Files in richelbilderbeek/beastscriptr
'BEAUti' from R

.Rbuildignore
.gitignore
.travis.yml
CONTRIBUTING.md
DESCRIPTION
Faq.md
LICENSE
NAMESPACE
NEWS.md R/are_clock_models.R R/are_equal_xml_files.R R/are_equal_xml_lines.R R/are_equivalent_xmls.R R/are_ids.R R/are_init_clock_models.R R/are_init_mrca_priors.R R/are_init_site_models.R R/are_init_tree_priors.R R/are_initial_phylogenies.R R/are_mrca_alignment_ids_in_fastas.R R/are_mrca_priors.R R/are_mrca_taxa_names_in_fastas.R R/are_mrca_taxa_non_intersecting.R R/are_rln_clock_models.R R/are_site_models.R R/are_tree_priors.R R/beautier.R R/clock_model_to_xml_lh_distr.R R/clock_model_to_xml_operators.R R/clock_model_to_xml_prior_distr.R R/clock_model_to_xml_state.R R/clock_model_to_xml_tracelog.R R/clock_model_to_xml_treelogger.R R/clock_models_to_xml_operators.R R/clock_models_to_xml_prior_distr.R R/clock_models_to_xml_state.R R/clock_models_to_xml_tracelog.R R/compare_lines.R R/count_trailing_spaces.R R/create_beast2_input.R R/create_beast2_input_1_12.R R/create_beast2_input_beast.R R/create_beast2_input_data.R R/create_beast2_input_data_sequences.R R/create_beast2_input_distr.R R/create_beast2_input_file.R R/create_beast2_input_file_1_12.R R/create_beast2_input_init.R R/create_beast2_input_loggers.R R/create_beast2_input_map.R R/create_beast2_input_operators.R R/create_beast2_input_run.R R/create_beast2_input_state.R R/create_beast2_input_xml.R R/create_clock_model.R R/create_clock_models.R R/create_distr.R R/create_gamma_site_model.R R/create_mcmc.R R/create_misc_options.R R/create_mrca_prior.R R/create_param.R R/create_random.R R/create_random_name.R R/create_site_model.R R/create_site_models.R R/create_tree_prior.R R/create_tree_priors.R R/create_yule_tree_priors.R R/default_param_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_phylo.R R/fasta_to_sequences.R R/fastas_to_phylos.R R/files_exist.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/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_path.R R/get_beautier_paths.R R/get_clock_model_name.R R/get_clock_model_names.R R/get_clock_models_ids.R R/get_distr_n_params.R R/get_distr_names.R R/get_file_base_sans_ext.R R/get_first_clock_model_index.R R/get_freq_equilibrium_names.R R/get_has_non_strict_clock_model.R R/get_n_taxa.R R/get_operator_id_pre.R R/get_param_names.R R/get_phylo_crown_age.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_unlinked_clock_models.R R/get_unlinked_site_models.R R/get_unlinked_tree_priors.R R/get_xml_closing_tag.R R/get_xml_opening_tag.R R/has_shared_rln_clock_models.R R/has_xml_closing_tag.R R/has_xml_opening_tag.R R/has_xml_short_closing_tag.R R/indent.R R/init_clock_models.R R/init_distr.R R/init_gamma_site_model.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_alpha_param.R R/is_bd_tree_prior.R R/is_beta_distr.R R/is_beta_param.R R/is_cbs_tree_prior.R R/is_ccp_tree_prior.R R/is_cep_tree_prior.R R/is_clock_model.R R/is_clock_model_name.R R/is_clock_rate_param.R R/is_distr.R R/is_distr_name.R R/is_exp_distr.R R/is_freq_equilibrium_name.R R/is_gamma_distr.R R/is_gamma_site_model.R R/is_gtr_site_model.R R/is_hky_site_model.R R/is_id.R R/is_in_patterns.R R/is_index_of_first_shared_clock_model.R R/is_index_of_non_first_shared_clock_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_inv_gamma_distr.R R/is_jc69_site_model.R R/is_kappa_1_param.R R/is_kappa_2_param.R R/is_lambda_param.R R/is_laplace_distr.R R/is_log_normal_distr.R R/is_m_param.R R/is_mcmc.R R/is_mean_param.R R/is_misc_options.R R/is_mrca_prior.R R/is_mu_param.R R/is_normal_distr.R R/is_one_div_x_distr.R R/is_one_na.R R/is_param.R R/is_param_name.R R/is_phylo.R R/is_poisson_distr.R R/is_rate_ac_param.R R/is_rate_ag_param.R R/is_rate_at_param.R R/is_rate_cg_param.R R/is_rate_ct_param.R R/is_rate_gt_param.R R/is_rln_clock_model.R R/is_s_param.R R/is_scale_param.R R/is_sigma_param.R R/is_site_model.R R/is_site_model_name.R R/is_strict_clock_model.R R/is_tn93_site_model.R R/is_tree_prior.R R/is_tree_prior_name.R R/is_uniform_distr.R R/is_xml.R R/is_yule_tree_prior.R R/mcmc_to_xml_run.R R/mrca_prior_to_xml_lh_distr.R R/mrca_prior_to_xml_operators.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/mrca_priors_to_xml_operators.R R/mrca_priors_to_xml_state.R R/mrca_priors_to_xml_tracelog.R R/parameter_to_xml.R R/phylo_to_xml_state.R R/remove_multiline.R R/rln_clock_model_to_xml_mean_rate_prior.R R/rnd_phylo_to_xml_state.R R/rnd_phylo_xml_init.R R/site_model_to_xml_lh_distr.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_subst_model.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_state.R R/site_models_to_xml_tracelog.R R/tree_models_to_xml_tracelog.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_operators.R R/tree_priors_to_xml_state.R R/tree_priors_to_xml_tracelog.R README.md
appveyor.yml
beautier.Rproj
code_of_conduct.md create_pdf.R examples.md
inst/CITATION
inst/WORDLIST
inst/extdata/2_4.xml
inst/extdata/aco_hky_nd2.xml
inst/extdata/aco_mcmc_chainlength_10_store_every_1.xml
inst/extdata/aco_nd2_2_4.xml
inst/extdata/aco_nd2_nd3_2_4.xml
inst/extdata/aco_nd2_nd3_nd4_2_4.xml
inst/extdata/aco_nd2_nd3_nd4_complex_2_4.xml
inst/extdata/aco_nd2_nd3_nd4_shared_clock_2_4.xml
inst/extdata/aco_nd2_rln_rln_2_4.xml
inst/extdata/aco_nd2_shared_site_model_2_4.xml
inst/extdata/aco_nd2_strict_rln_2_4.xml
inst/extdata/aco_nd2_strict_strict_2_4.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_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/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_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_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_30.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_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_two_mrca_priors.xml
inst/extdata/test_output_5.fas
inst/extdata/test_output_6.fas
inst/extdata/tn93_2_4.xml
inst/extdata/tn93_gcc_1_2_4.xml
inst/extdata/tn93_gcc_2_2_4.xml
inst/extdata/yule_2_4.xml
install_beast2
install_r_packages.R man/are_equivalent_xml_lines.Rd man/are_equivalent_xml_lines_all.Rd man/are_equivalent_xml_lines_loggers.Rd man/are_equivalent_xml_lines_operators.Rd man/are_equivalent_xml_lines_section.Rd man/bd_tree_prior_to_xml_prior_distr.Rd man/beautier.Rd man/cbs_tree_prior_to_xml_prior_distr.Rd man/ccp_tree_prior_to_xml_prior_distr.Rd man/cep_tree_prior_to_xml_prior_distr.Rd man/create_alpha_param.Rd man/create_bd_tree_prior.Rd man/create_beast2_input.Rd man/create_beast2_input_1_12.Rd man/create_beast2_input_distr_lh.Rd man/create_beast2_input_distr_prior.Rd man/create_beast2_input_file.Rd man/create_beast2_input_file_1_12.Rd man/create_beast2_input_screenlog.Rd man/create_beast2_input_tracelog.Rd man/create_beast2_input_treelogs.Rd man/create_beast2_input_xml.Rd man/create_beta_distr.Rd man/create_beta_param.Rd man/create_cbs_tree_prior.Rd man/create_ccp_tree_prior.Rd man/create_cep_tree_prior.Rd man/create_clock_model.Rd man/create_clock_models.Rd man/create_clock_rate_param.Rd man/create_distr.Rd man/create_exp_distr.Rd man/create_gamma_distr.Rd man/create_gamma_site_model.Rd man/create_gtr_site_model.Rd man/create_hky_site_model.Rd man/create_inv_gamma_distr.Rd man/create_jc69_site_model.Rd man/create_jc69_site_models.Rd man/create_kappa_1_param.Rd man/create_kappa_2_param.Rd man/create_lambda_param.Rd man/create_laplace_distr.Rd man/create_log_normal_distr.Rd man/create_m_param.Rd man/create_mcmc.Rd man/create_mean_param.Rd man/create_misc_options.Rd man/create_mrca_prior.Rd man/create_mu_param.Rd man/create_normal_distr.Rd man/create_one_div_x_distr.Rd man/create_param.Rd man/create_poisson_distr.Rd man/create_rate_ac_param.Rd man/create_rate_ag_param.Rd man/create_rate_at_param.Rd man/create_rate_cg_param.Rd man/create_rate_ct_param.Rd man/create_rate_gt_param.Rd man/create_rln_clock_model.Rd man/create_rnd_alpha_param.Rd man/create_rnd_bd_tree_prior.Rd man/create_rnd_beta_distr.Rd man/create_rnd_beta_param.Rd man/create_rnd_bool.Rd man/create_rnd_cbs_tree_prior.Rd man/create_rnd_ccp_tree_prior.Rd man/create_rnd_cep_tree_prior.Rd man/create_rnd_clock_model.Rd man/create_rnd_clock_rate_param.Rd man/create_rnd_distr.Rd man/create_rnd_estimate.Rd man/create_rnd_exp_distr.Rd man/create_rnd_freq_equilibrium.Rd man/create_rnd_gamma_distr.Rd man/create_rnd_gamma_site_model.Rd man/create_rnd_gtr_site_model.Rd man/create_rnd_hky_site_model.Rd man/create_rnd_inv_gamma_distr.Rd man/create_rnd_jc69_site_model.Rd man/create_rnd_kappa_1_param.Rd man/create_rnd_kappa_2_param.Rd man/create_rnd_lambda_param.Rd man/create_rnd_laplace_distr.Rd man/create_rnd_log_normal_distr.Rd man/create_rnd_m_param.Rd man/create_rnd_mean_param.Rd man/create_rnd_mrca_prior.Rd man/create_rnd_mrca_priors.Rd man/create_rnd_mu_param.Rd man/create_rnd_normal_distr.Rd man/create_rnd_one_div_x_distr.Rd man/create_rnd_param.Rd man/create_rnd_poisson_distr.Rd man/create_rnd_rate_ac_param.Rd man/create_rnd_rate_ag_param.Rd man/create_rnd_rate_at_param.Rd man/create_rnd_rate_cg_param.Rd man/create_rnd_rate_ct_param.Rd man/create_rnd_rate_gt_param.Rd man/create_rnd_rln_clock_model.Rd man/create_rnd_s_param.Rd man/create_rnd_scale_param.Rd man/create_rnd_sigma_param.Rd man/create_rnd_site_model.Rd man/create_rnd_strict_clock_model.Rd man/create_rnd_tn93_site_model.Rd man/create_rnd_tree_prior.Rd man/create_rnd_two_mrca_priors.Rd man/create_rnd_uniform_distr.Rd man/create_rnd_yule_tree_prior.Rd man/create_s_param.Rd man/create_scale_param.Rd man/create_sigma_param.Rd man/create_site_model.Rd man/create_site_models.Rd man/create_strict_clock_model.Rd man/create_strict_clock_models.Rd man/create_tn93_site_model.Rd man/create_tree_prior.Rd man/create_tree_priors.Rd man/create_uniform_distr.Rd man/create_yule_tree_prior.Rd man/create_yule_tree_priors.Rd man/default_params_doc.Rd man/distr_to_xml_beta.Rd man/distr_to_xml_exp.Rd man/distr_to_xml_gamma.Rd man/distr_to_xml_inv_gamma.Rd man/distr_to_xml_laplace.Rd man/distr_to_xml_log_normal.Rd man/distr_to_xml_normal.Rd man/distr_to_xml_one_div_x.Rd man/distr_to_xml_poisson.Rd man/distr_to_xml_uniform.Rd man/fasta_to_phylo.Rd man/fastas_to_phylos.Rd man/get_alignment_id.Rd man/get_alignment_ids.Rd man/get_beautier_path.Rd man/get_beautier_paths.Rd man/get_fasta_filename.Rd man/get_taxa_names.Rd man/init_bd_tree_prior.Rd man/init_ccp_tree_prior.Rd man/init_cep_tree_prior.Rd man/init_gtr_site_model.Rd man/init_hky_site_model.Rd man/init_jc69_site_model.Rd man/init_rln_clock_model.Rd man/init_strict_clock_model.Rd man/init_tn93_site_model.Rd man/init_yule_tree_prior.Rd man/is_init_beta_distr.Rd man/is_init_cep_tree_prior.Rd man/is_init_exp_distr.Rd man/is_init_gamma_distr.Rd man/is_init_inv_gamma_distr.Rd man/is_init_laplace_distr.Rd man/is_init_log_normal_distr.Rd man/is_init_normal_distr.Rd man/is_init_one_div_x_distr.Rd man/is_init_poisson_distr.Rd man/is_init_uniform_distr.Rd man/parameter_to_xml_alpha.Rd man/parameter_to_xml_beta.Rd man/parameter_to_xml_clock_rate.Rd man/parameter_to_xml_kappa_1.Rd man/parameter_to_xml_kappa_2.Rd man/parameter_to_xml_lambda.Rd man/parameter_to_xml_m.Rd man/parameter_to_xml_mean.Rd man/parameter_to_xml_mu.Rd man/parameter_to_xml_rate_ac.Rd man/parameter_to_xml_rate_ag.Rd man/parameter_to_xml_rate_at.Rd man/parameter_to_xml_rate_cg.Rd man/parameter_to_xml_rate_ct.Rd man/parameter_to_xml_rate_gt.Rd man/parameter_to_xml_s.Rd man/parameter_to_xml_scale.Rd man/parameter_to_xml_sigma.Rd man/yule_tree_prior_to_xml_prior_distr.Rd
pics/AppVeyor.png
pics/Codecov.png
pics/TravisCI.png
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
road_map.md
scripts/check_dead_links
scripts/install_r_packages.R
scripts/install_r_packages.sh
scripts/sbatch_test_random_1.sh
scripts/sbatch_test_random_nonsense_1.sh
scripts/test-create_beast2_input.R scripts/test-create_beast2_input_file.R scripts/test-create_beast2_input_file_1_12.R scripts/test_brute_force_1.R scripts/test_brute_force_2_shared_tree_priors.R scripts/test_brute_force_2_unlinked.R scripts/test_random_1.R
scripts/test_random_1.sh
scripts/test_random_nonsense_1.R
scripts/test_random_nonsense_1.sh
tests/spelling.R tests/testthat.R tests/testthat/test-are_clock_models.R tests/testthat/test-are_equal_xml_files.R tests/testthat/test-are_equal_xml_lines.R tests/testthat/test-are_equivalent_xml_files.R tests/testthat/test-are_equivalent_xml_lines.R tests/testthat/test-are_equivalent_xml_lines_section.R tests/testthat/test-are_ids.R tests/testthat/test-are_init_clock_models.R tests/testthat/test-are_init_tree_priors.R tests/testthat/test-are_mrca_alignment_ids_in_fastas.R tests/testthat/test-are_mrca_priors.R tests/testthat/test-are_mrca_taxa_names_in_fastas.R tests/testthat/test-are_mrca_taxa_non_intersecting.R tests/testthat/test-are_rln_clock_models.R tests/testthat/test-are_site_models.R tests/testthat/test-are_tree_priors.R tests/testthat/test-clock_model_to_xml_lh_distr.R tests/testthat/test-clock_model_to_xml_tracelog.R tests/testthat/test-clock_models_to_xml_operators.R tests/testthat/test-clock_models_to_xml_prior_distr.R tests/testthat/test-clock_models_to_xml_state.R 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tests/testthat/test-create_beast2_input_operators.R tests/testthat/test-create_beast2_input_run.R tests/testthat/test-create_beast2_input_state.R tests/testthat/test-create_clock_model.R tests/testthat/test-create_clock_models.R tests/testthat/test-create_distr.R tests/testthat/test-create_gamma_distr.R tests/testthat/test-create_gamma_site_model.R tests/testthat/test-create_jc69_site_models.R tests/testthat/test-create_mcmc.R tests/testthat/test-create_misc_options.R tests/testthat/test-create_mrca_prior.R tests/testthat/test-create_param.R tests/testthat/test-create_random.R tests/testthat/test-create_random_name.R tests/testthat/test-create_sigma_param.R tests/testthat/test-create_site_model.R tests/testthat/test-create_site_models.R tests/testthat/test-create_strict_clock_model.R tests/testthat/test-create_tree_prior.R tests/testthat/test-create_tree_priors.R tests/testthat/test-create_yule_tree_prior.R tests/testthat/test-create_yule_tree_priors.R tests/testthat/test-distr_to_xml.R tests/testthat/test-extract_xml_operators_from_lines.R tests/testthat/test-extract_xml_section_from_lines.R tests/testthat/test-fasta_file_to_sequences.R tests/testthat/test-fasta_to_phylo.R tests/testthat/test-fastas_to_phylos.R tests/testthat/test-find_clock_model.R tests/testthat/test-find_first_xml_opening_tag_line.R tests/testthat/test-find_last_xml_closing_tag_line.R tests/testthat/test-get_alignment_id.R tests/testthat/test-get_alignment_ids.R tests/testthat/test-get_beautier_path.R tests/testthat/test-get_beautier_paths.R tests/testthat/test-get_clock_model_name.R tests/testthat/test-get_clock_models_ids.R tests/testthat/test-get_distr_n_params.R tests/testthat/test-get_file_base_sans_ext.R tests/testthat/test-get_first_clock_model_index.R tests/testthat/test-get_has_non_strict_clock_model.R tests/testthat/test-get_n_taxa.R tests/testthat/test-get_operator_id_pre.R tests/testthat/test-get_phylo_crown_age.R tests/testthat/test-get_site_model_n_distrs.R tests/testthat/test-get_site_model_n_params.R tests/testthat/test-get_site_models_n_distrs.R tests/testthat/test-get_site_models_n_params.R tests/testthat/test-get_taxa_names.R tests/testthat/test-get_tree_prior_n_distrs.R tests/testthat/test-get_tree_prior_n_params.R tests/testthat/test-get_tree_priors_n_distrs.R tests/testthat/test-get_tree_priors_n_params.R tests/testthat/test-get_unlinked_clock_models.R tests/testthat/test-get_unlinked_site_models.R tests/testthat/test-get_unlinked_tree_priors.R tests/testthat/test-get_xml_closing_tag.R tests/testthat/test-get_xml_opening_tag.R tests/testthat/test-has_shared_rln_clock_models.R tests/testthat/test-has_xml_closing_tag.R tests/testthat/test-has_xml_opening_tag.R tests/testthat/test-has_xml_short_closing_tag.R tests/testthat/test-helper.R tests/testthat/test-indent.R tests/testthat/test-init_clock_models.R tests/testthat/test-init_distr.R tests/testthat/test-init_gamma_site_model.R tests/testthat/test-init_mrca_priors.R tests/testthat/test-init_param.R tests/testthat/test-init_site_models.R tests/testthat/test-init_tree_priors.R tests/testthat/test-interspace.R tests/testthat/test-is_alpha_param.R tests/testthat/test-is_beta_distr.R tests/testthat/test-is_cbs_tree_prior.R tests/testthat/test-is_ccp_tree_prior.R tests/testthat/test-is_clock_model.R tests/testthat/test-is_distr.R tests/testthat/test-is_exp_distr.R tests/testthat/test-is_gamma_distr.R tests/testthat/test-is_gamma_site_model.R tests/testthat/test-is_hky_site_model.R tests/testthat/test-is_id.R tests/testthat/test-is_in_patterns.R tests/testthat/test-is_index_of_first_shared_clock_model.R tests/testthat/test-is_init_clock_model.R tests/testthat/test-is_init_distr.R tests/testthat/test-is_init_gamma_site_model.R tests/testthat/test-is_init_param.R tests/testthat/test-is_init_site_model.R tests/testthat/test-is_init_tree_prior.R tests/testthat/test-is_inv_gamma_distr.R tests/testthat/test-is_jc69_site_model.R tests/testthat/test-is_laplace_distr.R tests/testthat/test-is_log_normal_distr.R tests/testthat/test-is_mcmc.R tests/testthat/test-is_misc_options.R tests/testthat/test-is_mrca_prior.R tests/testthat/test-is_normal_distr.R tests/testthat/test-is_one_div_x_distr.R tests/testthat/test-is_one_na.R tests/testthat/test-is_param.R tests/testthat/test-is_phylo.R tests/testthat/test-is_poisson_distr.R tests/testthat/test-is_rln_clock_model.R tests/testthat/test-is_site_model.R tests/testthat/test-is_site_model_name.R tests/testthat/test-is_tree_prior.R tests/testthat/test-is_tree_prior_name.R tests/testthat/test-is_uniform_distr.R tests/testthat/test-is_xml.R tests/testthat/test-is_yule_tree_prior.R tests/testthat/test-mcmc_to_xml_run.R tests/testthat/test-parameter_to_xml.R tests/testthat/test-remove_multiline.R tests/testthat/test-rnd_phylo_to_xml_init.R tests/testthat/test-site_model_to_xml_state.R tests/testthat/test-site_model_to_xml_tracelog.R tests/testthat/test-site_models_to_xml_operators.R tests/testthat/test-site_models_to_xml_state.R tests/testthat/test-site_models_to_xml_tracelog.R tests/testthat/test-tree_models_to_xml_tracelog.R tests/testthat/test-tree_prior_to_xml_prior_distr.R tests/testthat/test-tree_priors_to_xml_operators.R tests/testthat/test-tree_priors_to_xml_state.R tests/testthat/test-tree_priors_to_xml_tracelog.R
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vignettes/demo.R vignettes/demo.Rmd
vignettes/demo.html
vignettes/examples.R vignettes/examples.Rmd
vignettes/examples.html
vignettes/from_1_12_0_to_1_12_1.R vignettes/from_1_12_0_to_1_12_1.Rmd
vignettes/from_1_12_0_to_1_12_1.html
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vignettes/jc69_2_4.png
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richelbilderbeek/beastscriptr documentation built on Aug. 14, 2018, 1:20 a.m.