install.packages('beautier')state sectiongtr_site_model has the list elements
of a valid gtr_site_model object.beautier: A package to create a BEAST2 input file.inference_model is a valid BEAUti inference model.is_monophyletic has a valid value.tracelog has the list elements
of a valid tracelog object.mrca_prior_name is a valid MRCA prior name.param has the list elements
of the right type for a valid param object.tn93_site_model has the list elements
of a valid tn93_site_model object.tracelog is valid.beauti_options is a valid beauti_options object.tn93_site_model is a valid
TN93 nucleotide substitution model.beast tag of a BEAST2 parameter file.branchRateModel section
of the XML as text.alignment_id is valid.data section of a BEAST2 XML parameter fileinit section of a BEAST2 XML parameter file<data ..> XMLgtr_site_model is a valid
GTR nucleotide substitution model.mode is a valid logging mode.treelog has the list elements
of a valid treelog object.treelog is valid.clock_rate,
as needed by create_strict_clock_modelsort is a valid logging sorting option.screenlog is valid.screenlog has the list elements
of a valid screenlog object.store_every holds a valid valuestop if the file is absentdistribution tag
with the likelihood ID,
of a BEAST2 parameter file.substModel sectionsite_model has the list elements
of the right type for a valid site_model object.site_model has the list elements
of a valid site_model object.param has the list elements
of a valid param object.create_rln_clock_model,
and create_strict_clock_modelstate' section of a BEAST2 XML parameter filerun' section of a BEAST2 XML parameter fileTreeLogger<beast ...> XMLsubstModel sectionsubstModel sectionsubstModel sectioncreate_gtr_site_model,
create_hky_site_model,
create_jc69_site_model
and create_tn93_site_modeltracelog object, as used for testingtreelog object to be used in testingtracelog objectcreate_param.
This function does nothing. It is intended to inherit documentation from.screenlog objectsiteModel tag
of a BEAST2 parameter file.parameters within the siteModel section
of a BEAST2 parameter file.distribution tag
with the treeLikelihood ID,
of a BEAST2 parameter file.substModel sectionscreenlog section of the logger section
of a BEAST2 XML parameter filecreate_bd_tree_prior,
create_cbs_tree_prior,
create_ccp_tree_prior,
create_cep_tree_prior
and create_yule_tree_priorsection
present among the lines of
the text?state sectionfreq_equilibrium as XMLinst/extdata folderinst/extdata folderstate sectiontreelog objectscreenlog object, to be used in testingfreq_equilibrium argumentstate sectioncreate_gamma_distrcreate_gtr_site_modelcreate_clock_modelcreate_distrname is a valid freq_equilibrium argument valuecreate_poisson_distrcreate_hky_site_modelcreate_tn93_site_modelcreate_log_normal_distrcreate_hky_site_modelcreate_beta_distrbeauti_optionsinference_model uses
a relaxed log-normal clock model.create_inv_gamma_distrcreate_uniform_distrinference_model uses tip dating.inference_model uses a strict clock model.create_log_normal_distrcreate_gamma_site_modelcreate_beta_distrcreate_inv_gamma_distrcreate_exp_distrcreate_exp_distrcreate_normal_distrcreate_gtr_site_modelcreate_normal_distrinit sectioncreate_one_div_x_distrNA) or valid MRCA prior.state sectioncreate_one_div_x_distrcreate_laplace_distrcreate_laplace_distrcreate_site_modelcreate_jc69_site_modelcreate_uniform_distrcreate_strict_clock_modelstate sectioncreate_poisson_distroperators sectiontaxonset section in the prior section of the
distribution section of a BEAST2 XML parameter file.distribution's prior section (which is part of
a posterior distribution section) of a BEAST2 XML parameter file.state sectionstate sectionprior section in the prior section of
the prior section of the distribution section
of a BEAST2 XML parameter file for a Yule tree prioroperators section from the site models.