beautier2.6.12 package

Determine if the object is a valid 'rate CT' parameter

Determine if the object is a valid 'rate GT' parameter

Determine if the object is a valid relaxed log normal clock model

Determine if the object is a valid kappa 1 parameter

Determine if the object is a valid s parameter

Determine if the object is a valid scale parameter

Determine if the object is a valid sigma parameter

Determine if the object is a valid site_model

Determines if the name is a valid site_model name

Determine if the object is a valid strict clock model, as returned by ...

Determine if the object is a valid TN93 site model,

Determine if an object is a valid tree prior

Determines if the name is a valid tree prior name

Determine if the object is a valid uniform distribution as created by ...

Checks if the text is a valid XML node, that is, it has a opening and ...

Determine if the object is a valid Yule tree prior,

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

Internal function

Internal function

Converts an MCMC object to the run section's XML

Converts an MCMC object to the run section's XML for a default MCMC

Converts an MCMC object to the run section's XML for a Nested-Sampling...

Creates the distribution section in the prior section of the distribut...

Internal function to create the XML of an MRCA prior, as used in the `...

Creates the taxonset section in the prior section of the distributio...

Internal function

Creates the the distribution's prior section (which is part of a pos...

Determine if the object is a valid kappa 2 parameter

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

Check there are no files in the default beautier folder

Remove all lines that are only whitespace

Remove consecutive lines

Rename the filenames in an inference model

Determine if the object is a valid kappa parameter

Determine if the object is a valid lambda parameter

Determine if the object is a valid Laplace distribution, as created by...

Determine if the object is a valid log-normal distribution, as created...

Determine if the object is a valid m parameter

Determine if the object is a valid MCMC

Determine if the object is a valid Nested-Sampling MCMC, as used in [1...

Determine if the object is a valid mean parameter

Determine if an MRCA prior's alignment IDs is present in the FASTA fil...

Determine if an MRCA prior's alignment IDs are present in the FASTA fi...

Determine of the object is an empty (NA) or valid MRCA prior.

See if x is one MRCA prior with a distribution

Determine if the object is a valid mu parameter

Determine if the object is a valid normal distribution as created by `...

Determines if the environment is AppVeyor

Determines if the environment is a continuous integration service

Determines if the environment is GitHub Actions

Determines if the environment is Travis CI

Check if the argument is one boolean

Determine if the object is a valid 1/x distribution, as created by `cr...

Determines if the argument is a double

Determine if an object is one empty string

Determines if the argument is a whole number

Determines if x is one NA

Determines if the argument is one string

General function to create a distribution.

Determine if the object is a valid parameter

Determines if the name is a valid parameter name

Checks if the input is a phylogeny

Determine if the object is a valid Poisson distribution as created by ...

Determine if the object is a valid 'rate AC' parameter

Determine if the object is a valid 'rate AG' parameter

Determine if the object is a valid 'rate AT' parameter

Determine if the object is a valid 'rate CG' parameter

Create a trait set string.

Initializes a Relaxed Log-Normal clock model

Initializes all site models

Initializes a strict clock model

Creates the init section of a BEAST2 XML parameter file

Creates the map section of a BEAST2 XML parameter file

Creates the operators section of a BEAST2 XML parameter file

Initializes a TN93 site model

Initializes a Birth-Death tree prior

Initializes a beta distribution

Initializes a Coalescent Constant Population tree prior

Initializes a Coalescent Exponential Population tree prior

Initializes all clock models

Initializes a distribution

Initializes an exponential distribution

Initializes a gamma distribution

Initializes a gamma site model

Initializes a GTR site model

Initializes an HKY site model

Initialize an inference model

Initializes an inverse gamma distribution

Initializes a JC69 site model

Initializes an Laplace distribution

Initializes an log-normal distribution

Initialize the MRCA prior.

Initializes all MRCA priors

Initializes an normal distribution

Initializes an one-divided-by-x distribution

Initializes a parameter

Initializes an Poisson distribution

Initializes all tree priors

Initializes a uniform distribution

Initializes a Yule tree prior

Puts spaces in between the lines

Determine if the object is a valid alpha parameter

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

Determine if the object is a valid clock_rate parameter

Determine if the MCMC is a default MCMC

Determine if the object is a valid distribution

Determines if the name is a valid distribution name

Determine if the object is a valid exponential distribution as created...

Checks if name is a valid freq_equilibrium argument value

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

Determine if the object is a valid freq parameter

Determine if the object is a valid gamma distribution, as created by `...

Is object x a gamma site model?

Determine if the object is a valid GTR site model, as created by `crea...

Determine if the object is a valid HKY site model, as created by `crea...

Determine if the object is a valid ID

Is there at least one regular expression having a match with the line?

Determine if the input is an inference model

Determine if x is an initialized Birth-Death tree_prior object

Determine if x is an initialized beta distribution object as created b...

Determine if x is an initialized Coalescent Bayesian Skyline tree_prio...

Determine if x is an initialized Coalescent Constant Population tree_p...

Determine if x is an initialized Coalescent Exponential Population tre...

Determine if x is an initialized clock_model object, as created by `cr...

Determine if x is an initialized distribution object as created by `cr...

Determine if x is an initialized exponential distribution object as cr...

Determine if x is an initialized gamma distribution object

Determine if x is an initialized gamma site model, as created by `crea...

Determine if x is an initialized GTR site model as created by `create_...

Determine if x is an initialized HKY site model as created by `create_...

Determine if x is an initialized inverse-gamma distribution as created...

Determine if the object is a valid b_pop_sizes parameter

Determine if the object is a valid Birth Death tree prior

Determine if the object is a valid beauti_options

Determine if the object is a valid beta distribution, as created by `c...

Determine if x is an initialized JC69 site model as created by `create...

Determine if the object is a valid beta parameter

Determine if x is an initialized Laplace distribution as created by `c...

Determine if the object is a valid constant coalescent Bayesian skylin...

Determine if the object is a valid constant coalescence population tre...

Determine if x is an initialized log_normal distribution object as cre...

Determine if x is an initialized MRCA prior

Determine if x is an initialized normal distribution object as created...

Determine if x is an initialized one_div_x distribution object as crea...

Determine if x is an initialized parameter, as created by create_param

Determine if the object is a valid coalescent exponential population t...

Determine if the object is a valid clock_model

Determines if the name is a valid clock model name

Determine if x is an initialized Poisson distribution object as create...

Determine if x is an initialized relaxed log-normal clock_model object

Determine if x is an initialized site model, as created by `create_sit...

Determine if x is an initialized strict clock_model object

Determine if x is an initialized tn93 site model as created by `create...

Determine if x is an initialized tree_prior objects

Determine if x is an initialized uniform distribution object as create...

Determine if x is an initialized Yule tree_prior object

Determine if the object is a valid inverse-gamma distribution as creat...

Determine if the object is a valid JC69 site model

Internal function

Determine if x consists out of clock_models objects

Determine if two MCMCs are equal.

Determine if two screenlogs are equal.

Determine if two tracelogs are equal.

Determine if two treelogs are equal.

Determine if XML files result in equal trees

Determine if XML lines result in equal trees

Internal function

Determine if XML lines result in equivalent trees

Determine if XML lines result in equivalent trees

Determine if XML operator lines result in equivalent trees

Determine if XML operator lines result in equivalent trees

Determine if XML lines result in equivalent trees

Checks if all filenames have a FASTA filename extension

Determine if x consists out of IDs

Determine if x consists out of initialized clock_models objects

Determine if x consists out of initialized MRCA priors

Determine if x consists out of initialized site_models objects

Determine if x consists out of initialized tree_priors objects

Determine if the MRCA priors' alignment IDs are present in the FASTA f...

Determine if x consists out of MRCA priors

Determine if the MRCA priors' taxa names are present in the FASTA file...

Are the clock models Relaxed Log-Normal clock models?

Determine if x consists out of site_models objects

Determine if x consists out of tree_priors objects

Internal function

Internal function

Creates the tree prior section in the prior section of the prior secti...

beautier: A package to create a BEAST2 input file.

Internal function

Creates the tree prior section in the prior section of the prior secti...

Creates the tree prior section in the prior section of the prior secti...

Convert a CCP tree prior to the XML as part of the state section

Creates the tree prior section in the prior section of the prior secti...

Check if the alignment_id is valid.

Check if the beauti_options is a valid beauti_options object.

Check if the clock model is a valid clock model.

Check if the object is a list of one or more clock models.

Internal function

Checks if the input FASTA file and the inference model agree.

Function to check if a file exists. Calls stop if the file is absent

Check if the filename is valid

Checks if the parameter is a valid gamma site model

Checks if the gamma site model has the right list elements' names

Check if the gtr_site_model is a valid GTR nucleotide substitution m...

Check if the gtr_site_model has the list elements of a valid `gtr_si...

Check if the supplied object is a valid Bayesian phylogenetic inferenc...

Check if the inference_model is a valid BEAUti inference model.

Check if is_monophyletic has a valid value.

Check if the supplied mode is a valid logging mode.

Check if the supplied sort is a valid logging sorting option.

Check if the MCMC is a valid MCMC object.

Check if the MCMC has the list elements of a valid MCMC object.

Check if the MCMC has the list elements with valid values for being a ...

Check if the MRCA prior is a valid MRCA prior.

Check if mrca_prior_name is a valid MRCA prior name.

Check if the MRCA prior, which is a list, has all the named elements.

Check the MRCA prior's taxon names are valid.

Check if this an MCMC that uses Nested Sampling to estimate a marginal...

Check if the parameter is a valid parameter

Check if the param has the list elements of a valid param object.

Check if the param has the list elements of the right type for a val...

Check if the phylogeny is a valid phylogeny object.

Check if the rename function is a valid filename rename function

Check if the clock model is a valid clock model.

Check if a screenlog is valid.

Check if the screenlog has the list elements of a valid screenlog ...

Check if the screenlog has the list elements with valid values for bei...

Check if the site model is a valid site model

Check if the site_model has the list elements of a valid `site_model...

Check if the site_model has the list elements of the right type for ...

Check if the object is a list of one or more site models.

Check if store_every holds a valid value

Check if the clock model is a valid clock model.

Check if the tn93_site_model is a valid TN93 nucleotide substitution...

Check if the tn93_site_model has the list elements of a valid `tn93_...

Check if a tracelog is valid.

Check if the tracelog has the list elements of a valid tracelog ob...

Check if the tracelog has the list elements with valid values for bein...

Check if the tree prior is a valid tree prior

Check if the object is a list of one or more tree priors.

Check if a treelog is valid.

Check if the treelog has the list elements of a valid treelog obje...

Check if the treelog has the list elements with valid values for being...

Internal function

Internal function

Internal function

Internal function

Convert a clock model to the XML of the TreeLogger

Internal function

Internal function

Count the number of spaces before the first character

Create a parameter called alpha

Create a parameter called b_pop_sizes.

Create a Birth-Death tree prior

Create the <beast ...> XML

Create a BEAST2 XML input text

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

Creates the data section of a BEAST2 XML parameter file

Creates the data section of a BEAST2 XML parameter file

Creates the distribution section of a BEAST2 XML parameter file.

Creates the XML text for the distribution tag with the likelihood ...

Creates the prior section in the distribution section of a BEAST2 XML ...

Create a BEAST2 input file

Create a BEAST2 input file from an inference model

Create a BEAST2 XML input text from an inference model

Function to create a set of BEAUti options.

Function to create the BEAUti options for version 2.4.

Function to create the BEAUti options for version 2.6.

Create the default beautier temporary folder

Create a beta distribution

Create a parameter called beta

Internal function to create the branchRateModel section of the XML a...

Create a Coalescent Bayesian Skyline tree prior

Create a Coalescent Constant Population tree prior

Create a Coalescent Exponential Population tree prior

General function to create a clock model

Create a clock model from name

Creates all supported clock models, which is a list of the types retur...

Create clock models from their names

Create a parameter called clock_rate, as needed by `create_strict_cl...

Internal function

Create the <data ..> XML

General function to create a distribution.

Create an exponential distribution

Create a parameter called freq

Create a gamma distribution

Create a gamma site model, part of a site model

Create a GTR site model

Converts a GTR site model to XML, used in the substModel section

Create an HKY site model

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

Create a Bayesian phylogenetic inference model.

Create an inverse-gamma distribution

Create a JC69 site model

Converts a JC69 site model to XML, used in the substModel section

Create a parameter called kappa 1

Create a parameter called kappa 2

Create a parameter called kappa

Create a parameter called lambda

Create a Laplace distribution

Create a log-normal distribution

Creates the three logger sections of a BEAST2 XML parameter file

Create a parameter called m

Create an MCMC configuration.

Create a parameter called mean

Create a Most Recent Common Ancestor prior

Create a parameter called mu

Create an normal distribution

Create an inference model to measure the evidence of.

Create an MCMC object to estimate the marginal likelihood using Nested...

Create a 1/x distribution

General function to create a parameter.

Create a Poisson distribution

Create a parameter called 'rate AC'

Create a parameter called 'rate AG'

Create a parameter called 'rate AT'

Internal function

Create a parameter called 'rate CG'

Create a parameter called 'rate CT'

Create a parameter called 'rate GT'

Internal function

Create a relaxed log-normal clock model

Create a parameter called s

Create a parameter called scale

Create a screenlog object

Creates the screenlog section of the logger section of a BEAST2 XM...

Create a parameter called sigma

General function to create a site model.

Create a site model from name

Internal function to creates the XML text for the parameters within ...

Internal function to creates the XML text for the siteModel tag of a...

Creates all supported site models which is a list of the types returne...

Create site models from their names

Internal function.

Create a strict clock model

Internal function

Internal function to create the substModel section

Create a filename for a temporary screenlog file

Create a filename for a temporary tracelog file

Create a filename for a temporary treelog file

Create a testing inference model.

Create an MCMC configuration for testing.

Create an inference model to be tested by Nested Sampling

Create an NS MCMC object for testing

Create a screenlog object, to be used in testing

Create a tracelog object, as used for testing

Create a treelog object to be used in testing

Create a TN93 site model

Converts a TN93 site model to XML, used in the substModel section

Create a tracelog object

Internal function

Creates the XML text for the distribution tag with the `treeLikeliho...

Internal function to create a tree prior

Creates all supported tree priors, which is a list of the types return...

Create a treelog object

Creates the XML text for the logger tag with ID treelog. This sect...

Internal function

Internal function

Create a uniform distribution

Create the XML declaration of the BEAST2 XML input file

Create a Yule tree prior

Documentation of parameters (for example, create_param. This functio...

Documentation of general function arguments. This function does nothin...

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

Extract everything between first loggers and last loggers line

Extract everything between first operators and last operators line

Get the lines of an XML section, including the section tags

Convert a FASTA file to a table of sequences

Finds a clock model with a certain ID

Find the first line that satisfies a regex

Find the line number of the first section's opening tag

Find the index of the last line that matches a regex

Find the highest line number of a section's closing tag

Creates the freq_equilibrium as XML

Internal function

Internal function

Internal function.

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

Deprecated function

Conclude the ID from a FASTA filename.

Get the alignment IDs from one or more files.

Get the alignment ID from one or more FASTA filenames.

Get the path to the beautier temporary files folder

Get the full path of a file in the inst/extdata folder

Get the full paths of files in the inst/extdata folder

Get a temporary filename

Get the BEAUti name for a clock model

Get the clock model names

Collect the IDs of the list of clock models

Obtain the crown age of a phylogeny.

Get the default namespace element value of the beast XML tag.

Get the default namespace element value of the beast XML tag for B...

Get the default namespace element value of the beast XML tag for B...

Get the number of parameters a distribution uses

Get the distribution names

Get the path of a FASTA file used in testing

Get the base of the filename base without extension

Returns valid values for the freq_equilibrium argument

Get the number of distributions in a gamma site model

Get the number of distributions a site model has

Determines if there is at least one non-strict clock model in the list...

Get the filenames stored in an inference model.

Get the possible log modes

Get the possible log sorts

Get the filenames stored in an MCMC.

Extract the number of taxa from a file

Get the prefix of operator IDs

Get the parameter names

Get a function that, from a filename, returns the part without the dir...

Get a function that removes the hex string from filenames.

Get a function to replace the directory of a filename

Get the number of distributions a site model has

Get the number of distributions a site model has

Get the site models' names

Get the number of distributions a site model has

Get the number of distributions one or more site models have

Extract the names of taxa from a file

Get the number of distributions a tree prior has

Get the number of parameters a tree prior has

Get the tree prior names

Get the number of distributions a tree prior has

Get the number of parameters a list of tree priors has

Get the XML closing tag

Get the XML opening tag

Internal function

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

Determines if the inference model has an MRCA prior.

See if the inference model has one MRCA prior with a distribution

Determine if the inference_model uses a relaxed log-normal clock mod...

Determine if the inference_model uses a strict clock model.

Determine if the inference_model uses tip dating.

Is an XML closing tag with the value of sectionpresent among the lin...

Is an XML opening tag with value 'section' present among the lines of ...

Is an XML closing tag with short closing text in one of the lines of t...

Internal function

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

Indent text for a certain number of spaces. If the text is only whites...

Rename the filenames within an MCMC

Internal function

Internal function

Internal function

Internal function

Internal function

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

Internal function

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

Internal function

Internal function to convert a site model to XML, used in the state ...

Creates the site model's XML for the tracelog section

Write the XML operators section from the site models.

Represent the site models as XML

Creates the site models' XML for the tracelog section

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

Internal function

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

Internal function

Internal function

Creates the distribution section in the prior section of the distribut...

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

Creates the tree prior's XML for the tracelog section

Creates the distribution section in the prior section of the distribut...

Creates the tree priors' XML for the tracelog section

Unindents text

Internal function

Creates the prior section in the prior section of the prior section ...