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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
