Man pages for richelbilderbeek/beastscriptr
'BEAUti' from R

alpha_parameter_to_xmlInternal function
are_clock_modelsDetermine if x consists out of clock_models objects
are_equal_mcmcsDetermine if two MCMCs are equal.
are_equal_screenlogsDetermine if two screenlogs are equal.
are_equal_tracelogsDetermine if two tracelogs are equal.
are_equal_treelogsDetermine if two treelogs are equal.
are_equal_xml_filesDetermine if XML files result in equal trees
are_equal_xml_linesDetermine if XML lines result in equal trees
are_equivalent_xml_filesInternal function
are_equivalent_xml_linesDetermine if XML lines result in equivalent trees
are_equivalent_xml_lines_allDetermine if XML lines result in equivalent trees
are_equivalent_xml_lines_loggersDetermine if XML operator lines result in equivalent trees
are_equivalent_xml_lines_operatorsDetermine if XML operator lines result in equivalent trees
are_equivalent_xml_lines_sectionDetermine if XML lines result in equivalent trees
are_fasta_filenamesChecks if all filenames have a FASTA filename extension
are_idsDetermine if x consists out of IDs
are_init_clock_modelsDetermine if x consists out of initialized clock_models...
are_init_mrca_priorsDetermine if x consists out of initialized MRCA priors
are_init_site_modelsDetermine if x consists out of initialized site_models...
are_init_tree_priorsDetermine if x consists out of initialized tree_priors...
are_mrca_align_ids_in_fastaDetermine if the MRCA priors' alignment IDs are present in...
are_mrca_priorsDetermine if x consists out of MRCA priors
are_mrca_taxon_names_in_fastaDetermine if the MRCA priors' taxa names are present in the...
are_rln_clock_modelsAre the clock models Relaxed Log-Normal clock models?
are_site_modelsDetermine if x consists out of site_models objects
are_tree_priorsDetermine if x consists out of tree_priors objects
bd_tree_prior_to_xml_prior_distrCreates the tree prior section in the prior section of the...
beautier-package'beautier': A package to create a 'BEAST2' input file.
beta_parameter_to_xmlInternal function
b_pop_sizes_parameter_to_xmlInternal function
b_pop_sizes_param_to_xmlInternal function
cbs_tree_prior_to_xml_prior_distrCreates the tree prior section in the prior section of the...
ccp_tree_prior_to_xml_prior_distrCreates the tree prior section in the prior section of the...
ccp_tree_prior_to_xml_stateConvert a CCP tree prior to the XML as part of the 'state'...
cep_tree_prior_to_xml_prior_distrCreates the tree prior section in the prior section of the...
check_alignment_idCheck if the 'alignment_id' is valid.
check_beauti_optionsCheck if the 'beauti_options' is a valid 'beauti_options'...
check_clock_modelCheck if the clock model is a valid clock model.
check_clock_modelsCheck if the object is a list of one or more clock models.
check_empty_beautier_folderInternal function
check_file_and_model_agreeChecks if the input FASTA file and the inference model agree.
check_file_existsFunction to check if a file exists. Calls 'stop' if the file...
check_filenameCheck if the 'filename' is valid
check_gamma_site_modelChecks if the parameter is a valid gamma site model
check_gamma_site_model_namesChecks if the gamma site model has the right list elements'...
check_gtr_site_modelCheck if the 'gtr_site_model' is a valid GTR nucleotide...
check_gtr_site_model_namesCheck if the 'gtr_site_model' has the list elements of a...
check_inference_modelCheck if the supplied object is a valid Bayesian phylogenetic...
check_inference_modelsCheck if the 'inference_model' is a valid BEAUti inference...
check_is_monophyleticCheck if 'is_monophyletic' has a valid value.
check_log_modeCheck if the supplied 'mode' is a valid logging mode.
check_log_sortCheck if the supplied 'sort' is a valid logging sorting...
check_mcmcCheck if the MCMC is a valid MCMC object.
check_mcmc_list_element_namesCheck if the MCMC has the list elements of a valid MCMC...
check_mcmc_valuesCheck if the MCMC has the list elements with valid values for...
check_mrca_priorCheck if the MRCA prior is a valid MRCA prior.
check_mrca_prior_nameCheck if 'mrca_prior_name' is a valid MRCA prior name.
check_mrca_prior_namesCheck if the MRCA prior, which is a list, has all the named...
check_mrca_prior_taxa_namesCheck the MRCA prior's taxon names are valid.
check_ns_mcmcCheck if this an MCMC that uses Nested Sampling to estimate a...
check_paramCheck if the parameter is a valid parameter
check_param_namesCheck if the 'param' has the list elements of a valid 'param'...
check_param_typesCheck if the 'param' has the list elements of the right type...
check_phylogenyCheck if the phylogeny is a valid phylogeny object.
check_rename_funCheck if the rename function is a valid filename rename...
check_rln_clock_modelCheck if the clock model is a valid clock model.
check_screenlogCheck if a 'screenlog' is valid.
check_screenlog_namesCheck if the 'screenlog' has the list elements of a valid...
check_screenlog_valuesCheck if the screenlog has the list elements with valid...
check_site_modelCheck if the site model is a valid site model
check_site_model_namesCheck if the 'site_model' has the list elements of a valid...
check_site_modelsCheck if the object is a list of one or more site models.
check_site_model_typesCheck if the 'site_model' has the list elements of the right...
check_store_everyCheck if 'store_every' holds a valid value
check_strict_clock_modelCheck if the clock model is a valid clock model.
check_tn93_site_modelCheck if the 'tn93_site_model' is a valid TN93 nucleotide...
check_tn93_site_model_namesCheck if the 'tn93_site_model' has the list elements of a...
check_tracelogCheck if a 'tracelog' is valid.
check_tracelog_namesCheck if the 'tracelog' has the list elements of a valid...
check_tracelog_valuesCheck if the tracelog has the list elements with valid values...
check_treelogCheck if a 'treelog' is valid.
check_treelog_namesCheck if the 'treelog' has the list elements of a valid...
check_treelog_valuesCheck if the treelog has the list elements with valid values...
check_tree_priorCheck if the tree prior is a valid tree prior
check_tree_priorsCheck if the object is a list of one or more tree priors.
clock_model_to_xml_operatorsInternal function
clock_model_to_xml_prior_distrInternal function
clock_model_to_xml_stateInternal function
clock_model_to_xml_tracelogInternal function
clock_model_to_xml_treeloggerConvert a clock model to the XML of the 'TreeLogger'
clock_rate_param_to_xmlInternal function
compare_linesInternal function
count_trailing_spacesCount the number of spaces before the first character
create_alpha_paramCreate a parameter called alpha
create_bd_tree_priorCreate a Birth-Death tree prior
create_beast2_beast_xmlCreate the '<beast ...>' XML
create_beast2_inputCreate a BEAST2 XML input text
create_beast2_input_beastCreates the XML text for the 'beast' tag of a BEAST2...
create_beast2_input_dataCreates the 'data' section of a BEAST2 XML parameter file
create_beast2_input_data_sequencesCreates the data section of a BEAST2 XML parameter file
create_beast2_input_distrCreates the distribution section of a BEAST2 XML parameter...
create_beast2_input_distr_lhCreates the XML text for the 'distribution' tag with the...
create_beast2_input_distr_priorCreates the prior section in the distribution section of a...
create_beast2_input_fileCreate a BEAST2 input file
create_beast2_input_file_from_modelCreate a BEAST2 input file from an inference model
create_beast2_input_from_modelCreate a BEAST2 XML input text from an inference model
create_beast2_input_initCreates the 'init' section of a BEAST2 XML parameter file
create_beast2_input_mapCreates the map section of a BEAST2 XML parameter file
create_beast2_input_operatorsCreates the operators section of a BEAST2 XML parameter file
create_beast2_input_runCreates the "run" section of a BEAST2 XML parameter file
create_beast2_input_stateCreates the "state" section of a BEAST2 XML parameter file
create_beautier_tempfolderCreate the default 'beautier' temporary folder
create_beauti_optionsFunction to create a set of 'BEAUti' options.
create_beauti_options_v2_4Function to create the BEAUti options for version 2.4.
create_beauti_options_v2_6Function to create the BEAUti options for version 2.6.
create_beta_distrCreate a beta distribution
create_beta_paramCreate a parameter called beta
create_b_pop_sizes_paramCreate a parameter called 'b_pop_sizes'.
create_branch_rate_model_xmlInternal function to create the 'branchRateModel' section of...
create_cbs_tree_priorCreate a Coalescent Bayesian Skyline tree prior
create_ccp_tree_priorCreate a Coalescent Constant Population tree prior
create_cep_tree_priorCreate a Coalescent Exponential Population tree prior
create_clock_modelGeneral function to create a clock model
create_clock_model_from_nameCreate a clock model from name
create_clock_modelsCreates all supported clock models, which is a list of the...
create_clock_models_from_namesCreate clock models from their names
create_clock_rate_paramCreate a parameter called 'clock_rate', as needed by...
create_clock_rate_state_node_parameter_xmlInternal function
create_data_xmlCreate the '<data ..>' XML
create_distrGeneral function to create a distribution.
create_exp_distrCreate an exponential distribution
create_freq_paramCreate a parameter called freq
create_gamma_distrCreate a gamma distribution
create_gamma_site_modelCreate a gamma site model, part of a site model
create_gtr_site_modelCreate a GTR site model
create_gtr_subst_model_xmlConverts a GTR site model to XML, used in the 'substModel'...
create_hky_site_modelCreate an HKY site model
create_hky_subst_model_xmlConverts a site model to XML, used in the 'substModel'...
create_inference_modelCreate a Bayesian phylogenetic inference model.
create_inv_gamma_distrCreate an inverse-gamma distribution
create_jc69_site_modelCreate a JC69 site model
create_jc69_subst_model_xmlConverts a JC69 site model to XML, used in the 'substModel'...
create_kappa_1_paramCreate a parameter called kappa 1
create_kappa_2_paramCreate a parameter called kappa 2
create_kappa_paramCreate a parameter called kappa
create_lambda_paramCreate a parameter called lambda
create_laplace_distrCreate a Laplace distribution
create_loggers_xmlCreates the three logger sections of a BEAST2 XML parameter...
create_log_normal_distrCreate a log-normal distribution
create_mcmcCreate an MCMC configuration.
create_mean_paramCreate a parameter called mean
create_m_paramCreate a parameter called m
create_mrca_priorCreate a Most Recent Common Ancestor prior
create_mu_paramCreate a parameter called mu
create_normal_distrCreate an normal distribution
create_ns_inference_modelCreate an inference model to measure the evidence of.
create_ns_mcmcCreate an MCMC object to estimate the marginal likelihood...
create_one_div_x_distrCreate a 1/x distribution
create_paramGeneral function to create a parameter.
create_poisson_distrCreate a Poisson distribution
create_rate_ac_paramCreate a parameter called 'rate AC'
create_rate_ag_paramCreate a parameter called 'rate AG'
create_rate_at_paramCreate a parameter called 'rate AT'
create_rate_categories_state_node_xmlInternal function
create_rate_cg_paramCreate a parameter called 'rate CG'
create_rate_ct_paramCreate a parameter called 'rate CT'
create_rate_gt_paramCreate a parameter called 'rate GT'
create_rln_clock_branch_rate_model_xmlInternal function
create_rln_clock_modelCreate a relaxed log-normal clock model
create_scale_paramCreate a parameter called scale
create_screenlogCreate a 'screenlog' object
create_screenlog_xmlCreates the 'screenlog' section of the 'logger' section of a...
create_sigma_paramCreate a parameter called sigma
create_site_modelGeneral function to create a site model.
create_site_model_from_nameCreate a site model from name
create_site_model_parameters_xmlInternal function to creates the XML text for the...
create_site_modelsCreates all supported site models which is a list of the...
create_site_models_from_namesCreate site models from their names
create_site_model_xmlInternal function to creates the XML text for the 'siteModel'...
create_s_paramCreate a parameter called s
create_strict_clock_branch_rate_model_xmlInternal function.
create_strict_clock_modelCreate a strict clock model
create_strict_clock_rate_scaler_operator_xmlInternal function
create_subst_model_xmlInternal function to create the 'substModel' section
create_temp_screenlog_filenameCreate a filename for a temporary 'screenlog' file
create_temp_tracelog_filenameCreate a filename for a temporary 'tracelog' file
create_temp_treelog_filenameCreate a filename for a temporary 'treelog' file
create_test_inference_modelCreate a testing inference model.
create_test_mcmcCreate an MCMC configuration for testing.
create_test_ns_inference_modelCreate an inference model to be tested by Nested Sampling
create_test_ns_mcmcCreate an NS MCMC object for testing
create_test_screenlogCreate a 'screenlog' object, to be used in testing
create_test_tracelogCreate a 'tracelog' object, as used for testing
create_test_treelogCreate a 'treelog' object to be used in testing
create_tn93_site_modelCreate a TN93 site model
create_tn93_subst_model_xmlConverts a TN93 site model to XML, used in the 'substModel'...
create_tracelogCreate a 'tracelog' object
create_tracelog_xmlInternal function
create_trait_set_stringCreate a trait set string.
create_tree_likelihood_distr_xmlCreates the XML text for the 'distribution' tag with the...
create_treelogCreate a 'treelog' object
create_treelog_xmlCreates the XML text for the 'logger' tag with ID 'treelog'....
create_tree_priorInternal function to create a tree prior
create_tree_priorsCreates all supported tree priors, which is a list of the...
create_ucld_mean_state_node_param_xmlInternal function
create_ucld_stdev_state_node_param_xmlInternal function
create_uniform_distrCreate a uniform distribution
create_xml_declarationCreate the XML declaration of the BEAST2 XML input file
create_yule_tree_priorCreate a Yule tree prior
default_parameters_docDocumentation of parameters (for example, 'create_param'....
default_params_docDocumentation of general function arguments. This function...
distr_to_xmlInternal function
distr_to_xml_betaInternal function
distr_to_xml_expInternal function
distr_to_xml_inv_gammaInternal function
distr_to_xml_laplaceInternal function
distr_to_xml_log_normalInternal function
distr_to_xml_normalInternal function
distr_to_xml_one_div_xInternal function
distr_to_xml_poissonInternal function
distr_to_xml_uniformInternal function
extract_xml_loggers_from_linesExtract everything between first loggers and last loggers...
extract_xml_operators_from_linesExtract everything between first operators and last operators...
extract_xml_section_from_linesGet the lines of an XML section, including the section tags
fasta_file_to_sequencesConvert a FASTA file to a table of sequences
find_clock_modelFinds a clock model with a certain ID
find_first_regex_lineFind the first line that satisfies a regex
find_first_xml_opening_tag_lineFind the line number of the first section's opening tag
find_last_regex_lineFind the index of the last line that matches a regex
find_last_xml_closing_tag_lineFind the highest line number of a section's closing tag
freq_equilibrium_to_xmlCreates the 'freq_equilibrium' as XML
freq_param_to_xmlInternal function
gamma_distr_to_xmlInternal function
gamma_site_models_to_xml_prior_distrDeprecated function
gamma_site_model_to_xml_prior_distrInternal function.
gamma_site_model_to_xml_stateConverts a gamma site model to XML, used in the 'state'...
get_alignment_idConclude the ID from a FASTA filename.
get_alignment_idsGet the alignment IDs from one or more files.
get_alignment_ids_from_fasta_filenamesGet the alignment ID from one or more FASTA filenames.
get_beautier_folderGet the path to the beautier temporary files folder
get_beautier_pathGet the full path of a file in the 'inst/extdata' folder
get_beautier_pathsGet the full paths of files in the 'inst/extdata' folder
get_beautier_tempfilenameGet a temporary filename
get_clock_model_nameGet the BEAUti name for a clock model
get_clock_model_namesGet the clock model names
get_clock_models_idsCollect the IDs of the list of clock models
get_crown_ageObtain the crown age of a phylogeny.
get_default_beast_namespaceGet the default 'namespace' element value of the 'beast' XML...
get_default_beast_namespace_v2_4Get the default 'namespace' element value of the 'beast' XML...
get_default_beast_namespace_v2_6Get the default 'namespace' element value of the 'beast' XML...
get_distr_namesGet the distribution names
get_distr_n_paramsGet the number of parameters a distribution uses
get_fasta_filenameGet the path of a FASTA file used in testing
get_file_base_sans_extGet the base of the filename base without extension
get_freq_equilibrium_namesReturns valid values for the 'freq_equilibrium' argument
get_gamma_site_model_n_distrsGet the number of distributions in a gamma site model
get_gamma_site_model_n_paramsGet the number of distributions a site model has
get_has_non_strict_clock_modelDetermines if there is at least one non-strict clock model in...
get_inference_model_filenamesGet the filenames stored in an inference model.
get_log_modesGet the possible log modes
get_log_sortsGet the possible log sorts
get_mcmc_filenamesGet the filenames stored in an MCMC.
get_n_taxaExtract the number of taxa from a file
get_operator_id_preGet the prefix of operator IDs
get_param_namesGet the parameter names
get_remove_dir_funGet a function that, from a filename, returns the part...
get_remove_hex_funGet a function that removes the hex string from filenames.
get_replace_dir_funGet a function to replace the directory of a filename
get_site_model_namesGet the site models' names
get_site_model_n_distrsGet the number of distributions a site model has
get_site_model_n_paramsGet the number of distributions a site model has
get_site_models_n_distrsGet the number of distributions a site model has
get_site_models_n_paramsGet the number of distributions one or more site models have
get_taxa_namesExtract the names of taxa from a file
get_tree_prior_namesGet the tree prior names
get_tree_prior_n_distrsGet the number of distributions a tree prior has
get_tree_prior_n_paramsGet the number of parameters a tree prior has
get_tree_priors_n_distrsGet the number of distributions a tree prior has
get_tree_priors_n_paramsGet the number of parameters a list of tree priors has
get_xml_closing_tagGet the XML closing tag
get_xml_opening_tagGet the XML opening tag
gtr_site_model_to_xml_prior_distrInternal function
gtr_site_model_to_xml_stateConverts a site model to XML, used in the 'state' section
has_mrca_priorDetermines if the inference model has an MRCA prior.
has_mrca_prior_with_distrSee if the inference model has one MRCA prior with a...
has_rln_clock_modelDetermine if the 'inference_model' uses a relaxed log-normal...
has_strict_clock_modelDetermine if the 'inference_model' uses a strict clock model.
has_tip_datingDetermine if the 'inference_model' uses tip dating.
has_xml_closing_tagIs an XML closing tag with the value of 'section' present...
has_xml_opening_tagIs an XML opening tag with value 'section' present among the...
has_xml_short_closing_tagIs an XML closing tag with short closing text in one of the...
hky_site_model_to_xml_prior_distrInternal function
hky_site_model_to_xml_stateConverts a site model to XML, used in the 'state' section
indentIndent text for a certain number of spaces. If the text is...
init_bd_tree_priorInitializes a Birth-Death tree prior
init_beta_distrInitializes a beta distribution
init_ccp_tree_priorInitializes a Coalescent Constant Population tree prior
init_cep_tree_priorInitializes a Coalescent Exponential Population tree prior
init_clock_modelsInitializes all clock models
init_distrInitializes a distribution
init_exp_distrInitializes an exponential distribution
init_gamma_distrInitializes a gamma distribution
init_gamma_site_modelInitializes a gamma site model
init_gtr_site_modelInitializes a GTR site model
init_hky_site_modelInitializes an HKY site model
init_inference_modelInitialize an inference model
init_inv_gamma_distrInitializes an inverse gamma distribution
init_jc69_site_modelInitializes a JC69 site model
init_laplace_distrInitializes an Laplace distribution
init_log_normal_distrInitializes an log-normal distribution
init_mrca_priorInitialize the MRCA prior.
init_mrca_priorsInitializes all MRCA priors
init_normal_distrInitializes an normal distribution
init_one_div_x_distrInitializes an one-divided-by-x distribution
init_paramInitializes a parameter
init_poisson_distrInitializes an Poisson distribution
init_rln_clock_modelInitializes a Relaxed Log-Normal clock model
init_site_modelsInitializes all site models
init_strict_clock_modelInitializes a strict clock model
init_tn93_site_modelInitializes a TN93 site model
init_tree_priorsInitializes all tree priors
init_uniform_distrInitializes a uniform distribution
init_yule_tree_priorInitializes a Yule tree prior
interspacePuts spaces in between the lines
is_alpha_paramDetermine if the object is a valid alpha parameter
is_bd_tree_priorDetermine if the object is a valid Birth Death tree prior
is_beauti_optionsDetermine if the object is a valid 'beauti_options'
is_beta_distrDetermine if the object is a valid beta distribution, as...
is_beta_paramDetermine if the object is a valid beta parameter
is_b_pop_sizes_paramDetermine if the object is a valid b_pop_sizes parameter
is_cbs_tree_priorDetermine if the object is a valid constant coalescent...
is_ccp_tree_priorDetermine if the object is a valid constant coalescence...
is_cep_tree_priorDetermine if the object is a valid coalescent exponential...
is_clock_modelDetermine if the object is a valid clock_model
is_clock_model_nameDetermines if the name is a valid clock model name
is_clock_rate_paramDetermine if the object is a valid clock_rate parameter
is_default_mcmcDetermine if the MCMC is a default MCMC
is_distrDetermine if the object is a valid distribution
is_distr_nameDetermines if the name is a valid distribution name
is_exp_distrDetermine if the object is a valid exponential distribution...
is_freq_equilibrium_nameChecks if 'name' is a valid 'freq_equilibrium' argument value
is_freq_paramDetermine if the object is a valid freq parameter
is_gamma_distrDetermine if the object is a valid gamma distribution, as...
is_gamma_site_modelIs object x a gamma site model?
is_gtr_site_modelDetermine if the object is a valid GTR site model, as created...
is_hky_site_modelDetermine if the object is a valid HKY site model, as created...
is_idDetermine if the object is a valid ID
is_inference_modelDetermine if the input is an inference model
is_init_bd_tree_priorDetermine if x is an initialized Birth-Death tree_prior...
is_init_beta_distrDetermine if x is an initialized beta distribution object as...
is_init_cbs_tree_priorDetermine if x is an initialized Coalescent Bayesian Skyline...
is_init_ccp_tree_priorDetermine if x is an initialized Coalescent Constant...
is_init_cep_tree_priorDetermine if x is an initialized Coalescent Exponential...
is_init_clock_modelDetermine if x is an initialized clock_model object, as...
is_init_distrDetermine if x is an initialized distribution object as...
is_init_exp_distrDetermine if x is an initialized exponential distribution...
is_init_gamma_distrDetermine if x is an initialized gamma distribution object
is_init_gamma_site_modelDetermine if x is an initialized gamma site model, as created...
is_init_gtr_site_modelDetermine if x is an initialized GTR site model as created by...
is_init_hky_site_modelDetermine if x is an initialized HKY site model as created by...
is_init_inv_gamma_distrDetermine if x is an initialized inverse-gamma distribution...
is_init_jc69_site_modelDetermine if x is an initialized JC69 site model as created...
is_init_laplace_distrDetermine if x is an initialized Laplace distribution as...
is_init_log_normal_distrDetermine if x is an initialized log_normal distribution...
is_init_mrca_priorDetermine if x is an initialized MRCA prior
is_init_normal_distrDetermine if x is an initialized normal distribution object...
is_init_one_div_x_distrDetermine if x is an initialized one_div_x distribution...
is_init_paramDetermine if x is an initialized parameter, as created by...
is_init_poisson_distrDetermine if x is an initialized Poisson distribution object...
is_init_rln_clock_modelDetermine if x is an initialized relaxed log-normal...
is_init_site_modelDetermine if x is an initialized site model, as created by...
is_init_strict_clock_modelDetermine if x is an initialized strict clock_model object
is_init_tn93_site_modelDetermine if x is an initialized tn93 site model as created...
is_init_tree_priorDetermine if x is an initialized tree_prior objects
is_init_uniform_distrDetermine if x is an initialized uniform distribution object...
is_init_yule_tree_priorDetermine if x is an initialized Yule tree_prior object
is_in_patternsIs there at least one regular expression having a match with...
is_inv_gamma_distrDetermine if the object is a valid inverse-gamma distribution...
is_jc69_site_modelDetermine if the object is a valid JC69 site model
is_kappa_1_paramDetermine if the object is a valid kappa 1 parameter
is_kappa_2_paramDetermine if the object is a valid kappa 2 parameter
is_kappa_paramDetermine if the object is a valid kappa parameter
is_lambda_paramDetermine if the object is a valid lambda parameter
is_laplace_distrDetermine if the object is a valid Laplace distribution, as...
is_log_normal_distrDetermine if the object is a valid log-normal distribution,...
is_mcmcDetermine if the object is a valid MCMC
is_mcmc_nested_samplingDetermine if the object is a valid Nested-Sampling MCMC, as...
is_mean_paramDetermine if the object is a valid mean parameter
is_m_paramDetermine if the object is a valid m parameter
is_mrca_align_id_in_fastaDetermine if an MRCA prior's alignment IDs is present in the...
is_mrca_align_ids_in_fastasDetermine if an MRCA prior's alignment IDs are present in the...
is_mrca_priorDetermine of the object is an empty ('NA') or valid MRCA...
is_mrca_prior_with_distrSee if x is one MRCA prior with a distribution
is_mu_paramDetermine if the object is a valid mu parameter
is_normal_distrDetermine if the object is a valid normal distribution as...
is_on_appveyorDetermines if the environment is AppVeyor
is_on_ciDetermines if the environment is a continuous integration...
is_one_boolCheck if the argument is one boolean
is_one_div_x_distrDetermine if the object is a valid 1/x distribution, as...
is_one_doubleDetermines if the argument is a double
is_one_empty_stringDetermine if an object is one empty string
is_one_intDetermines if the argument is a whole number
is_one_naDetermines if x is one NA
is_one_stringDetermines if the argument is one string
is_one_string_that_is_a_numberGeneral function to create a distribution.
is_on_github_actionsDetermines if the environment is GitHub Actions
is_on_travisDetermines if the environment is Travis CI
is_paramDetermine if the object is a valid parameter
is_param_nameDetermines if the name is a valid parameter name
is_phyloChecks if the input is a phylogeny
is_poisson_distrDetermine if the object is a valid Poisson distribution as...
is_rate_ac_paramDetermine if the object is a valid 'rate AC' parameter
is_rate_ag_paramDetermine if the object is a valid 'rate AG' parameter
is_rate_at_paramDetermine if the object is a valid 'rate AT' parameter
is_rate_cg_paramDetermine if the object is a valid 'rate CG' parameter
is_rate_ct_paramDetermine if the object is a valid 'rate CT' parameter
is_rate_gt_paramDetermine if the object is a valid 'rate GT' parameter
is_rln_clock_modelDetermine if the object is a valid relaxed log normal clock...
is_scale_paramDetermine if the object is a valid scale parameter
is_sigma_paramDetermine if the object is a valid sigma parameter
is_site_modelDetermine if the object is a valid site_model
is_site_model_nameDetermines if the name is a valid site_model name
is_s_paramDetermine if the object is a valid s parameter
is_strict_clock_modelDetermine if the object is a valid strict clock model, as...
is_tn93_site_modelDetermine if the object is a valid TN93 site model,
is_tree_priorDetermine if an object is a valid tree prior
is_tree_prior_nameDetermines if the name is a valid tree prior name
is_uniform_distrDetermine if the object is a valid uniform distribution as...
is_xmlChecks if the text is a valid XML node, that is, it has a...
is_yule_tree_priorDetermine if the object is a valid Yule tree prior,
jc69_site_model_to_xml_stateConverts a site model to XML, used in the 'state' section
kappa_param_to_xmlInternal function
mcmc_to_xml_runConverts an MCMC object to the run section's XML
mcmc_to_xml_run_defaultConverts an MCMC object to the run section's XML for a...
mcmc_to_xml_run_nested_samplingConverts an MCMC object to the run section's XML for a...
m_param_to_xmlInternal function
mrca_priors_to_xml_prior_distrCreates the the 'distribution"s prior section (which is part...
mrca_prior_to_xml_prior_distrCreates the distribution section in the prior section of the...
mrca_prior_to_xml_stateInternal function to create the XML of an MRCA prior, as used...
mrca_prior_to_xml_taxonsetCreates the 'taxonset' section in the prior section of the...
mrca_prior_to_xml_tracelogInternal function
no_taxa_to_xml_treeInternal function
parameter_to_xmlInternal function
parameter_to_xml_kappa_1Internal function
parameter_to_xml_kappa_2Internal function
parameter_to_xml_lambdaInternal function
parameter_to_xml_meanInternal function
parameter_to_xml_muInternal function
parameter_to_xml_rate_acInternal function
parameter_to_xml_rate_agInternal function
parameter_to_xml_rate_atInternal function
parameter_to_xml_rate_cgInternal function
parameter_to_xml_rate_ctInternal function
parameter_to_xml_rate_gtInternal function
parameter_to_xml_scaleInternal function
parameter_to_xml_sigmaInternal function
remove_beautier_folderCheck there are no files in the default beautier folder
remove_empty_linesRemove all lines that are only whitespace
remove_multilineRemove consecutive lines
rename_inference_model_filenamesRename the filenames in an inference model
rename_mcmc_filenamesRename the filenames within an MCMC
rln_clock_model_to_xml_mean_rate_priorInternal function
rln_clock_model_to_xml_operatorsInternal function
rln_clock_model_to_xml_prior_distrInternal function
rln_clock_model_to_xml_stateInternal function
rln_clock_model_to_xml_tracelogInternal function
rnd_phylo_to_xml_initCreates the XML of a random phylogeny, as used in the 'init'...
site_models_to_xml_operatorsWrite the XML 'operators' section from the site models.
site_models_to_xml_prior_distrRepresent the site models as XML
site_models_to_xml_tracelogCreates the site models' XML for the tracelog section
site_model_to_xml_operatorsConverts a site model to XML, used in the 'operators' section
site_model_to_xml_prior_distrInternal function
site_model_to_xml_stateInternal function to convert a site model to XML, used in the...
site_model_to_xml_tracelogCreates the site model's XML for the tracelog section
s_parameter_to_xmlInternal function
strict_clock_model_to_xml_operatorsInternal function
strict_clock_model_to_xml_prior_distrInternal function
strict_clock_model_to_xml_stateInternal function
strict_clock_model_to_xml_tracelogInternal function
taxa_to_xml_treeInternal function
tipdate_taxa_to_xml_traitInternal function
tipdate_taxa_to_xml_treeInternal function
tn93_site_model_to_xml_prior_distrInternal function
tn93_site_model_to_xml_stateConverts a site model to XML, used in the 'state' section
tree_model_to_tracelog_xmlInternal function
tree_priors_to_xml_prior_distrCreates the distribution section in the prior section of the...
tree_priors_to_xml_tracelogCreates the tree priors' XML for the tracelog section
tree_prior_to_xml_operatorsInternal function
tree_prior_to_xml_prior_distrCreates the distribution section in the prior section of the...
tree_prior_to_xml_stateCreates the XML of a tree prior, as used in the 'state'...
tree_prior_to_xml_tracelogCreates the tree prior's XML for the tracelog section
unindentUnindents text
yule_tree_prior_to_xml_operatorsInternal function
yule_tree_prior_to_xml_prior_distrCreates the 'prior' section in the prior section of the prior...
richelbilderbeek/beastscriptr documentation built on Nov. 5, 2023, 8:36 p.m.