Files in ropensci/beautier
'BEAUti' from R

.Rbuildignore

.Rinstignore

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/custom.md .github/ISSUE_TEMPLATE/feature_request.md .github/pull_request_template.md

.github/workflows/R-CMD-check.yaml

.github/workflows/build_singularity.yaml

.github/workflows/check_bash_style.yaml

.github/workflows/check_links.yaml

.github/workflows/check_markdown.yaml

.github/workflows/valid_json_schema.json

.gitignore

.markdownlint.jsonc

.markdownlintignore

.spellcheck.yml

.wordlist.txt

CODE_OF_CONDUCT.md CONTRIBUTING.md

CRAN-SUBMISSION

DESCRIPTION

LICENSE

Meta/vignette.rds

NAMESPACE

R/create_branch_rate_model_stuff_xml.R

R/create_branch_rate_model_xml.R R/create_clock_model.R R/create_clock_model_from_name.R R/create_clock_models.R R/create_clock_models_from_names.R R/create_clock_rate_state_node_parameter_xml.R R/create_data_xml.R R/create_distr.R R/create_gamma_site_model.R R/create_inference_model.R R/create_loggers_xml.R R/create_mcmc.R R/create_mcmc_nested_sampling.R R/create_mrca_prior.R R/create_ns_inference_model.R R/create_param.R R/create_rate_categories_state_node_xml.R R/create_rln_clock_branch_rate_model_xml.R R/create_screenlog.R R/create_screenlog_xml.R R/create_site_model.R R/create_site_model_from_name.R R/create_site_model_parameters_xml.R R/create_site_model_xml.R R/create_site_models.R R/create_site_models_from_names.R R/create_strict_clock_branch_rate_model_xml.R R/create_strict_clock_rate_scaler_operator_xml.R R/create_subst_model_xml.R R/create_temp_screenlog_filename.R R/create_temp_tracelog_filename.R R/create_temp_treelog_filename.R R/create_test_inference_model.R R/create_test_mcmc.R R/create_test_ns_inference_model.R R/create_test_ns_mcmc.R R/create_test_screenlog.R R/create_test_tracelog.R R/create_test_treelog.R R/create_tracelog.R R/create_tracelog_xml.R R/create_trait_set_string.R R/create_tree_likelihood_distr_xml.R R/create_tree_prior.R R/create_tree_priors.R R/create_treelog.R R/create_treelog_xml.R R/create_ucld_mean_state_node_param_xml.R R/create_ucld_stdev_state_node_param_xml.R R/default_params_doc.R R/distr_to_xml.R R/extract_xml_loggers_from_lines.R R/extract_xml_operators_from_lines.R R/extract_xml_section_from_lines.R R/fasta_to_sequences.R R/find_clock_model.R R/find_first_regex_line.R R/find_first_xml_opening_tag_line.R R/find_last_regex_line.R R/find_last_xml_closing_tag_line.R R/freq_equilibrium_to_xml.R R/freq_param_to_xml.R R/gamma_distr_to_xml.R R/gamma_site_model_to_xml_prior_distr.R R/gamma_site_model_to_xml_state.R R/gamma_site_models_to_xml_prior_distr.R R/get_alignment_id.R R/get_alignment_ids.R R/get_beautier_folder.R R/get_beautier_path.R R/get_beautier_paths.R R/get_beautier_tempfilename.R R/get_clock_model_name.R R/get_clock_model_names.R R/get_clock_models_ids.R R/get_crown_age.R R/get_default_beast_namespace.R R/get_distr_n_params.R R/get_distr_names.R R/get_file_base_sans_ext.R R/get_freq_equilibrium_names.R R/get_gamma_site_model_n_distrs.R R/get_gamma_site_model_n_params.R R/get_has_non_strict_clock_model.R R/get_inference_model_filenames.R R/get_log_modes.R R/get_log_sorts.R R/get_mcmc_filenames.R R/get_n_taxa.R R/get_operator_id_pre.R R/get_param_names.R R/get_remove_dir_fun.R R/get_remove_hex_fun.R R/get_replace_dir_fun.R R/get_site_model_n_distrs.R R/get_site_model_n_params.R R/get_site_model_names.R R/get_site_models_n_distrs.R R/get_site_models_n_params.R R/get_taxa_names.R R/get_test_filenames.R R/get_tree_prior_n_distrs.R R/get_tree_prior_n_params.R R/get_tree_prior_names.R R/get_tree_priors_n_distrs.R R/get_tree_priors_n_params.R R/get_xml_closing_tag.R R/get_xml_opening_tag.R R/gtr_site_model_to_xml_prior.R R/gtr_site_model_to_xml_state.R R/has_mrca_prior.R R/has_mrca_prior_with_distr.R R/has_rln_clock_model.R R/has_strict_clock_model.R R/has_tip_dating.R R/has_xml_closing_tag.R R/has_xml_opening_tag.R R/has_xml_short_closing_tag.R R/hky_site_model_to_xml_prior_distr.R R/hky_site_model_to_xml_state.R R/import-standalone-obj-type.R R/import-standalone-types-check.R R/indent.R R/init_clock_models.R R/init_distr.R R/init_gamma_site_model.R R/init_inference_model.R R/init_mrca_prior.R R/init_mrca_priors.R R/init_param.R R/init_site_models.R R/init_tree_priors.R R/interspace.R R/is_beauti_options.R R/is_clock_model.R R/is_clock_model_name.R R/is_default_mcmc.R R/is_distr.R R/is_distr_name.R R/is_freq_equilibrium_name.R R/is_gamma_site_model.R R/is_id.R R/is_in_patterns.R R/is_inference_model.R R/is_init_clock_model.R R/is_init_distr.R R/is_init_gamma_site_model.R R/is_init_mrca_prior.R R/is_init_param.R R/is_init_site_model.R R/is_init_tree_prior.R R/is_m_param.R R/is_mcmc.R R/is_mrca_align_id_in_fasta.R R/is_mrca_align_ids_in_fastas.R R/is_mrca_prior.R R/is_mrca_prior_with_distr.R R/is_on_ci.R R/is_one_bool.R R/is_one_double.R R/is_one_empty_string.R R/is_one_int.R R/is_one_na.R R/is_one_string.R R/is_one_string_that_is_a_number.R R/is_param.R R/is_param_name.R R/is_phylo.R R/is_site_model.R R/is_site_model_name.R R/is_tree_prior.R R/is_tree_prior_name.R R/is_xml.R R/jc69_site_model_to_xml_state.R R/kappa_param_to_xml.R R/m_param_to_xml.R R/mcmc_to_xml_run.R R/mrca_prior_to_xml_prior_distr.R R/mrca_prior_to_xml_state.R R/mrca_prior_to_xml_taxonset.R R/mrca_prior_to_xml_tracelog.R R/mrca_priors_to_xml_distr.R R/parameter_to_xml.R R/remove_beautier_folder.R R/remove_empty_lines.R R/remove_multiline.R R/rename_inference_model_filenames.R R/rename_mcmc_filenames.R R/rln_clock_model_to_xml_mean_rate_prior.R R/rln_clock_model_to_xml_operators.R R/rln_clock_model_to_xml_prior_distr.R R/rln_clock_model_to_xml_state.R R/rln_clock_model_to_xml_tracelog.R R/rnd_phylo_xml_init.R R/s_parameter_to_xml.R R/site_model_to_xml_operators.R R/site_model_to_xml_prior.R R/site_model_to_xml_state.R R/site_model_to_xml_tracelog.R R/site_models_to_xml_operators.R R/site_models_to_xml_prior_distr.R R/site_models_to_xml_tracelog.R R/strict_clock_model_to_xml_operators.R R/strict_clock_model_to_xml_prior_distr.R R/strict_clock_model_to_xml_state.R R/strict_clock_model_to_xml_tracelog.R R/taxa_to_xml_tree.R R/tipdate_taxa_to_xml_trait.R R/tn93_site_model_to_xml_prior_distr.R R/tn93_site_model_to_xml_state.R R/tree_model_to_tracelog_xml.R R/tree_prior_to_xml_operators.R R/tree_prior_to_xml_prior_distr.R R/tree_prior_to_xml_state.R R/tree_prior_to_xml_tracelog.R R/tree_priors_to_xml_distr.R R/tree_priors_to_xml_tracelog.R R/unindent.R R/yule_tree_prior_to_xml_operators.R README.md

Singularity

beautier.Rproj

codemeta.json

cran-comments.md

doc/aco_hky_nd2_tn93.png

doc/all_default.png

doc/anthus_2_4.png

doc/bd_2_4.png

doc/beautier_logo.png

doc/birth_rate_normal_2_4.png

doc/code_of_conduct.md doc/demo.R doc/demo.Rmd

doc/demo.html

doc/demo.md doc/examples.R doc/examples.Rmd

doc/examples.html

doc/examples.md doc/faq.md

doc/hky_prop_invariant_0_5_2_4.png

doc/jc69_2_4.png

doc/mrca_crown_age.png

doc/mrca_prior_all.png

doc/mrca_prior_crown_age.png

doc/rln_2_4.png

doc/road_map.md

doc/strict_clock_rate_0_5_2_4.png

inst/CITATION

inst/WORDLIST

inst/extdata/2_4.xml

inst/extdata/2_6_0.xml

inst/extdata/2_6_2.xml

inst/extdata/Felinecoronavirus_Envelope_1.fas

inst/extdata/Felinecoronavirus_Envelope_1.txt

inst/extdata/Felinecoronavirus_Envelope_1.xml

inst/extdata/Felinecoronavirus_Envelope_1_no_quotes.txt

inst/extdata/G_VII_pre2003.xml

inst/extdata/G_VII_pre2003_dates_4.txt

inst/extdata/G_VII_pre2003_msa.fas

inst/extdata/G_VII_pre2003_no_tip.xml

inst/extdata/Heleioporus_species_ND2_Pop1.fasta

inst/extdata/THAILAND_TEST.clust_1.dated.fa

inst/extdata/THAILAND_TEST.clust_1.dated.txt

inst/extdata/aco_hky_nd2.xml

inst/extdata/aco_mcmc_chainlength_10_store_every_1.xml

inst/extdata/anthus_15_15.xml

inst/extdata/anthus_15_26.xml

inst/extdata/anthus_15_na.xml

inst/extdata/anthus_aco.fas

inst/extdata/anthus_aco_sub.fas

inst/extdata/anthus_aco_sub.xml

inst/extdata/anthus_aco_sub_20181016.xml

inst/extdata/anthus_aco_sub_20181016_all.xml

inst/extdata/anthus_aco_sub_20181016_all_monophyletic.xml

inst/extdata/anthus_aco_sub_20181016_all_one_div_x.xml

inst/extdata/anthus_aco_sub_20181016_all_one_div_x_monophyletic.xml

inst/extdata/anthus_aco_sub_20181016_all_one_div_x_rln.xml

inst/extdata/anthus_aco_sub_2_5_1.xml

inst/extdata/anthus_aco_sub_2_6.xml

inst/extdata/anthus_aco_sub_calibrated.xml

inst/extdata/anthus_aco_sub_calibrated_no_prior.xml

inst/extdata/anthus_aco_sub_calibrated_rln.xml

inst/extdata/anthus_aco_sub_calibrated_rln_monophyletic.xml

inst/extdata/anthus_aco_sub_cbs_groupsize_4_dim.xml

inst/extdata/anthus_aco_sub_two_mrca_priors.xml

inst/extdata/anthus_na_15.xml

inst/extdata/anthus_na_na.xml

inst/extdata/anthus_nd2.fas

inst/extdata/anthus_nd2_sub.fas

inst/extdata/anthus_nd3.fas

inst/extdata/anthus_nd4.fas

inst/extdata/babette_issue_26.xml

inst/extdata/bd_2_4.xml

inst/extdata/bd_6_taxa_2_4.xml

inst/extdata/bd_birth_rate_normal_death_rate_gamma_2_4.xml

inst/extdata/birth_rate_beta_2_4.xml

inst/extdata/birth_rate_exp_2_4.xml

inst/extdata/birth_rate_gamma_2_4.xml

inst/extdata/birth_rate_inv_gamma_2_4.xml

inst/extdata/birth_rate_laplace_2_4.xml

inst/extdata/birth_rate_log_normal_2_4.xml

inst/extdata/birth_rate_normal_2_4.xml

inst/extdata/birth_rate_one_div_x_2_4.xml

inst/extdata/birth_rate_poisson_2_4.xml

inst/extdata/birth_rate_uniform_2_4.xml

inst/extdata/cbs_2_4.xml

inst/extdata/cbs_6_taxa_2_4.xml

inst/extdata/ccp_2_4.xml

inst/extdata/ccp_6_taxa_2_4.xml

inst/extdata/ccp_pop_size_gamma_2_4.xml

inst/extdata/cep_2_4.xml

inst/extdata/cep_6_taxa_2_4.xml

inst/extdata/gtr_2_4.xml

inst/extdata/gtr_2_6.xml

inst/extdata/gtr_gcc_1_2_4.xml

inst/extdata/gtr_gcc_2_2_4.xml

inst/extdata/gtr_gcc_2_shape_1_5_2_4.xml

inst/extdata/gtr_gcc_2_shape_1_5_prop_invariant_0_5_2_4.xml

inst/extdata/gtr_no_rate_estimation_2_4.xml

inst/extdata/hky_2_4.xml

inst/extdata/hky_2_6.xml

inst/extdata/hky_gcc_1_2_4.xml

inst/extdata/hky_gcc_2_2_4.xml

inst/extdata/hky_gcc_4_2_4.xml

inst/extdata/hky_kappa_2_4.xml

inst/extdata/hky_prop_invariant_0_5_2_4.xml

inst/extdata/issue_135_mrca_estimate_beauti.xml

inst/extdata/issue_135_mrca_estimate_beautier.xml

inst/extdata/issue_135_mrca_no_estimate_beauti.xml

inst/extdata/issue_135_mrca_no_estimate_beautier.xml

inst/extdata/issue_135_no_mrca_estimate_beauti.xml

inst/extdata/issue_135_no_mrca_estimate_beautier.xml

inst/extdata/issue_135_no_mrca_no_estimate_beauti.xml

inst/extdata/issue_135_no_mrca_no_estimate_beautier.xml

inst/extdata/issue_137_lognormal_estimate_beauti.xml

inst/extdata/issue_138_v2_6_7.xml

inst/extdata/issue_142.xml

inst/extdata/jc69_2_4.xml

inst/extdata/jc69_gcc_2_2_4.xml

inst/extdata/jc69_gcc_2_shape_1_5_2_4.xml

inst/extdata/jc69_gcc_2_shape_1_5_prop_invariant_0_5_2_4.xml

inst/extdata/rln_2_4.xml

inst/extdata/rln_2_6.xml

inst/extdata/rln_and_tipdates_babette_issue_26_v2_6.xml

inst/extdata/rln_mrca_2_5.xml

inst/extdata/rln_mrca_one_div_x_2_5.xml

inst/extdata/rln_tipdates_2_6.xml

inst/extdata/rln_uclstdev_beta_2_4.xml

inst/extdata/strict_clock_2_4.xml

inst/extdata/strict_clock_rate_0_5_2_4.xml

inst/extdata/test_output_0.fas

inst/extdata/test_output_0_n_init_attempts.xml

inst/extdata/test_output_0_pre_burnin.xml

inst/extdata/test_output_0_tipdates.tsv

inst/extdata/test_output_2.fas

inst/extdata/test_output_5.fas

inst/extdata/test_output_6.fas

inst/extdata/tipdates_2_6.xml

inst/extdata/tn93_2_4.xml

inst/extdata/tn93_2_6.xml

inst/extdata/tn93_gcc_1_2_4.xml

inst/extdata/tn93_gcc_2_2_4.xml

inst/extdata/tn93_kappas_not_estimated.xml

inst/extdata/yule_2_4.xml

man/figures/AppVeyor.png

man/figures/Codecov.png

man/figures/GitHubActions.png

man/figures/beautier_logo.png

mlc_config.json

pics/AppVeyor.png

pics/Codecov.png

pics/GitHubActions.png

pics/README.md

pics/aco_hky_nd2.png

pics/aco_hky_nd2_tn93.png

pics/aco_nd2_hky.png

pics/aco_nd2_same_clock_model.png

pics/aco_nd2_same_site_model.png

pics/aco_strict_nd2_rln.png

pics/all_default.png

pics/anthus_2_4.png

pics/beast_logo.png

pics/beautier_logo.png

pics/beautier_logo_1_11.png

pics/beautier_logo_1_12_2.png

pics/beautier_logo_1_12_a.png

pics/beautier_logo_1_12_b.png

pics/beautier_logo_1_13.png

pics/belle.png

pics/birth_death_2_4.png

pics/birth_rate_normal_2_4.png

pics/butterfly.png

pics/butterfly_mono_background.png

pics/butterfly_mono_background_2.png

pics/cbs_group_sizes_dimension_4_2_4.png

pics/clade_age_prior.png

pics/coalescent_exponential_population.png

pics/hky_estimate_prop_invariant_2_4.png

pics/hky_example.png

pics/hky_gcc_4_2_4.png

pics/hky_gcc_5_shape_1_5_2_4.png

pics/hky_prop_invariant_0_5_2_4.png

pics/jc69_2_4.png

pics/mrca_prior_all.png

pics/mrca_prior_crown_age.png

pics/priors.png

pics/r_logo.png

pics/r_logo_flipped.png

pics/relaxed_clock_log_normal_2_4.png

pics/rln_rate_2_4.png

pics/strict_clock_rate_0_5_2_4.png

scripts/build_cran.sh

scripts/build_singularity_container.sh

scripts/check_no_local_files

scripts/create_singularity_container.sh

scripts/demo_container.R scripts/find_functions_with_missing_rd_tags.R

scripts/install_beast2

scripts/install_r_packages.R

scripts/install_r_packages.sh

scripts/issue_105.R

scripts/run_container.sh

tests/testthat/test-create_branch_rate_model_stuff_xml.R

tests/testthat/test-create_log_normal_distr.R

tests/testthat/test-hky_site_model_to_xml_prior_distr.R

vignettes/.gitignore

vignettes/aco_hky_nd2_tn93.png

vignettes/all_default.png

vignettes/anthus_2_4.png

vignettes/bd_2_4.png

vignettes/beautier_logo.png

vignettes/birth_rate_normal_2_4.png

vignettes/demo.Rmd vignettes/examples.Rmd

vignettes/hky_prop_invariant_0_5_2_4.png

vignettes/inference_models.Rmd

vignettes/jc69_2_4.png

vignettes/mrca_crown_age.png

vignettes/mrca_prior_all.png

vignettes/mrca_prior_crown_age.png

vignettes/rln_2_4.png

vignettes/strict_clock_rate_0_5_2_4.png

ropensci/beautier documentation built on July 9, 2024, 6:14 a.m.

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ropensci/beautier
'BEAUti' from R

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'BEAUti' from R

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ropensci/beautier 'BEAUti' from R

Files in ropensci/beautier 'BEAUti' from R

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ropensci/beautier
'BEAUti' from R

Files in ropensci/beautier
'BEAUti' from R