install.packages('beautier')beauti_options is a valid beauti_options object.is_monophyletic has a valid value.inference_model is a valid BEAUti inference model.state sectionstop if the file is absentalignment_id is valid.gtr_site_model is a valid
GTR nucleotide substitution model.beautier: A package to create a BEAST2 input file.tracelog is valid.tn93_site_model has the list elements
of a valid tn93_site_model object.mode is a valid logging mode.tn93_site_model is a valid
TN93 nucleotide substitution model.param has the list elements
of the right type for a valid param object.sort is a valid logging sorting option.treelog is valid.treelog has the list elements
of a valid treelog object.store_every holds a valid valueparam has the list elements
of a valid param object.TreeLoggerinit section of a BEAST2 XML parameter filesite_model has the list elements
of a valid site_model object.site_model has the list elements
of the right type for a valid site_model object.distribution tag
with the likelihood ID,
of a BEAST2 parameter file.<data ..> XMLcreate_rln_clock_model,
and create_strict_clock_modelbranchRateModel section
of the XML as text.beast tag of a BEAST2 parameter file.data section of a BEAST2 XML parameter filesubstModel sectionrun' section of a BEAST2 XML parameter filestate' section of a BEAST2 XML parameter fileclock_rate,
as needed by create_strict_clock_modelsubstModel sectionsubstModel sectionscreenlog section of the logger section
of a BEAST2 XML parameter filecreate_gtr_site_model,
create_hky_site_model,
create_jc69_site_model
and create_tn93_site_modelscreenlog objectparameters within the siteModel section
of a BEAST2 parameter file.siteModel tag
of a BEAST2 parameter file.tracelog objecttreelog objectgtr_site_model has the list elements
of a valid gtr_site_model object.tracelog objectsubstModel sectionmrca_prior_name is a valid MRCA prior name.screenlog has the list elements
of a valid screenlog object.screenlog is valid.tracelog has the list elements
of a valid tracelog object.<beast ...> XMLcreate_param.
This function does nothing. It is intended to inherit documentation from.screenlog objectcreate_bd_tree_prior,
create_cbs_tree_prior,
create_ccp_tree_prior,
create_cep_tree_prior
and create_yule_tree_priorstate sectionfreq_equilibrium argumentdistribution tag
with the treeLikelihood ID,
of a BEAST2 parameter file.treelog objectinst/extdata folderinst/extdata folderstate sectionsection
present among the lines of
the text?state sectioninference_model uses
a relaxed log-normal clock model.substModel sectioncreate_clock_modelcreate_gamma_distrcreate_distrfreq_equilibrium as XMLcreate_exp_distrinference_model uses tip dating.inference_model uses a strict clock model.create_normal_distrcreate_uniform_distrcreate_normal_distrcreate_one_div_x_distrcreate_log_normal_distrcreate_tn93_site_modelcreate_beta_distrbeauti_optionscreate_poisson_distrcreate_gtr_site_modelcreate_beta_distrcreate_hky_site_modelcreate_jc69_site_modelstate sectioncreate_laplace_distrcreate_laplace_distrcreate_exp_distrname is a valid freq_equilibrium argument valuecreate_uniform_distrcreate_gtr_site_modelcreate_gamma_site_modelcreate_poisson_distroperators sectionstate sectioncreate_hky_site_modelcreate_inv_gamma_distrcreate_log_normal_distrcreate_inv_gamma_distrNA) or valid MRCA prior.create_site_modeltaxonset section in the prior section of the
distribution section of a BEAST2 XML parameter file.create_one_div_x_distrinit sectioncreate_strict_clock_modelprior section in the prior section of
the prior section of the distribution section
of a BEAST2 XML parameter file for a Yule tree priorstate sectiondistribution's prior section (which is part of
a posterior distribution section) of a BEAST2 XML parameter file.operators section from the site models.state section