| Determine if x is an initialized Coalescent Exponential Population tree_prior object | is_init_cep_tree_prior |
| Determine if x is an initialized clock_model object, as created by 'create_clock_model' | is_init_clock_model |
| Determine if x is an initialized distribution object as created by 'create_distr' | is_init_distr |
| Determine if x is an initialized exponential distribution object as created by 'create_exp_distr' | is_init_exp_distr |
| Determine if x is an initialized gamma distribution object | is_init_gamma_distr |
| Determine if x is an initialized gamma site model, as created by 'create_gamma_site_model' | is_init_gamma_site_model |
| Determine if x is an initialized GTR site model as created by 'create_gtr_site_model' | is_init_gtr_site_model |
| Determine if x is an initialized HKY site model as created by 'create_hky_site_model' | is_init_hky_site_model |
| Determine if x is an initialized inverse-gamma distribution as created by 'create_inv_gamma_distr' | is_init_inv_gamma_distr |
| Determine if x is an initialized JC69 site model as created by 'create_jc69_site_model' | is_init_jc69_site_model |
| Determine if x is an initialized Laplace distribution as created by 'create_laplace_distr' | is_init_laplace_distr |
| Determine if x is an initialized log_normal distribution object as created by 'create_log_normal_distr' | is_init_log_normal_distr |
| Determine if x is an initialized MRCA prior | is_init_mrca_prior |
| Determine if x is an initialized normal distribution object as created by 'create_normal_distr' | is_init_normal_distr |
| Determine if x is an initialized one_div_x distribution object as created by 'create_one_div_x_distr' | is_init_one_div_x_distr |
| Determine if x is an initialized parameter, as created by create_param | is_init_param |
| Determine if x is an initialized Poisson distribution object as created by 'create_poisson_distr' | is_init_poisson_distr |
| Determine if x is an initialized relaxed log-normal clock_model object | is_init_rln_clock_model |
| Determine if x is an initialized site model, as created by 'create_site_model' | is_init_site_model |
| Determine if x is an initialized strict clock_model object | is_init_strict_clock_model |
| Determine if x is an initialized tn93 site model as created by 'create_tn93_site_model' | is_init_tn93_site_model |
| Determine if x is an initialized tree_prior objects | is_init_tree_prior |
| Determine if x is an initialized uniform distribution object as created by 'create_uniform_distr' | is_init_uniform_distr |
| Determine if x is an initialized Yule tree_prior object | is_init_yule_tree_prior |
| Determine if the object is a valid inverse-gamma distribution as created by 'create_inv_gamma_distr' | is_inv_gamma_distr |
| Determine if the object is a valid JC69 site model | is_jc69_site_model |
| Determine if the object is a valid kappa 1 parameter | is_kappa_1_param |
| Determine if the object is a valid kappa 2 parameter | is_kappa_2_param |
| Determine if the object is a valid kappa parameter | is_kappa_param |
| Determine if the object is a valid lambda parameter | is_lambda_param |
| Determine if the object is a valid Laplace distribution, as created by 'create_laplace_distr' | is_laplace_distr |
| Determine if the object is a valid log-normal distribution, as created by 'create_log_normal_distr' | is_log_normal_distr |
| Determine if the object is a valid m parameter | is_m_param |
| Determine if the object is a valid MCMC | is_mcmc |
| Determine if the object is a valid Nested-Sampling MCMC, as used in [1] | is_mcmc_nested_sampling is_nested_sampling_mcmc |
| Determine if the object is a valid mean parameter | is_mean_param |
| Determine if an MRCA prior's alignment IDs is present in the FASTA file | is_mrca_align_id_in_fasta |
| Determine if an MRCA prior's alignment IDs are present in the FASTA files | is_mrca_align_ids_in_fastas |
| Determine of the object is an empty ('NA') or valid MRCA prior. | is_mrca_prior |
| See if x is one MRCA prior with a distribution | is_mrca_prior_with_distr |
| Determine if the object is a valid mu parameter | is_mu_param |
| Determine if the object is a valid normal distribution as created by 'create_normal_distr' | is_normal_distr |
| Determines if the environment is AppVeyor | is_on_appveyor |
| Determines if the environment is a continuous integration service | is_on_ci |
| Determines if the environment is GitHub Actions | is_on_github_actions |
| Determines if the environment is Travis CI | is_on_travis |
| Check if the argument is one boolean | is_one_bool |
| Determine if the object is a valid 1/x distribution, as created by 'create_one_div_x_distr' | is_one_div_x_distr |
| Determines if the argument is a double | is_one_double |
| Determine if an object is one empty string | is_one_empty_string |
| Determines if the argument is a whole number | is_one_int |
| Determines if x is one NA | is_one_na |
| Determines if the argument is one string | is_one_string |
| General function to create a distribution. | is_one_string_that_is_a_number |
| Determine if the object is a valid parameter | is_param |
| Determines if the name is a valid parameter name | is_param_name |
| Checks if the input is a phylogeny | is_phylo |
| Determine if the object is a valid Poisson distribution as created by 'create_poisson_distr' | is_poisson_distr |
| Determine if the object is a valid 'rate AC' parameter | is_rate_ac_param |
| Determine if the object is a valid 'rate AG' parameter | is_rate_ag_param |
| Determine if the object is a valid 'rate AT' parameter | is_rate_at_param |
| Determine if the object is a valid 'rate CG' parameter | is_rate_cg_param |
| Determine if the object is a valid 'rate CT' parameter | is_rate_ct_param |
| Determine if the object is a valid 'rate GT' parameter | is_rate_gt_param |
| Determine if the object is a valid relaxed log normal clock model | is_rln_clock_model |
| Determine if the object is a valid s parameter | is_s_param |
| Determine if the object is a valid scale parameter | is_scale_param |
| Determine if the object is a valid sigma parameter | is_sigma_param |
| Determine if the object is a valid site_model | is_site_model |
| Determines if the name is a valid site_model name | is_site_model_name |
| Determine if the object is a valid strict clock model, as returned by 'create_strict_clock_model' | is_strict_clock_model |
| Determine if the object is a valid TN93 site model, | is_tn93_site_model |
| Determine if an object is a valid tree prior | is_tree_prior |
| Determines if the name is a valid tree prior name | is_tree_prior_name |
| Determine if the object is a valid uniform distribution as created by 'create_uniform_distr' | is_uniform_distr |
| Checks if the text is a valid XML node, that is, it has a opening and matching closing tag | is_xml |
| Determine if the object is a valid Yule tree prior, | is_yule_tree_prior |
| Converts a site model to XML, used in the 'state' section | jc69_site_model_to_xml_state |
| Internal function | kappa_param_to_xml |
| Internal function | m_param_to_xml |
| Converts an MCMC object to the run section's XML | mcmc_to_xml_run |
| Converts an MCMC object to the run section's XML for a default MCMC | mcmc_to_xml_run_default |
| Converts an MCMC object to the run section's XML for a Nested-Sampling MCMC | mcmc_to_xml_run_nested_sampling |
| Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file. | mrca_prior_to_xml_prior_distr |
| Internal function to create the XML of an MRCA prior, as used in the 'state' section | mrca_prior_to_xml_state |
| Creates the 'taxonset' section in the prior section of the distribution section of a BEAST2 XML parameter file. | mrca_prior_to_xml_taxonset |
| Internal function | mrca_prior_to_xml_tracelog |
| Creates the the 'distribution''s prior section (which is part of a posterior distribution section) of a BEAST2 XML parameter file. | mrca_priors_to_xml_prior_distr |
| 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 |
| Check there are no files in the default beautier folder | remove_beautier_folder |
| Remove all lines that are only whitespace | remove_empty_lines |
| Remove consecutive lines | remove_multiline |
| Rename the filenames in an inference model | rename_inference_model_filenames |
| Rename the filenames within an MCMC | rename_mcmc_filenames |
| Internal function | 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 |
| Creates the XML of a random phylogeny, as used in the 'init' section | rnd_phylo_to_xml_init |
| Internal function | s_parameter_to_xml |
| Converts a site model to XML, used in the 'operators' section | site_model_to_xml_operators |
| Internal function | site_model_to_xml_prior_distr |
| Internal function to convert a site model to XML, used in the `state` section | site_model_to_xml_state |
| Creates the site model's XML for the tracelog section | site_model_to_xml_tracelog |
| Write the XML 'operators' section from the site models. | site_models_to_xml_operators |
| Represent the site models as XML | site_models_to_xml_prior_distr |
| Creates the site models' XML for the tracelog section | site_models_to_xml_tracelog |
| 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 |
| Converts a site model to XML, used in the 'state' section | tn93_site_model_to_xml_state |
| Internal function | tree_model_to_tracelog_xml |
| Internal function | tree_prior_to_xml_operators |
| Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file. | tree_prior_to_xml_prior_distr |
| Creates the XML of a tree prior, as used in the 'state' section | tree_prior_to_xml_state |
| Creates the tree prior's XML for the tracelog section | tree_prior_to_xml_tracelog |
| Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file. | tree_priors_to_xml_prior_distr |
| Creates the tree priors' XML for the tracelog section | tree_priors_to_xml_tracelog |
| Unindents text | unindent |
| Internal function | yule_tree_prior_to_xml_operators |
| Creates the 'prior' section in the prior section of the prior section of the distribution section of a BEAST2 XML parameter file for a Yule tree prior | yule_tree_prior_to_xml_prior_distr |
