|
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 |
