
Function reference
-
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
-
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 aBEAST2
input file.
-
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 validbeauti_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 validgtr_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 validparam
object.
-
check_param_types()
- Check if the
param
has the list elements of the right type for a validparam
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 validscreenlog
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 validsite_model
object.
-
check_site_model_types()
- Check if the
site_model
has the list elements of the right type for a validsite_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 validtn93_site_model
object.
-
check_tracelog()
- Check if a
tracelog
is valid.
-
check_tracelog_names()
- Check if the
tracelog
has the list elements of a validtracelog
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 validtreelog
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()
- Converts a clock model to the
operators
section of the XML as text
-
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_models_to_xml_operators()
- Deprecated
-
clock_models_to_xml_prior_distr()
- Deprecated function
-
clock_models_to_xml_state()
- Deprecated internal function
-
clock_models_to_xml_tracelog()
- Deprecated internal function
-
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_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 thelikelihood
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_rln_xml()
- Internal function
-
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
, andcreate_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 bycreate_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_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_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_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 thelogger
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
parameter
s within thesiteModel
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
andcreate_tn93_site_model
-
create_site_models_from_names()
- Create site models from their names
-
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
-
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()
- 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 thetreeLikelihood
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
andcreate_yule_tree_prior
-
create_treelog()
- Create a
treelog
object
-
create_treelog_xml()
- Creates the XML text for the
logger
tag with IDtreelog
. 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
-
gamma_distr_to_xml()
- Internal function
-
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_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_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_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?
-
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 validfreq_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,
-
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.
-
mrca_priors_to_xml_tracelog()
- Creates the MRCA priors' XML for the tracelog section
-
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_s()
- 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()
- Used by
clock_models_to_xml_prior_distr
-
rln_clock_model_to_xml_prior_distr()
- Internal function
-
rnd_phylo_to_xml_init()
- Creates the XML of a random phylogeny,
as used in the
init
section
-
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_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
-
taxa_to_xml_tree()
- Internal function
-
tipdate_taxa_to_xml_trait()
- Internal function
-
tipdate_taxa_to_xml_tree()
- Internal function
-
tree_model_to_tracelog_xml()
- Internal function
-
tree_models_to_xml_tracelog()
- Creates the tree models' XML for the tracelog section
-
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_operators()
- Deprecated
-
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