Determine if two MCMCs are equal.
Internal function
Determine if two tracelogs are equal.
Determine if XML files result in equal trees
Determine if x consists out of clock_models objects
Internal function
Determine if XML lines result in equivalent trees
Determine if two screenlogs are equal.
Determine if x consists out of initialized clock_models objects
are_equivalent_xml_lines_operators
Determine if XML operator lines result in equivalent trees
Determine if x consists out of initialized site_models objects
Determine if two treelogs are equal.
Determine if x consists out of initialized MRCA priors
are_mrca_align_ids_in_fasta
Determine if the MRCA priors' alignment IDs are present in the FASTA files
are_equivalent_xml_lines_loggers
Determine if XML operator lines result in equivalent trees
are_equivalent_xml_lines_all
Determine if XML lines result in equivalent trees
Determine if XML lines result in equal trees
Determine if x consists out of MRCA priors
Determine if x consists out of IDs
beautier: A package to create a BEAST2 input file.
Checks if all filenames have a FASTA filename extension
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
are_equivalent_xml_lines_section
Determine if XML lines result in equivalent trees
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
Internal function
Check if the object is a list of one or more clock models.
check_empty_beautier_folder
Internal function
Determine if x consists out of initialized tree_priors objects
are_mrca_taxon_names_in_fasta
Determine if the MRCA priors' taxa names are present in the FASTA files
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
Are the clock models Relaxed Log-Normal clock models?
ccp_tree_prior_to_xml_state
Convert a CCP tree prior
to the XML as part of the state section
Checks if the parameter is a valid gamma site model
check_mrca_prior_taxa_names
Check the MRCA prior's taxon names are valid.
Check if the `filename` is valid
Internal function
check_file_and_model_agree
Checks if the input FASTA file and the inference model agree.
b_pop_sizes_parameter_to_xml
Internal function
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 if mrca_prior_name is a valid MRCA prior name.
check_gamma_site_model_names
Checks if the gamma site model has the right list elements' names
Check if the MRCA prior,
which is a list, has all the named elements.
check_gtr_site_model_names
Check if the gtr_site_model has the list elements
of a valid gtr_site_model object.
Check if the alignment_id is valid.
Check if the MRCA prior is a valid MRCA prior.
Check if the site_model has the list elements
of a valid site_model object.
Check if the site_model has the list elements
of the right type for a valid site_model object.
Check if the param has the list elements
of the right type for a valid param object.
clock_model_to_xml_prior_distr
Internal function
Determine if x consists out of site_models objects
Check if this an MCMC that uses Nested Sampling
to estimate a marginal likelihood.
Check if the gtr_site_model is a valid
GTR nucleotide substitution model.
Check if the supplied mode is a valid logging mode.
Determine if x consists out of tree_priors objects
Check if the parameter is a valid parameter
Internal function
Check if the supplied object is a valid
Bayesian phylogenetic inference model.
Check if the MCMC has the list elements with valid values
for being a valid MCMC object.
Function to check if a file exists.
Calls stop if the file is absent
Check if the supplied sort is a valid logging sorting option.
Check if the phylogeny is a valid phylogeny object.
check_tn93_site_model_names
Check if the tn93_site_model has the list elements
of a valid tn93_site_model object.
clock_model_to_xml_treelogger
Convert a clock model to the XML of the TreeLogger
Check if a screenlog is valid.
Check if the object is a list of one or more site models.
Check if the param has the list elements
of a valid param object.
Internal function
Check if a tracelog is valid.
Check if the tracelog has the list elements
of a valid tracelog object.
Check if the screenlog has the list elements
of a valid screenlog object.
Check if the beauti_options is a valid beauti_options object.
Check if the rename function is a valid filename rename function
Check if the tracelog has the list elements with valid values
for being a valid tracelog object.
Check if the site model is a valid site model
Check if store_every holds a valid value
Check if the treelog has the list elements with valid values
for being a valid treelog object.
Count the number of spaces before the first character
create_beast2_input_state
Creates the 'state' section of a BEAST2 XML parameter file
Creates the 'run' section of a BEAST2 XML parameter file
Internal function
create_beast2_input_distr_prior
Creates the prior section in 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.
clock_model_to_xml_tracelog
Internal function
clock_model_to_xml_operators
Internal function
Function to create a set of `BEAUti` options.
Create an HKY site model
Create a parameter called clock_rate,
as needed by create_strict_clock_model
Create a Bayesian phylogenetic inference model.
Create the <beast ...> XML
create_beast2_input_from_model
Create a BEAST2 XML input text from an inference model
Creates the init section of a BEAST2 XML parameter file
Create a BEAST2 XML input text
Create the <data ..> XML
Check if the clock model is a valid clock model.
Check if the tree prior is a valid tree prior
create_clock_rate_state_node_parameter_xml
Internal function
Check if the clock model is a valid clock model.
Create a Laplace distribution
Create a relaxed log-normal clock model
create_beast2_input_file_from_model
Create a BEAST2 input file from an inference model
create_beauti_options_v2_4
Function to create the BEAUti options for version 2.4.
Create a parameter called alpha
Create a parameter called kappa
create_hky_subst_model_xml
Converts a site model to XML,
used in the substModel section
Check if the MCMC is a valid MCMC object.
Check if the inference_model is a valid BEAUti inference model.
create_beast2_input_data_sequences
Creates the data section of a BEAST2 XML parameter file
Check if the treelog has the list elements
of a valid treelog object.
Check if is_monophyletic has a valid value.
Create a Most Recent Common Ancestor prior
create_beast2_input_distr
Creates the distribution section of a BEAST2 XML parameter file.
Check if the screenlog has the list elements with valid values
for being a valid screenlog object.
check_mcmc_list_element_names
Check if the MCMC has the list elements of a valid MCMC object.
Create a 1/x distribution
General function to create a distribution.
Create a parameter called sigma
Check if the object is a list of one or more tree priors.
Create a Coalescent Bayesian Skyline tree prior
create_branch_rate_model_xml
Internal function to create the branchRateModel section
of the XML as text.
Create an normal distribution
Create an inverse-gamma distribution
Create a GTR site model
General function to create a clock model
create_clock_model_from_name
Create a clock model from name
Create an MCMC configuration.
Create a parameter called lambda
Create a screenlog object, to be used in testing
Create a Poisson distribution
Create a Coalescent Constant Population tree prior
create_gtr_subst_model_xml
Converts a GTR site model to XML,
used in the substModel section
Create a BEAST2 input file
Check if the tn93_site_model is a valid
TN93 nucleotide substitution model.
Check if a treelog is valid.
Creates the screenlog section of the logger section
of a BEAST2 XML parameter file
Check if the clock model is a valid clock model.
create_beast2_input_beast
Creates the XML text for the beast tag of a BEAST2 parameter file.
General function to create a parameter.
Create a parameter called `b_pop_sizes`.
Creates the data section of a BEAST2 XML parameter file
create_beast2_input_operators
Creates the operators section of a BEAST2 XML parameter file
Internal function
extract_xml_operators_from_lines
Extract everything between first operators and last operators line
Create a Coalescent Exponential Population tree prior
Create a beta distribution
Create a parameter called 'rate CT'
Create a gamma distribution
Create a gamma site model, part of a site model
Create a parameter called beta
Create a JC69 site model
create_jc69_subst_model_xml
Converts a JC69 site model to XML,
used in the substModel section
Create a parameter called 'rate AC'
create_tn93_subst_model_xml
Converts a TN93 site model to XML,
used in the substModel section
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
Creates the three logger sections of a BEAST2 XML parameter file
Create a treelog object to be used in testing
Create a parameter called mu
create_site_models_from_names
Create site models from their names
Get the full path of a file in the inst/extdata folder
Create a log-normal distribution
Create a parameter called m
create_beauti_options_v2_6
Function to create the BEAUti options for version 2.6.
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
find_last_xml_closing_tag_line
Find the highest line number of a section's closing tag
Get the alignment IDs from one or more files.
Create a parameter called s
create_strict_clock_rate_scaler_operator_xml
Internal function
gamma_site_model_to_xml_state
Converts a gamma site model to XML,
used in the state section
create_ns_inference_model
Create an inference model to measure the evidence of.
Create a parameter called kappa 1
Create a parameter called 'rate CG'
Create a Birth-Death tree prior
get_default_beast_namespace_v2_4
Get the default `namespace` element value of the `beast` XML tag
for BEAST 2.4
Creates all supported clock models,
which is a list of the types returned by
create_rln_clock_model,
and create_strict_clock_model
Creates the map section of a BEAST2 XML parameter file
Internal function to create the substModel section
Get a function that, from a filename, returns the part
without the directory.
Create an NS MCMC object for testing
Create a tracelog object
Create a parameter called scale
Create a screenlog object
Get the parameter names
Internal function
Create a parameter called 'rate GT'
create_strict_clock_model
Create a strict clock model
create_strict_clock_branch_rate_model_xml
Internal function.
create_temp_screenlog_filename
Create a filename for a temporary `screenlog` file
Create a parameter called 'rate AG'
Get the number of parameters a distribution uses
Create a parameter called mean
create_rln_clock_branch_rate_model_xml
Internal function
get_inference_model_filenames
Get the filenames stored in an inference model.
Create a TN93 site model
Create a tracelog object, as used for testing
create_temp_tracelog_filename
Create a filename for a temporary `tracelog` file
create_site_model_parameters_xml
Internal function to creates the XML text for the
parameters within the siteModel section
of a BEAST2 parameter file.
extract_xml_section_from_lines
Get the lines of an XML section, including the section tags
get_gamma_site_model_n_params
Get the number of distributions a site model has
Internal function
Internal function
Internal function
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_clock_models_from_names
Create clock models from their names
Get a function that removes the hex string from filenames.
Obtain the crown age of a phylogeny.
Get the XML closing tag
create_temp_treelog_filename
Create a filename for a temporary `treelog` file
create_beautier_tempfolder
Create the default `beautier` temporary folder
Internal function
Create a trait set string.
Create a treelog object
create_test_inference_model
Create a testing inference model.
Internal function
Get the number of parameters a list of tree priors has
Create an exponential distribution
Determines if the argument is one string
extract_xml_loggers_from_lines
Extract everything between first loggers and last loggers line
Initializes a Relaxed Log-Normal clock model
gamma_site_model_to_xml_prior_distr
Internal function.
Checks if name is a valid freq_equilibrium argument value
get_default_beast_namespace_v2_6
Get the default `namespace` element value of the `beast` XML tag
for BEAST 2.6
mrca_prior_to_xml_taxonset
Creates the taxonset section in the prior section of the
distribution section of a BEAST2 XML parameter file.
Determine if x is an initialized MRCA prior
Get the distribution names
Internal function
Conclude the ID from a FASTA filename.
Determine if the object is a valid mean parameter
get_alignment_ids_from_fasta_filenames
Get the alignment ID from one or more FASTA filenames.
Determine if the object is a valid
constant coalescence population tree prior
Determines if the name is a valid distribution name
Initializes all site models
Get the filenames stored in an MCMC.
General function to create a site model.
Get the site models' names
Internal function to creates the XML text for the siteModel tag
of a BEAST2 parameter file.
find_first_xml_opening_tag_line
Find the line number of the first section's opening tag
Internal function to create a tree prior
Create a parameter called kappa 2
is_one_string_that_is_a_number
General function to create a distribution.
Create a parameter called freq
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 a uniform distribution
Create an MCMC object to estimate the marginal likelihood
using Nested Sampling.
Convert a FASTA file to a table of sequences
Create an MCMC configuration for testing.
Determines if the name is a valid parameter name
Create a parameter called 'rate AT'
create_rate_categories_state_node_xml
Internal function
create_site_model_from_name
Create a site model from name
Get the possible log sorts
Find the index of the last line that matches a regex
Extract the number of taxa from a file
Initializes all clock models
Get the path to the beautier temporary files folder
tree_model_to_tracelog_xml
Internal function
Determine if the inference_model uses tip dating.
Determine if the inference_model uses a strict clock model.
Is object x a gamma site model?
Initializes a Coalescent Exponential Population tree prior
get_default_beast_namespace
Get the default `namespace` element value of the `beast` XML tag.
create_ucld_mean_state_node_param_xml
Internal function
Get the prefix of operator IDs
Initializes an Laplace distribution
create_ucld_stdev_state_node_param_xml
Internal function
Get the clock model names
Initializes a TN93 site model
Initialize the MRCA prior.
Create the XML declaration of the BEAST2 XML input file
Create a Yule tree prior
get_freq_equilibrium_names
Returns valid values for the freq_equilibrium argument
Initializes a distribution
Get a function to replace the directory of a filename
Initializes an one-divided-by-x distribution
Internal function
Internal function
create_test_ns_inference_model
Create an inference model to be tested by Nested Sampling
create_tree_likelihood_distr_xml
Creates the XML text for the distribution tag
with the treeLikelihood ID,
of a BEAST2 parameter file.
Internal function
Internal function
Get the tree prior names
Creates the freq_equilibrium as XML
get_beautier_tempfilename
Get a temporary filename
Get the number of parameters a tree prior has
Documentation of parameters (for example, create_param.
This function does nothing. It is intended to inherit documentation from.
Initializes a GTR site model
get_gamma_site_model_n_distrs
Get the number of distributions in a gamma site model
Is an XML closing tag with the value of section
present among the lines of
the text?
Get the path of a FASTA file used in testing
gtr_site_model_to_xml_state
Converts a site model to XML,
used in the state section
Determine if the object is a valid distribution
hky_site_model_to_xml_prior_distr
Internal function
Initializes a gamma site model
Extract the names of taxa from a file
Determine if the object is a valid Birth Death tree prior
Get the number of distributions one or more site models have
Internal function
Documentation of general function arguments.
This function does nothing.
It is intended to inherit function argument documentation.
has_xml_short_closing_tag
Is an XML closing tag with short closing text in
one of the lines of the text?
Determine if the object is a valid MCMC
Find the first line that satisfies a regex
Get the number of distributions a site model has
Is an XML opening tag with value 'section' present among the lines of
the text?
Determine if the object is a valid
'rate AT' parameter
Determine if the MCMC is a default MCMC
Initializes a beta distribution
Get the full paths of files in the inst/extdata folder
Determine if the object is a valid
'rate AG' parameter
Determine if the object is a valid
scale parameter
Determine if the object is a valid beauti_options
Determine if the object is a valid
gamma distribution,
as created by create_gamma_distr
Determine if the inference_model uses
a relaxed log-normal clock model.
Initializes a Birth-Death tree prior
strict_clock_model_to_xml_prior_distr
Internal function
Finds a clock model with a certain ID
Initializes an normal distribution
Determines if the inference model has an MRCA prior.
Determine if x is an initialized normal distribution object
as created by create_normal_distr
Initializes a uniform distribution
Determine if x is an initialized relaxed log-normal clock_model object
Determine if the object is a valid constant coalescent Bayesian skyline prior
Initializes all tree priors
Determine if the object is a valid
Poisson distribution
as created by create_poisson_distr
Initializes an HKY site model
Determine if the object is a valid
alpha parameter
Initializes a parameter
Determine if x is an initialized clock_model object,
as created by create_clock_model
Initialize an inference model
Initializes a Yule tree prior
Determines if the name is a valid tree prior name
Puts spaces in between the lines
Initializes a strict clock model
gamma_site_models_to_xml_prior_distr
Deprecated function
Determines if the name is a valid clock model name
Internal function
has_mrca_prior_with_distr
See if the inference model has one MRCA prior with a distribution
Determine if the object is a valid freq parameter
Determine if x is an initialized Coalescent Constant Population
tree_prior object
Get the possible log modes
Collect the IDs of the list of clock models
site_model_to_xml_operators
Converts a site model to XML,
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.
Determine if the object is a valid parameter
Determine if x is an initialized uniform distribution object
as created by create_uniform_distr
Internal function to convert a site model to XML,
used in the `state` section
Determine if the object is a valid
clock_rate parameter
Determine if the object is a valid GTR site model,
as created by create_gtr_site_model
Get the number of distributions a site model has
Determine if the object is a valid lambda parameter
Internal function
Determines if the environment is GitHub Actions
Determine if x is an initialized gamma site model,
as created by create_gamma_site_model
Determine if x is an initialized GTR site model
as created by create_gtr_site_model
Determine if x is an initialized gamma distribution object
Determine if the object is a valid HKY site model,
as created by create_hky_site_model
Get the BEAUti name for a clock model
Determine if x is an initialized HKY site model
as created by create_hky_site_model
Determine if x is an initialized inverse-gamma distribution
as created by create_inv_gamma_distr
Internal function to create the XML of an MRCA prior,
as used in the state section
Initializes an log-normal distribution
Determine if the object is a valid relaxed log normal clock model
Get the base of the filename base without extension
Get the number of distributions a tree prior has
Initializes an Poisson distribution
Determine if the object is a valid ID
Get the number of distributions a tree prior has
Determine if x is an initialized log_normal distribution object
as created by create_log_normal_distr
Determine if the object is a valid kappa parameter
Determine if the object is a valid
m parameter
Initializes a Coalescent Constant Population tree prior
Determine if x is an initialized exponential distribution object
as created by create_exp_distr
Determine if the object is a valid
sigma parameter
is_mrca_align_ids_in_fastas
Determine if an MRCA prior's alignment IDs are present in the FASTA files
is_init_strict_clock_model
Determine if x is an initialized strict clock_model object
Determine if the object is a valid
b_pop_sizes parameter
Get the number of distributions a site model has
Determine if the object is a valid JC69 site model
Determine if the object is a valid kappa 1 parameter
Determine if the object is a valid
log-normal distribution,
as created by create_log_normal_distr
Determine if the object is a valid
exponential distribution
as created by create_exp_distr
Get the XML opening tag
hky_site_model_to_xml_state
Converts a site model to XML,
used in the state section
gtr_site_model_to_xml_prior_distr
Internal function
Initializes a gamma distribution
Indent text for a certain number of spaces.
If the text is only whitespace, leave it as such
Determine if x is an initialized Birth-Death tree_prior object
Initializes an exponential distribution
tipdate_taxa_to_xml_trait
Internal function
Determine if x is an initialized tree_prior objects
Determine if x is an initialized Poisson distribution object
as created by create_poisson_distr
is_mrca_align_id_in_fasta
Determine if an MRCA prior's alignment IDs is present in the FASTA file
Determine if the object is a valid
coalescent exponential population tree prior
Determine if the object is a valid clock_model
rln_clock_model_to_xml_mean_rate_prior
Internal function
See if x is one MRCA prior with a distribution
Determine if the object is a valid
s parameter
Determine if the object is a valid
mu parameter
Determines if the argument is a whole number
Initializes a JC69 site model
Initializes an inverse gamma distribution
Is there at least one regular expression having a match with the line?
Determine if the object is a valid TN93 site model,
Determine if x is an initialized parameter,
as created by create_param
Determine if x is an initialized tn93 site model
as created by create_tn93_site_model
Determines if the name is a valid site_model name
Initializes all MRCA priors
Rename the filenames within an MCMC
Converts an MCMC object to the run section's XML for a default MCMC
Determine if the object is a valid
'rate GT' parameter
Determine if the object is a valid strict clock model,
as returned by create_strict_clock_model
Determine if the object is a valid
beta distribution,
as created by create_beta_distr
Internal function
Determine if the input is an inference model
Determine if the object is a valid site_model
Determine if x is an initialized JC69 site model
as created by create_jc69_site_model
Determine if x is an initialized Coalescent Exponential Population
tree_prior object
strict_clock_model_to_xml_tracelog
Internal function
Determine if x is an initialized Yule tree_prior object
strict_clock_model_to_xml_state
Internal function
Determine if x is an initialized Laplace distribution
as created by create_laplace_distr
Determine if the object is a valid
beta parameter
Internal function
Determine if the object is a valid
inverse-gamma distribution
as created by create_inv_gamma_distr
Determines if the environment is a continuous integration service
Determine if x is an initialized distribution object
as created by create_distr
Determine if the object is a valid Nested-Sampling MCMC,
as used in [1]
Creates the XML of a random phylogeny,
as used in the init section
Internal function
Determine if x is an initialized beta distribution object
as created by create_beta_distr
Determine if x is an initialized Coalescent Bayesian Skyline
tree_prior object
Determine if the object is a valid
Laplace distribution,
as created by create_laplace_distr
Determine if x is an initialized one_div_x distribution object
as created by create_one_div_x_distr
Internal function
Determine if an object is one empty string
rln_clock_model_to_xml_operators
Internal function
Internal function
Determine if the object is a valid kappa 2 parameter
Check there are no files in the default beautier folder
Checks if the input is a phylogeny
Determine of the object is an empty (NA) or valid MRCA prior.
rln_clock_model_to_xml_state
Internal function
mcmc_to_xml_run_nested_sampling
Converts an MCMC object to the run section's XML for a Nested-Sampling MCMC
Internal function
Determine if an object is a valid tree prior
Internal function
Internal function
site_models_to_xml_prior_distr
Represent the site models as XML
Converts an MCMC object to the run section's XML
Determine if x is an initialized site model,
as created by create_site_model
Internal function
Determine if the object is a valid
1/x distribution,
as created by create_one_div_x_distr
Check if the argument is one boolean
tn93_site_model_to_xml_prior_distr
Internal function
Determines if the environment is Travis CI
Determines if x is one NA
jc69_site_model_to_xml_state
Converts a site model to XML,
used in the state section
Remove all lines that are only whitespace
Internal function
Determines if the argument is a double
Determine if the object is a valid
'rate AC' parameter
Determines if the environment is AppVeyor
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
Determine if the object is a valid
normal distribution
as created by create_normal_distr
rln_clock_model_to_xml_tracelog
Internal function
Internal function
Internal function
site_model_to_xml_prior_distr
Internal function
Internal function
Determine if the object is a valid
uniform distribution
as created by create_uniform_distr
mrca_prior_to_xml_tracelog
Internal function
Internal function
Determine if the object is a valid
'rate CT' parameter
Determine if the object is a valid
'rate CG' parameter
mrca_prior_to_xml_prior_distr
Creates the distribution section in the prior section of the
distribution section of a BEAST2 XML parameter file.
Determine if the object is a valid Yule tree prior,
Checks if the text is a valid XML node, that is,
it has a opening and matching closing tag
site_models_to_xml_operators
Write the XML operators section from the site models.
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.
site_models_to_xml_tracelog
Creates the site models' XML for the tracelog section
Internal function
yule_tree_prior_to_xml_operators
Internal function
Internal function
strict_clock_model_to_xml_operators
Internal function
Creates the XML of a tree prior,
as used in the state section
rename_inference_model_filenames
Rename the filenames in an inference model
Internal function
tree_prior_to_xml_operators
Internal function
Remove consecutive lines
tree_prior_to_xml_tracelog
Creates the tree prior's XML for the tracelog section
rln_clock_model_to_xml_prior_distr
Internal function
tree_priors_to_xml_prior_distr
Creates the distribution section in the prior section of the
distribution section of a BEAST2 XML parameter file.
Unindents text
tree_priors_to_xml_tracelog
Creates the tree priors' XML for the tracelog section
Internal function
tn93_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