Man pages for ropensci/beautier
'BEAUti' from R

are_clock_modelsDetermine if x consists out of clock_models objects
are_equal_mcmcsDetermine if two MCMCs are equal.
are_equivalent_xml_linesDetermine if XML lines result in equivalent trees
are_equivalent_xml_lines_allDetermine if XML lines result in equivalent trees
are_equivalent_xml_lines_loggersDetermine if XML operator lines result in equivalent trees
are_equivalent_xml_lines_operatorsDetermine if XML operator lines result in equivalent trees
are_equivalent_xml_lines_sectionDetermine if XML lines result in equivalent trees
are_site_modelsDetermine if x consists out of site_models objects
are_tree_priorsDetermine if x consists out of tree_priors objects
bd_tree_prior_to_xml_prior_distrCreates the tree prior section in the prior section of the...
beautier'beautier': A package to create a 'BEAST2' input file.
cbs_tree_prior_to_xml_prior_distrCreates the tree prior section in the prior section of the...
ccp_tree_prior_to_xml_prior_distrCreates the tree prior section in the prior section of the...
cep_tree_prior_to_xml_prior_distrCreates the tree prior section in the prior section of the...
check_beauti_optionsCheck if the 'beauti_options' is a valid 'beauti_options'...
check_clock_modelCheck if the clock model is a valid clock model.
check_clock_modelsCheck if the object is a list of one or more clock models.
check_inference_modelCheck if the supplied object is a valid Bayesian phylogenetic...
check_inference_modelsCheck if the 'inference_model' is a valid BEAUti inference...
check_mcmcCheck if the MCMC is a valid MCMC object.
check_mrca_priorCheck if the MRCA prior is a valid MRCA prior.
check_phylogenyCheck if the phylogeny is a valid phylogeny object.
check_rln_clock_modelCheck if the clock model is a valid clock model.
check_site_modelCheck if the site model is a valid site model
check_site_modelsCheck if the object is a list of one or more site models.
check_strict_clock_modelCheck if the clock model is a valid clock model.
check_tree_priorCheck if the tree prior is a valid tree prior
check_tree_priorsCheck if the object is a list of one or more tree priors.
create_alpha_paramCreate a parameter called alpha
create_bd_tree_priorCreate a Birth-Death tree prior
create_beast2_inputCreate a BEAST2 XML input text
create_beast2_input_distr_lhCreates the likelihood section in the distribution section of...
create_beast2_input_distr_priorCreates the prior section in the distribution section of a...
create_beast2_input_fileCreate a BEAST2 input file
create_beast2_input_file_from_modelCreate a BEAST2 input file from an inference model
create_beast2_input_screenlogCreates the 'screenlog' section of the 'logger' section of a...
create_beast2_input_tracelogCreates the 'tracelog' section of the 'logger' section of a...
create_beast2_input_treelogsCreates the 'tracelog' section of the 'logger' section of a...
create_beauti_optionsFunction to create a set of BEAUti options.
create_beta_distrCreate a beta distribution
create_beta_paramCreate a parameter called beta
create_cbs_tree_priorCreate a Coalescent Bayesian Skyline tree prior
create_ccp_tree_priorCreate a Coalescent Constant Population tree prior
create_cep_tree_priorCreate a Coalescent Exponential Population tree prior
create_clock_modelGeneral function to create a clock model
create_clock_model_from_nameCreate a clock model from name
create_clock_modelsCreates all supported clock models, which is a list of the...
create_clock_models_from_namesCreate clock models from their names
create_clock_rate_paramCreate a parameter called 'clock_rate', as needed by...
create_distrGeneral function to create a distribution.
create_exp_distrCreate an exponential distribution
create_gamma_distrCreate a gamma distribution
create_gamma_site_modelCreate a gamma site model, part of a site model
create_gtr_site_modelCreate a GTR site model
create_hky_site_modelCreate an HKY site model
create_inference_modelCreate a Bayesian phylogenetic inference model.
create_inv_gamma_distrCreate an inverse-gamma distribution
create_jc69_site_modelCreate a JC69 site model
create_kappa_1_paramCreate a parameter called kappa 1
create_kappa_2_paramCreate a parameter called kappa 2
create_lambda_paramCreate a parameter called lambda
create_laplace_distrCreate a Laplace distribution
create_log_normal_distrCreate a log-normal distribution
create_mcmcCreate an MCMC configuration.
create_mean_paramCreate a parameter called mean
create_m_paramCreate a parameter called m
create_mrca_priorCreate a Most Recent Common Ancestor prior
create_mu_paramCreate a parameter called mu
create_nested_sampling_mcmcCreate an MCMC object to estimate the marginal likelihood...
create_normal_distrCreate an normal distribution
create_one_div_x_distrCreate a 1/x distribution
create_paramGeneral function to create a parameter.
create_poisson_distrCreate a Poisson distribution
create_rate_ac_paramCreate a parameter called 'rate AC'
create_rate_ag_paramCreate a parameter called 'rate AG'
create_rate_at_paramCreate a parameter called 'rate AT'
create_rate_cg_paramCreate a parameter called 'rate CG'
create_rate_ct_paramCreate a parameter called 'rate CT'
create_rate_gt_paramCreate a parameter called 'rate GT'
create_rln_clock_modelCreate a relaxed log-normal clock model
create_scale_paramCreate a parameter called scale
create_sigma_paramCreate a parameter called sigma
create_site_modelGeneral function to create a site model.
create_site_model_from_nameCreate a site model from name
create_site_modelsCreates all supported site models which is a list of the...
create_site_models_from_namesCreate site models from their names
create_s_paramCreate a parameter called s
create_strict_clock_modelCreate a strict clock model
create_tn93_site_modelCreate a TN93 site model
create_tree_priorInternal function to create a tree prior
create_tree_prior_from_nameCreate a tree prior from name
create_tree_priorsCreates all supported tree priors, which is a list of the...
create_tree_priors_from_namesCreate tree priors from their names
create_uniform_distrCreate a uniform distribution
create_yule_tree_priorCreate a Yule tree prior
default_parameters_docDocumentation of parameters (for example, 'create_param'....
default_params_docDocumentation of general function arguments. This function...
distr_to_xml_betaConverts a beta distribution to XML
distr_to_xml_expConverts an exponential distribution to XML
distr_to_xml_gammaConverts a gamma distribution to XML
distr_to_xml_inv_gammaConverts an inverse-gamma distribution to XML
distr_to_xml_laplaceConverts a Laplace distribution to XML
distr_to_xml_log_normalConverts a log-normal distribution to XML
distr_to_xml_normalConverts a normal distribution to XML
distr_to_xml_one_div_xConverts a 1/x distribution to XML
distr_to_xml_poissonConverts a Poisson distribution to XML
distr_to_xml_uniformConverts a uniform distribution to XML
fastas_to_phylosCreate one or more random phylogenies.
fasta_to_phyloCreate a random phylogeny, with the same taxa names as the...
get_alignment_idConclude the ID from a FASTA filename.
get_alignment_idsGet the alignment ID from one or more FASTA filenames.
get_beautier_pathGet the full path of a file in the 'inst/extdata' folder
get_beautier_pathsGet the full paths of files in the 'inst/extdata' folder
get_clock_model_namesGet the clock model names
get_crown_ageObtain the crown age of a phylogeny.
get_fasta_filenameGet the path of a FASTA file used in testing
get_gamma_site_model_n_distrsGet the number of distributions in a gamma site model
get_site_model_namesGet the site models' names
get_taxa_namesExtract the names of taxa from a file
get_tree_prior_namesGet the tree prior names
has_mrca_priorDetermines if the inference model has an MRCA prior.
init_bd_tree_priorInitializes a Birth-Death tree prior
init_ccp_tree_priorInitializes a Coalescent Constant Population tree prior
init_cep_tree_priorInitializes a Coalescent Exponential Population tree prior
init_gtr_site_modelInitializes a GTR site model
init_hky_site_modelInitializes an HKY site model
init_jc69_site_modelInitializes a JC69 site model
init_rln_clock_modelInitializes a Relaxed Log-Normal clock model
init_strict_clock_modelInitializes a strict clock model
init_tn93_site_modelInitializes a TN93 site model
init_yule_tree_priorInitializes a Yule tree prior
is_bd_tree_priorDetermine if the object is a valid Birth Death tree prior
is_cbs_tree_priorDetermine if the object is a valid constant coalescent...
is_ccp_tree_priorDetermine if the object is a valid constant coalescence...
is_cep_tree_priorDetermine if the object is a valid coalescent exponential...
is_clock_modelDetermine if the object is a valid clock_model
is_init_beta_distrDetermine if x is an initialized beta distribution object as...
is_init_cep_tree_priorDetermine if x is an initialized Coalescent Exponential...
is_init_exp_distrDetermine if x is an initialized exponential distribution...
is_init_gamma_distrDetermine if x is an initialized gamma distribution object
is_init_inv_gamma_distrDetermine if x is an initialized inverse-gamma distribution...
is_init_laplace_distrDetermine if x is an initialized Laplace distribution as...
is_init_log_normal_distrDetermine if x is an initialized log_normal distribution...
is_init_normal_distrDetermine if x is an initialized normal distribution object...
is_init_one_div_x_distrDetermine if x is an initialized one_div_x distribution...
is_init_poisson_distrDetermine if x is an initialized Poisson distribution object...
is_init_uniform_distrDetermine if x is an initialized uniform distribution object...
is_mcmcDetermine if the object is a valid MCMC
is_mcmc_nested_samplingDetermine if the object is a valid Nested-Sampling MCMC, as...
is_one_naDetermines if x is one NA
is_phyloChecks if the input is a phylogeny
is_site_modelDetermine if the object is a valid site_model
is_tree_priorDetermine if an object is a valid tree prior
is_yule_tree_priorDetermine if the object is a valid Yule tree prior,
parameter_to_xml_alphaConverts an alpha parameter to XML
parameter_to_xml_betaConverts a beta parameter to XML
parameter_to_xml_clock_rateConverts a 'clockRate' parameter to XML
parameter_to_xml_kappa_1Converts a kappa 1 parameter to XML
parameter_to_xml_kappa_2Converts a kappa 2 parameter to XML
parameter_to_xml_lambdaConverts a lambda parameter to XML
parameter_to_xml_mConverts a m parameter to XML
parameter_to_xml_meanConverts a mean parameter to XML
parameter_to_xml_muConverts a mu parameter to XML
parameter_to_xml_rate_acConverts a 'rate AC' parameter to XML
parameter_to_xml_rate_agConverts a 'rate AG' parameter to XML
parameter_to_xml_rate_atConverts a 'rate AT' parameter to XML
parameter_to_xml_rate_cgConverts a 'rate CG' parameter to XML
parameter_to_xml_rate_ctConverts a 'rate CT' parameter to XML
parameter_to_xml_rate_gtConverts a 'rate GT' parameter to XML
parameter_to_xml_sConverts a s parameter to XML
parameter_to_xml_scaleConverts a scale parameter to XML
parameter_to_xml_sigmaConverts a sigma parameter to XML
yule_tree_prior_to_xml_prior_distrCreates the 'prior' section in the prior section of the prior...
ropensci/beautier documentation built on May 14, 2019, 8:52 p.m.