Package index

All functions

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 objects

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 objects

are_init_tree_priors(): Determine if x consists out of initialized tree_priors objects

are_mrca_align_ids_in_fasta(): Determine if the MRCA priors' alignment IDs are present in the FASTA files

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 FASTA files

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

b_pop_sizes_param_to_xml(): Internal function

b_pop_sizes_parameter_to_xml(): Internal function

bd_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 Birth-Death tree prior

beta_parameter_to_xml(): Internal function

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 Birth-Death tree prior

ccp_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_state(): Convert a CCP tree prior to the XML as part of the state section

cep_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 Exponential Population tree prior

check_alignment_id(): Check if the alignment_id is valid.

check_beauti_options(): Check if the beauti_options is a valid beauti_options object.

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 is absent

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' names

check_gtr_site_model(): Check if the gtr_site_model is a valid GTR nucleotide substitution model.

check_gtr_site_model_names(): Check if the gtr_site_model has the list elements of a valid gtr_site_model object.

check_inference_model(): Check if the supplied object is a valid Bayesian phylogenetic inference model.

check_inference_models(): Check if the inference_model is a valid BEAUti inference model.

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 option.

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 object.

check_mcmc_values(): Check if the MCMC has the list elements with valid values for being a valid MCMC object.

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 elements.

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 marginal likelihood.

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 object.

check_param_types(): Check if the param has the list elements of the right type for a valid param object.

check_phylogeny(): Check if the phylogeny is a valid phylogeny object.

check_rename_fun(): Check if the rename function is a valid filename rename function

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 screenlog object.

check_screenlog_values(): Check if the screenlog has the list elements with valid values for being a valid screenlog object.

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 site_model object.

check_site_model_types(): Check if the site_model has the list elements of the right type for a valid site_model object.

check_site_models(): Check if the object is a list of one or more site models.

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 substitution model.

check_tn93_site_model_names(): Check if the tn93_site_model has the list elements of a valid tn93_site_model object.

check_tracelog(): Check if a tracelog is valid.

check_tracelog_names(): Check if the tracelog has the list elements of a valid tracelog object.

check_tracelog_values(): Check if the tracelog has the list elements with valid values for being a valid tracelog object.

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.

check_treelog(): Check if a treelog is valid.

check_treelog_names(): Check if the treelog has the list elements of a valid treelog object.

check_treelog_values(): Check if the treelog has the list elements with valid values for being a valid treelog object.

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_b_pop_sizes_param(): Create a parameter called `b_pop_sizes`.

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 parameter file.

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 file.

create_beast2_input_distr_lh(): Creates the XML text for the distribution tag with the likelihood ID, of a BEAST2 parameter file.

create_beast2_input_distr_prior(): Creates the prior section in the distribution section of a BEAST2 XML parameter file

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_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_beautier_tempfolder(): Create the default `beautier` temporary folder

create_beta_distr(): Create a beta distribution

create_beta_param(): Create a parameter called beta

create_branch_rate_model_xml(): Internal function to create the branchRateModel section of the XML as text.

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 types returned by create_rln_clock_model, and create_strict_clock_model

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_strict_clock_model

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 section

create_hky_site_model(): Create an HKY site model

create_hky_subst_model_xml(): Converts a site model to XML, used in the substModel section

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 section

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_log_normal_distr(): Create a log-normal distribution

create_loggers_xml(): Creates the three logger sections of a BEAST2 XML parameter file

create_m_param(): Create a parameter called m

create_mcmc(): Create an MCMC configuration.

create_mean_param(): Create a parameter called mean

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 using Nested Sampling.

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_s_param(): Create a parameter called s

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 BEAST2 XML parameter file

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 parameters within the siteModel section of a BEAST2 parameter file.

create_site_model_xml(): Internal function to creates the XML text for the siteModel tag of a BEAST2 parameter file.

create_site_models(): 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_from_names(): Create site models from their names

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 section

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 treeLikelihood ID, of a BEAST2 parameter file.

create_tree_prior(): Internal function to create a tree prior

create_tree_priors(): 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_treelog(): Create a treelog object

create_treelog_xml(): 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_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. This function does nothing. It is intended to inherit documentation from.

default_params_doc(): Documentation of general function arguments. This function does nothing. It is intended to inherit function argument documentation.

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 line

extract_xml_operators_from_lines(): Extract everything between first operators and last operators line

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_model_to_xml_prior_distr(): Internal function.

gamma_site_model_to_xml_state(): Converts a gamma site model to XML, used in the state section

gamma_site_models_to_xml_prior_distr(): Deprecated function

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 tag.

get_default_beast_namespace_v2_4(): Get the default `namespace` element value of the `beast` XML tag for BEAST 2.4

get_default_beast_namespace_v2_6(): Get the default `namespace` element value of the `beast` XML tag for BEAST 2.6

get_distr_n_params(): Get the number of parameters a distribution uses

get_distr_names(): Get the distribution names

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 the list of one or more clock models

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 without the directory.

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_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_model_names(): Get the site models' names

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_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_prior_names(): Get the tree prior names

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 distribution

has_rln_clock_model(): Determine if the inference_model uses a relaxed log-normal clock model.

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 among the lines of the text?

has_xml_opening_tag(): Is an XML opening tag with value 'section' present among the lines of the text?

has_xml_short_closing_tag(): Is an XML closing tag with short closing text in one of the lines of the text?

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 only whitespace, leave it as such

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_b_pop_sizes_param(): Determine if the object is a valid b_pop_sizes 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 created by create_beta_distr

is_beta_param(): Determine if the object is a valid beta parameter

is_cbs_tree_prior(): Determine if the object is a valid constant coalescent Bayesian skyline prior

is_ccp_tree_prior(): Determine if the object is a valid constant coalescence population tree prior

is_cep_tree_prior(): Determine if the object is a valid coalescent exponential population tree prior

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 as created by create_exp_distr

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 created by create_gamma_distr

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 by create_gtr_site_model

is_hky_site_model(): Determine if the object is a valid HKY site model, as created by create_hky_site_model

is_id(): Determine if the object is a valid ID

is_in_patterns(): Is there at least one regular expression having a match with the line?

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 object

is_init_beta_distr(): Determine if x is an initialized beta distribution object as created by create_beta_distr

is_init_cbs_tree_prior(): Determine if x is an initialized Coalescent Bayesian Skyline tree_prior object

is_init_ccp_tree_prior(): Determine if x is an initialized Coalescent Constant Population tree_prior object

is_init_cep_tree_prior(): Determine if x is an initialized Coalescent Exponential Population tree_prior object

is_init_clock_model(): Determine if x is an initialized clock_model object, as created by create_clock_model

is_init_distr(): Determine if x is an initialized distribution object as created by create_distr

is_init_exp_distr(): Determine if x is an initialized exponential distribution object as created by create_exp_distr

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 by create_gamma_site_model

is_init_gtr_site_model(): Determine if x is an initialized GTR site model as created by create_gtr_site_model

is_init_hky_site_model(): Determine if x is an initialized HKY site model as created by create_hky_site_model

is_init_inv_gamma_distr(): Determine if x is an initialized inverse-gamma distribution as created by create_inv_gamma_distr

is_init_jc69_site_model(): Determine if x is an initialized JC69 site model as created by create_jc69_site_model

is_init_laplace_distr(): Determine if x is an initialized Laplace distribution as created by create_laplace_distr

is_init_log_normal_distr(): Determine if x is an initialized log_normal distribution object as created by create_log_normal_distr

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 as created by create_normal_distr

is_init_one_div_x_distr(): Determine if x is an initialized one_div_x distribution object as created by create_one_div_x_distr

is_init_param(): Determine if x is an initialized parameter, as created by create_param

is_init_poisson_distr(): Determine if x is an initialized Poisson distribution object as created by create_poisson_distr

is_init_rln_clock_model(): Determine if x is an initialized relaxed log-normal clock_model object

is_init_site_model(): Determine if x is an initialized site model, as created by create_site_model

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 by create_tn93_site_model

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 as created by create_uniform_distr

is_init_yule_tree_prior(): Determine if x is an initialized Yule tree_prior object

is_inv_gamma_distr(): Determine if the object is a valid inverse-gamma distribution as created by create_inv_gamma_distr

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 created by create_laplace_distr

is_log_normal_distr(): Determine if the object is a valid log-normal distribution, as created by create_log_normal_distr

is_m_param(): Determine if the object is a valid m parameter

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 used in [1]

is_mean_param(): Determine if the object is a valid mean parameter

is_mrca_align_id_in_fasta(): Determine if an MRCA prior's alignment IDs is present in the FASTA file

is_mrca_align_ids_in_fastas(): Determine if an MRCA prior's alignment IDs are present in the FASTA files

is_mrca_prior(): Determine of the object is an empty (NA) or valid MRCA prior.

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 created by create_normal_distr

is_on_appveyor(): Determines if the environment is AppVeyor

is_on_ci(): Determines if the environment is a continuous integration service

is_on_github_actions(): Determines if the environment is GitHub Actions

is_on_travis(): Determines if the environment is Travis CI

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 created by create_one_div_x_distr

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_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 created by create_poisson_distr

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 model

is_s_param(): Determine if the object is a valid s parameter

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_strict_clock_model(): Determine if the object is a valid strict clock model, as returned by create_strict_clock_model

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 created by create_uniform_distr

is_xml(): Checks if the text is a valid XML node, that is, it has a opening and matching closing tag

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

m_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 default MCMC

mcmc_to_xml_run_nested_sampling(): Converts an MCMC object to the run section's XML for a Nested-Sampling MCMC

mrca_prior_to_xml_prior_distr(): Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file.

mrca_prior_to_xml_state(): Internal function to create the XML of an MRCA prior, as used in the state section

mrca_prior_to_xml_taxonset(): Creates the taxonset section in the prior section of the distribution section of a BEAST2 XML parameter file.

mrca_prior_to_xml_tracelog(): Internal function

mrca_priors_to_xml_prior_distr(): Creates the the distribution's prior section (which is part of a posterior distribution section) of a BEAST2 XML parameter file.

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 section

s_parameter_to_xml(): Internal function

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 `state` section

site_model_to_xml_tracelog(): Creates the site model's XML for the tracelog section

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

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_prior_to_xml_operators(): Internal function

tree_prior_to_xml_prior_distr(): Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file.

tree_prior_to_xml_state(): Creates the XML of a tree prior, as used in the state section

tree_prior_to_xml_tracelog(): Creates the tree prior's XML for the tracelog section

tree_priors_to_xml_prior_distr(): Creates the distribution section in the prior section of the distribution section of a BEAST2 XML parameter file.

tree_priors_to_xml_tracelog(): Creates the tree priors' 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 section of the distribution section of a BEAST2 XML parameter file for a Yule tree prior

All functions

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