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 |