install.packages('beautier')beautier: A package to create a BEAST2 input file.state sectionmrca_prior_name is a valid MRCA prior name.gtr_site_model has the list elements
of a valid gtr_site_model object.alignment_id is valid.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.param has the list elements
of the right type for a valid param object.gtr_site_model is a valid
GTR nucleotide substitution model.mode is a valid logging mode.stop if the file is absentsort is a valid logging sorting option.tn93_site_model has the list elements
of a valid tn93_site_model object.TreeLoggerscreenlog is valid.param has the list elements
of a valid param object.tracelog is valid.tracelog has the list elements
of a valid tracelog object.screenlog has the list elements
of a valid screenlog object.beauti_options is a valid beauti_options object.store_every holds a valid valuestate' section of a BEAST2 XML parameter filerun' section of a BEAST2 XML parameter filedistribution tag
with the likelihood ID,
of a BEAST2 parameter file.clock_rate,
as needed by create_strict_clock_model<beast ...> XMLinit section of a BEAST2 XML parameter file<data ..> XMLsubstModel sectioninference_model is a valid BEAUti inference model.treelog has the list elements
of a valid treelog object.is_monophyletic has a valid value.branchRateModel section
of the XML as text.screenlog object, to be used in testingsubstModel sectiontn93_site_model is a valid
TN93 nucleotide substitution model.treelog is valid.screenlog section of the logger section
of a BEAST2 XML parameter filebeast tag of a BEAST2 parameter file.data section of a BEAST2 XML parameter filesubstModel sectionsubstModel sectiontreelog object to be used in testinginst/extdata foldercreate_gtr_site_model,
create_hky_site_model,
create_jc69_site_model
and create_tn93_site_modelstate sectioncreate_rln_clock_model,
and create_strict_clock_modelsubstModel sectiontracelog objectscreenlog objecttracelog object, as used for testingparameters within the siteModel section
of a BEAST2 parameter file.treelog objectname is a valid freq_equilibrium argument valuetaxonset section in the prior section of the
distribution section of a BEAST2 XML parameter file.siteModel tag
of a BEAST2 parameter file.create_bd_tree_prior,
create_cbs_tree_prior,
create_ccp_tree_prior,
create_cep_tree_prior
and create_yule_tree_priorinference_model uses tip dating.inference_model uses a strict clock model.freq_equilibrium argumentdistribution tag
with the treeLikelihood ID,
of a BEAST2 parameter file.freq_equilibrium as XMLcreate_param.
This function does nothing. It is intended to inherit documentation from.section
present among the lines of
the text?state sectioninst/extdata folderbeauti_optionscreate_gamma_distrinference_model uses
a relaxed log-normal clock model.create_normal_distrcreate_poisson_distrcreate_clock_modeloperators sectioncreate_uniform_distrcreate_gtr_site_modelcreate_gamma_site_modelcreate_gtr_site_modelcreate_hky_site_modelcreate_hky_site_modelcreate_inv_gamma_distrstate sectioncreate_log_normal_distrcreate_exp_distrcreate_log_normal_distrcreate_exp_distrstate sectioncreate_poisson_distrcreate_tn93_site_modelcreate_strict_clock_modelcreate_beta_distrcreate_jc69_site_modelcreate_laplace_distrcreate_inv_gamma_distrcreate_distrinit sectioncreate_beta_distrcreate_laplace_distrcreate_one_div_x_distrNA) or valid MRCA prior.create_site_modelcreate_one_div_x_distrstate sectionprior section in the prior section of
the prior section of the distribution section
of a BEAST2 XML parameter file for a Yule tree priorcreate_normal_distrcreate_uniform_distroperators section from the site models.distribution's prior section (which is part of
a posterior distribution section) of a BEAST2 XML parameter file.state sectionstate section