'BEAUti' from R


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Documentation for package ‘beautier’ version 2.2.1

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A B C D F G H I P Y

beautier-package 'beautier': A package to create a 'BEAST2' input file.

-- A --

are_clock_models Determine if x consists out of clock_models objects
are_equal_mcmcs Determine if two MCMCs are equal.
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_site_models Determine if x consists out of site_models objects
are_tree_priors Determine if x consists out of tree_priors objects

-- B --

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.

-- C --

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_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_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_mcmc Check if the MCMC is a valid MCMC object.
check_mrca_prior Check if the MRCA prior is a valid MRCA prior.
check_phylogeny Check if the phylogeny is a valid phylogeny object.
check_rln_clock_model Check if the clock model is a valid clock model.
check_site_model Check if the site model is a valid site model
check_site_models Check if the object is a list of one or more site models.
check_strict_clock_model Check if the clock model is a valid clock model.
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.
create_alpha_param Create a parameter called alpha
create_bd_tree_prior Create a Birth-Death tree prior
create_beast2_input Create a BEAST2 XML input text
create_beast2_input_distr_lh Creates the likelihood section in the distribution section of a BEAST2 XML 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_screenlog Creates the 'screenlog' section of the 'logger' section of a BEAST2 XML parameter file
create_beast2_input_tracelog Creates the 'tracelog' section of the 'logger' section of a BEAST2 XML parameter file
create_beast2_input_treelogs Creates the 'tracelog' section of the 'logger' section of a BEAST2 XML parameter file
create_beauti_options Function to create a set of BEAUti options.
create_beta_distr Create a beta distribution
create_beta_param Create a parameter called beta
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_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_model_from_name Create a clock model from name
create_clock_model_rln Create a relaxed log-normal clock model
create_clock_model_strict Create a strict clock model
create_clock_rate_param Create a parameter called 'clock_rate', as needed by 'create_strict_clock_model'
create_distr General function to create a distribution.
create_distr_beta Create a beta distribution
create_distr_exp Create an exponential distribution
create_distr_gamma Create a gamma distribution
create_distr_inv_gamma Create an inverse-gamma distribution
create_distr_laplace Create a Laplace distribution
create_distr_log_normal Create a log-normal distribution
create_distr_normal Create an normal distribution
create_distr_one_div_x Create a 1/x distribution
create_distr_poisson Create a Poisson distribution
create_distr_uniform Create a uniform 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_hky_site_model Create an HKY site model
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_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_mcmc Create an MCMC configuration.
create_mcmc_nested_sampling Create an MCMC object to estimate the marginal likelihood using Nested Sampling.
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_m_param Create a parameter called m
create_nested_sampling_mcmc Create an MCMC object to estimate the marginal likelihood using Nested Sampling.
create_normal_distr Create an normal distribution
create_one_div_x_distr Create a 1/x distribution
create_param General function to create a parameter.
create_param_alpha Create a parameter called alpha
create_param_beta Create a parameter called beta
create_param_clock_rate Create a parameter called 'clock_rate', as needed by 'create_strict_clock_model'
create_param_kappa_1 Create a parameter called kappa 1
create_param_kappa_2 Create a parameter called kappa 2
create_param_lambda Create a parameter called lambda
create_param_m Create a parameter called m
create_param_mean Create a parameter called mean
create_param_mu Create a parameter called mu
create_param_rate_ac Create a parameter called 'rate AC'
create_param_rate_ag Create a parameter called 'rate AG'
create_param_rate_at Create a parameter called 'rate AT'
create_param_rate_cg Create a parameter called 'rate CG'
create_param_rate_ct Create a parameter called 'rate CT'
create_param_rate_gt Create a parameter called 'rate GT'
create_param_s Create a parameter called s
create_param_scale Create a parameter called scale
create_param_sigma Create a parameter called sigma
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_scale_param Create a parameter called scale
create_sigma_param Create a parameter called sigma
create_site_model General function to create a site model.
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_site_model_from_name Create a site model from name
create_site_model_gtr Create a GTR site model
create_site_model_hky Create an HKY site model
create_site_model_jc69 Create a JC69 site model
create_site_model_tn93 Create a TN93 site model
create_strict_clock_model Create a strict clock model
create_s_param Create a parameter called s
create_tn93_site_model Create a TN93 site model
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_tree_priors_from_names Create tree priors from their names
create_tree_prior_bd Create a Birth-Death tree prior
create_tree_prior_cbs Create a Coalescent Bayesian Skyline tree prior
create_tree_prior_ccp Create a Coalescent Constant Population tree prior
create_tree_prior_cep Create a Coalescent Exponential Population tree prior
create_tree_prior_from_name Create a tree prior from name
create_tree_prior_yule Create a Yule tree prior
create_uniform_distr Create a uniform distribution
create_yule_tree_prior Create a Yule tree prior

-- D --

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_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

-- F --

fastas_to_phylos Create one or more random phylogenies.
fasta_to_phylo Create a random phylogeny, with the same taxa names as the FASTA file and the desired crown age

-- G --

get_alignment_id Conclude the ID from a FASTA filename.
get_alignment_ids 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_names Get the clock model names
get_crown_age Obtain the crown age of a phylogeny.
get_fasta_filename Get the path of a FASTA file used in testing
get_gamma_site_model_n_distrs Get the number of distributions in a gamma site model
get_site_model_names Get the site models' names
get_taxa_names Extract the names of taxa from a file
get_tree_prior_names Get the tree prior names

-- H --

has_mrca_prior Determines if the inference model has an MRCA prior.

-- I --

init_bd_tree_prior Initializes a Birth-Death tree prior
init_ccp_tree_prior Initializes a Coalescent Constant Population tree prior
init_cep_tree_prior Initializes a Coalescent Exponential Population tree prior
init_gtr_site_model Initializes a GTR site model
init_hky_site_model Initializes an HKY site model
init_jc69_site_model Initializes a JC69 site model
init_rln_clock_model Initializes a Relaxed Log-Normal clock model
init_strict_clock_model Initializes a strict clock model
init_tn93_site_model Initializes a TN93 site model
init_yule_tree_prior Initializes a Yule tree prior
is_bd_tree_prior Determine if the object is a valid Birth Death tree prior
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_init_beta_distr Determine if x is an initialized beta distribution object as created by 'create_beta_distr'
is_init_cep_tree_prior Determine if x is an initialized Coalescent Exponential Population tree_prior object
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_inv_gamma_distr Determine if x is an initialized inverse-gamma distribution as created by 'create_inv_gamma_distr'
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_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_poisson_distr Determine if x is an initialized Poisson distribution object as created by 'create_poisson_distr'
is_init_uniform_distr Determine if x is an initialized uniform distribution object as created by 'create_uniform_distr'
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_nested_sampling_mcmc Determine if the object is a valid Nested-Sampling MCMC, as used in [1]
is_one_na Determines if x is one NA
is_phylo Checks if the input is a phylogeny
is_site_model Determine if the object is a valid site_model
is_tree_prior Determine if an object is a valid tree prior
is_yule_tree_prior Determine if the object is a valid Yule tree prior,

-- P --

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

-- Y --

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