install.packages('beautier')state sectionbeautier: A package to create a BEAST2 input file.beauti_options is a valid beauti_options object.stop if the file is absentgtr_site_model is a valid
GTR nucleotide substitution model.mode is a valid logging mode.gtr_site_model has the list elements
of a valid gtr_site_model object.alignment_id is valid.sort is a valid logging sorting option.mrca_prior_name is a valid MRCA prior name.TreeLoggerbeast tag of a BEAST2 parameter file.site_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.is_monophyletic has a valid value.inference_model is a valid BEAUti inference model.store_every holds a valid value<beast ...> XMLtn93_site_model is a valid
TN93 nucleotide substitution model.param has the list elements
of a valid param object.run' section of a BEAST2 XML parameter fileparam has the list elements
of the right type for a valid param object.screenlog is valid.screenlog has the list elements
of a valid screenlog object.tracelog has the list elements
of a valid tracelog object.treelog has the list elements
of a valid treelog object.treelog is valid.distribution tag
with the likelihood ID,
of a BEAST2 parameter file.operators section of the
XML as texttreelog objectcreate_rln_clock_model,
and create_strict_clock_modelclock_rate,
as needed by create_strict_clock_modelinit section of a BEAST2 XML parameter filestate' section of a BEAST2 XML parameter file<data ..> XMLtracelog is valid.tn93_site_model has the list elements
of a valid tn93_site_model object.branchRateModel section
of the XML as text.substModel sectioninst/extdata foldersection
present among the lines of
the text?data section of a BEAST2 XML parameter filesiteModel tag
of a BEAST2 parameter file.substModel sectioncreate_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.tracelog objectdistribution tag
with the treeLikelihood ID,
of a BEAST2 parameter file.substModel sectionsubstModel sectiontreelog objecttracelog objectscreenlog section of the logger section
of a BEAST2 XML parameter filescreenlog objectcreate_param.
This function does nothing. It is intended to inherit documentation from.substModel sectioncreate_gtr_site_modelcreate_bd_tree_prior,
create_cbs_tree_prior,
create_ccp_tree_prior,
create_cep_tree_prior
and create_yule_tree_priorfreq_equilibrium as XMLstate sectioncreate_hky_site_modelcreate_clock_modelcreate_distrcreate_gamma_site_modelcreate_site_modelcreate_gtr_site_modelcreate_tn93_site_modelcreate_inv_gamma_distrinst/extdata folderinference_model uses tip dating.inference_model uses a strict clock model.freq_equilibrium argumentcreate_beta_distrcreate_exp_distrbeauti_optionsname is a valid freq_equilibrium argument valuestate sectioninference_model uses
a relaxed log-normal clock model.create_exp_distrcreate_beta_distrinit sectioncreate_hky_site_modelcreate_inv_gamma_distrcreate_normal_distroperators sectioncreate_gamma_distrcreate_one_div_x_distrcreate_log_normal_distrcreate_normal_distrcreate_uniform_distrcreate_jc69_site_modelcreate_laplace_distrcreate_poisson_distrcreate_laplace_distrcreate_one_div_x_distrcreate_log_normal_distrNA) or valid MRCA prior.create_poisson_distrdistribution's prior section (which is part of
a posterior distribution section) of a BEAST2 XML parameter file.taxonset section in the prior section of the
distribution section of a BEAST2 XML parameter file.create_uniform_distroperators section from the site models.prior section in the prior section of
the prior section of the distribution section
of a BEAST2 XML parameter file for a Yule tree priorcreate_strict_clock_modelstate sectionprior sectionstate section