All functions

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()

Determine if XML files result in equivalent trees

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

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

beautier

beautier: A package to create a BEAST2 input file.

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

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_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_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_lh_distr()

Converts a clock model to the branchRateModel section of the XML as text.

clock_model_to_xml_operators()

Converts a clock model to the operators section of the XML as text

clock_model_to_xml_prior_distr()

Converts a clock model to the prior section of the XML as text

clock_model_to_xml_state()

Converts a clock model to the state section of the XML as text

clock_model_to_xml_tracelog()

Creates the clock model's XML for the tracelog section

clock_model_to_xml_treelogger()

Convert a clock model to the XML of the TreeLogger

clock_models_to_xml_operators()

Create all clock models' operators' XML text

clock_models_to_xml_prior_distr()

Represent the clock models as XML

clock_models_to_xml_state()

Converts one or more clock models to the state section of the XML as text

clock_models_to_xml_state_check_deprecated()

Internal function to check if clock_models_to_xml_state uses deprecated arguments.

clock_models_to_xml_tracelog()

Creates the clock models' XML for the tracelog section

compare_lines()

Internal debug function to compare the actually created lines to expected lines using any diff tool

count_trailing_spaces()

Count the number of spaces before the first character

create_alpha_param()

Create a parameter called alpha

create_bd_tree_prior()

Create a Birth-Death tree prior

create_beast2_beast_xml()

Create the <beast ...> XML

create_beast2_input()

Create a BEAST2 XML input text

create_beast2_input_beast()

Creates the XML text for the beast tag of a BEAST2 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_beta_distr()

Create a beta distribution

create_beta_param()

Create a parameter called beta

create_branch_rate_model_rln_xml()

Internal function to call create_branch_rate_model_xml for a relaxed log-normal clock.

create_branch_rate_model_sc_xml()

Internal function to call create_branch_rate_model_xml for a strict clock.

create_branch_rate_model_stuff_xml()

Internal function called by create_branch_rate_model_xml

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_data_xml()

Create the <data ..> XML

create_distr()

General function to create a distribution.

create_exp_distr()

Create an exponential distribution

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_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_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_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_model()

Create a strict clock model

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

create_test_tracelog()

Create a tracelog object

create_test_treelog()

Create a treelog object

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()

Creates the tracelog section of the logger section of a BEAST2 XML parameter file

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_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()

Converts a distribution to XML

distr_to_xml_beta()

Converts a beta distribution to XML

distr_to_xml_exp()

Converts an exponential distribution to XML

distr_to_xml_gamma()

Converts a gamma distribution to XML

distr_to_xml_inv_gamma()

Converts an inverse-gamma distribution to XML

distr_to_xml_laplace()

Converts a Laplace distribution to XML

distr_to_xml_log_normal()

Converts a log-normal distribution to XML

distr_to_xml_normal()

Converts a normal distribution to XML

distr_to_xml_one_div_x()

Converts a 1/x distribution to XML

distr_to_xml_poisson()

Converts a Poisson distribution to XML

distr_to_xml_uniform()

Converts a uniform distribution to XML

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

gamma_site_model_to_xml_prior_distr()

Creates the gamma site models section in the distribution section of a BEAST2 XML parameter file

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()

Creates the gamma site models section in the distribution section of a BEAST2 XML parameter file

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_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_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_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

has_mrca_prior()

Determines if the inference model has an MRCA prior.

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?

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_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_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_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_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_int()

Determines if the argument is a whole number

is_one_na()

Determines if x is one NA

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,

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_lh_distr()

Converts an MRCA prior to the branchRateModel section of the XML as text.

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()

Creates the MRCA prior's XML for the tracelog section

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.

mrca_priors_to_xml_state()

Deprecated

mrca_priors_to_xml_tracelog()

Creates the MRCA priors' XML for the tracelog section

no_taxa_to_xml_tree()

Creates the 'tree' section of a BEAST2 XML parameter file, which is part of a 'state' section, without being indented, when there is no tip-dating

parameter_to_xml()

Converts a parameter to XML

parameter_to_xml_alpha()

Converts an alpha parameter to XML

parameter_to_xml_beta()

Converts a beta parameter to XML

parameter_to_xml_clock_rate()

Converts a clockRate parameter to XML

parameter_to_xml_kappa_1()

Converts a kappa 1 parameter to XML

parameter_to_xml_kappa_2()

Converts a kappa 2 parameter to XML

parameter_to_xml_lambda()

Converts a lambda parameter to XML

parameter_to_xml_m()

Converts a m parameter to XML

parameter_to_xml_mean()

Converts a mean parameter to XML

parameter_to_xml_mu()

Converts a mu parameter to XML

parameter_to_xml_rate_ac()

Converts a 'rate AC' parameter to XML

parameter_to_xml_rate_ag()

Converts a 'rate AG' parameter to XML

parameter_to_xml_rate_at()

Converts a 'rate AT' parameter to XML

parameter_to_xml_rate_cg()

Converts a 'rate CG' parameter to XML

parameter_to_xml_rate_ct()

Converts a 'rate CT' parameter to XML

parameter_to_xml_rate_gt()

Converts a 'rate GT' parameter to XML

parameter_to_xml_s()

Converts a s parameter to XML

parameter_to_xml_scale()

Converts a scale parameter to XML

parameter_to_xml_sigma()

Converts a sigma parameter to XML

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()

Used by clock_models_to_xml_prior_distr

rnd_phylo_to_xml_init()

Creates the XML of a random phylogeny, as used in the init section

site_model_to_xml_lh_distr()

Creates the XML text for the siteModel tag of a BEAST2 parameter file.

site_model_to_xml_operators()

Converts a site model to XML, used in the operators section

site_model_to_xml_prior_distr()

Converts a site model to XML, used in the prior section

site_model_to_xml_state()

Converts a site model to XML, used in the state section

site_model_to_xml_subst_model()

Converts a site model to XML, used in the substModel 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_state()

Deprecated function

site_models_to_xml_tracelog()

Creates the site models' XML for the tracelog section

taxa_to_xml_tree()

Creates the 'tree' section of a BEAST2 XML parameter file

tipdate_taxa_to_xml_tree()

Creates the tree section (part of the state section) when there is tip-dating

tree_models_to_xml_tracelog()

Creates the tree models' XML for the tracelog section

tree_prior_to_xml_operators()

Creates the XML of a tree prior, as used in the operators section

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_operators()

Creates the XML of a list of one or more tree priors, as used in the operators 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_state()

Converts one or more tree priors to the state section of the XML as text

tree_priors_to_xml_tracelog()

Creates the tree priors' XML for the tracelog section

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