Files in richelbilderbeek/pirouette

Create a Bayesian Posterior from a Phylogeny

.Rbuildignore

.github/.gitignore

.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/check_bash_style.yaml

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.lintr

CODE_OF_CONDUCT.md CONTRIBUTING.md

DESCRIPTION

LICENSE

NAMESPACE

NEWS.md R/alignment_params_to_posterior_trees.R R/check_alignment.R R/check_alignment_params.R R/check_beast2_installed.R R/check_error_fun.R R/check_error_measure_params.R R/check_experiment.R R/check_experiments.R R/check_experiments_all_inference_models_are_unique.R R/check_experiments_candidates_have_same_beast2_files.R R/check_experiments_candidates_have_same_mcmcs.R R/check_gen_and_cand_save_to_different_files.R R/check_inference_conditions.R R/check_inference_model_type_names.R R/check_inference_model_weights.R R/check_init_pir_params.R R/check_is_ns_beast2_pkg_installed.R R/check_model_type.R R/check_mutation_rate.R R/check_pir_out.R R/check_pir_out_errors_above_zero.R R/check_pir_params.R R/check_pir_paramses.R R/check_reconstructed_phylogeny.R R/check_root_sequence.R R/check_sim_tral_fun.R R/check_sim_twal_fun.R R/check_sim_twin_tree_fun.R R/check_tree_and_model.R R/check_tree_and_model_errors.R R/check_tree_and_models.R R/check_tree_type.R R/check_tree_types.R R/check_twin_phylogeny.R R/check_twinning_params.R R/check_twinning_params_names.R R/collapse_tree_and_model.R R/collect_pir_outs.R R/combine_brts_and_topology.R R/combine_models.R R/complete_treelog_filename.R R/convert_pir_out_to_long.R R/copy_true_alignment.R R/count_n_mutations.R R/create_alignment_params.R R/create_all_bd_experiments.R R/create_all_coal_experiments.R R/create_all_experiments.R R/create_blocked_dna.R R/create_cand_experiment.R R/create_copy_twin_tree_from_true_fun.R R/create_error_measure_params.R R/create_exemplary_dd_tree.R R/create_exemplary_dd_tree_giappo.R R/create_experiment.R R/create_gen_experiment.R R/create_generative_trees.R R/create_inference_conditions.R R/create_mono_nuc_dna.R R/create_pir_params.R R/create_rate_matrix.R R/create_sim_yule_twin_tree_fun.R R/create_standard_mutation_rate.R R/create_std_pir_params.R R/create_std_pir_paramses.R R/create_test_cand_experiment.R R/create_test_experiment.R R/create_test_gen_experiment.R R/create_test_marg_liks.R R/create_test_phylogeny.R R/create_test_pir_params_setup.R R/create_test_pir_run_output.R R/create_tral_file.R R/create_tree_and_model_errors_from_folder.R R/create_tree_and_model_errors_from_folders.R R/create_true_alignment.R R/create_twal_file.R R/create_twin_branching_times.R R/create_twin_tree.R R/create_twinning_params.R R/default_params_doc.R R/delete_beast2_state_files.R R/errorses_to_data_frame.R R/est_evidences.R R/get_alignment_n_taxa.R R/get_alignment_sequence_length.R R/get_alignment_sequences.R R/get_copy_tral_fun.R R/get_experiment_filenames.R R/get_experiments_filenames.R R/get_gamma_error_fun.R R/get_model_selections.R R/get_nltt_error_fun.R R/get_pir_params_filenames.R R/get_pir_plot_fill_colors.R R/get_pir_plot_line_colors.R R/get_pir_plot_theme.R R/get_pir_plot_tree_and_model_descriptions.R R/get_remove_hex_twin_fun.R R/get_sim_bd_twin_tree_fun.R R/get_sim_tral_with_lns_site_model_fun.R R/get_sim_tral_with_std_nsm_fun.R R/get_sim_tral_with_uns_site_model_fun.R R/get_sim_twal_with_same_n_mutation_fun.R R/get_sim_twal_with_std_nsm_fun.R R/get_sim_yule_twin_tree_fun.R R/get_temp_errors_filename.R R/get_temp_evidence_filename.R R/get_temp_fasta_filename.R R/get_temp_tree_filename.R R/get_test_alignment.R R/get_tree_and_model_descriptions.R R/get_tree_and_model_values.R R/has_candidate_experiments.R R/has_twinning.R R/init_experiment.R R/init_pir_params.R R/is_best_candidate.R R/is_dna_seq.R R/is_pir_params.R R/phylo_to_errors.R R/pir_plot.R R/pir_plot_from_file.R R/pir_plot_from_long.R R/pir_plots.R R/pir_rename.R R/pir_rename_to_std.R R/pir_run.R R/pir_run_distribution.R R/pir_run_true_tree.R R/pir_run_twin_tree.R R/pir_runs.R R/pir_save.R R/pir_to_pics.R R/pir_to_tables.R R/pirouette-package.R R/plot_alignment_from_file.R R/read_errors_csv.R R/relevel_inference_model.R R/relevel_tree_and_model.R R/renum_rng_seeds.R R/replicate_pir_params.R R/rm_pir_param_files.R R/select_candidate_evidences.R R/select_experiments.R R/shorten_experiments.R R/shorten_pir_params.R R/shorten_pir_paramses.R R/sim_alignment_with_n_mutations.R R/sim_alignment_with_std_nsm.R R/sim_alignment_with_std_nsm_from_params.R R/sim_bd_twin_tree.R R/sim_tral_with_lns_site_model.R R/sim_tral_with_nsm.R R/sim_tral_with_uns_site_model.R R/sim_true_alignment.R R/sim_twal_with_lns_site_model.R R/sim_twal_with_nsm.R R/sim_twal_with_same_n_mutation.R R/sim_twal_with_uns_site_model.R R/sim_twin_alignment.R R/to_evidence_filename.R R/to_twin_filename.R R/to_twin_filenames.R R/twin_to_yule_tree.R R/utils-pipe.R R/utils.R R/will_measure_evidence.R README.md

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doc/how_to_set_up_experiments.md doc/install.md doc/interpretation.md

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inst/CITATION

inst/extdata/alignment.fas

inst/extdata/test_output_3.fas

inst/extdata/test_output_3_evidence.fas

man/check_alignment.Rd man/check_alignment_params.Rd man/check_alignment_params_names.Rd man/check_beast2_installed.Rd man/check_candidates_save_to_same_files.Rd man/check_error_fun.Rd man/check_error_measure_params.Rd man/check_experiment.Rd man/check_experiments.Rd man/check_experiments_all_inference_models_are_unique.Rd man/check_experiments_candidates_have_same_mcmcs.Rd man/check_gen_and_cand_exps_save_to_different_files.Rd man/check_inference_conditions.Rd man/check_inference_model_type_names.Rd man/check_inference_model_weights.Rd man/check_init_pir_params.Rd man/check_is_ns_beast2_pkg_installed.Rd man/check_model_type.Rd man/check_mutation_rate.Rd man/check_pir_out.Rd man/check_pir_out_errors_above_zero.Rd man/check_pir_out_names.Rd man/check_pir_params.Rd man/check_pir_params_data_types.Rd man/check_pir_params_names.Rd man/check_pir_paramses.Rd man/check_reconstructed_phylogeny.Rd man/check_root_sequence.Rd man/check_sim_tral_fun.Rd man/check_sim_twal_fun.Rd man/check_sim_twin_tree_fun.Rd man/check_tree_and_model.Rd man/check_tree_and_model_errors.Rd man/check_tree_and_models.Rd man/check_tree_type.Rd man/check_tree_types.Rd man/check_twin_phylogeny.Rd man/check_twinning_params.Rd man/check_twinning_params_names.Rd man/collapse_tree_and_model.Rd man/collect_pir_outs.Rd man/combine_brts_and_topology.Rd man/combine_models.Rd man/complete_treelog_filename.Rd man/convert_pir_out_to_long.Rd man/convert_tree2brts.Rd man/copy_true_alignment.Rd man/count_n_mutations.Rd man/create_alignment_params.Rd man/create_all_bd_experiments.Rd man/create_all_coal_experiments.Rd man/create_all_experiments.Rd man/create_bd_tree.Rd man/create_blocked_dna.Rd man/create_cand_experiment.Rd man/create_copy_twtr_from_true_fun.Rd man/create_error_measure_params.Rd man/create_exemplary_dd_tree.Rd man/create_exemplary_dd_tree_giappo.Rd man/create_experiment.Rd man/create_gen_experiment.Rd man/create_inference_conditions.Rd man/create_mono_nuc_dna.Rd man/create_pir_params.Rd man/create_sim_yule_twin_tree_fun.Rd man/create_standard_mutation_rate.Rd man/create_std_pir_params.Rd man/create_std_pir_paramses.Rd man/create_test_alignment_params.Rd man/create_test_cand_experiment.Rd man/create_test_experiment.Rd man/create_test_gen_experiment.Rd man/create_test_marg_liks.Rd man/create_test_phylogeny.Rd man/create_test_pir_params.Rd man/create_test_pir_params_setup.Rd man/create_test_pir_run_output.Rd man/create_test_pir_run_output2.Rd man/create_tral_file.Rd man/create_tree_and_model_errors_from_folder.Rd man/create_tree_and_model_errors_from_folders.Rd man/create_true_alignment.Rd man/create_twal_file.Rd man/create_twin_branching_times.Rd man/create_twin_tree.Rd man/create_twinning_params.Rd man/create_yule_tree.Rd man/default_params_doc.Rd man/delete_beast2_state_files.Rd man/errorses_to_data_frame.Rd man/est_evidences.Rd

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man/get_alignment_n_taxa.Rd man/get_alignment_sequence_length.Rd man/get_alignment_sequences.Rd man/get_copy_tral_fun.Rd man/get_experiment_filenames.Rd man/get_experiments_filenames.Rd man/get_gamma_error_fun.Rd man/get_model_selections.Rd man/get_model_type_names.Rd man/get_nltt_error_fun.Rd man/get_pir_params_filenames.Rd man/get_pir_plot_fill_colors.Rd man/get_pir_plot_line_colors.Rd man/get_pir_plot_theme.Rd man/get_pir_plot_tree_and_model_descriptions.Rd man/get_remove_hex_twin_fun.Rd man/get_sim_bd_twin_tree_fun.Rd man/get_sim_tral_with_lns_nsm_fun.Rd man/get_sim_tral_with_std_nsm_fun.Rd man/get_sim_tral_with_uns_nsm_fun.Rd man/get_sim_twal_same_n_muts_fun.Rd man/get_sim_twal_with_std_nsm_fun.Rd man/get_sim_yule_twin_tree_fun.Rd man/get_temp_errors_filename.Rd man/get_temp_evidence_filename.Rd man/get_temp_fasta_filename.Rd man/get_temp_tree_filename.Rd man/get_test_alignment.Rd man/get_tree_and_model_descriptions.Rd man/get_tree_and_model_values.Rd man/get_tree_types.Rd man/get_twin_methods.Rd man/get_twin_models.Rd man/has_candidate_experiments.Rd man/has_twinning.Rd man/init_experiment.Rd man/init_pir_params.Rd man/is_best_candidate.Rd man/is_dna_seq.Rd man/is_pir_params.Rd man/phylo_to_errors.Rd man/pipe.Rd man/pir_plot.Rd man/pir_plot_from_file.Rd man/pir_plot_from_long.Rd man/pir_plots.Rd man/pir_rename.Rd man/pir_rename_to_std.Rd man/pir_run.Rd man/pir_run_distribution.Rd man/pir_run_true_tree.Rd man/pir_run_twin_tree.Rd man/pir_runs.Rd man/pir_save.Rd man/pir_to_pics.Rd man/pir_to_tables.Rd man/pirouette-package.Rd man/plot_alignment_from_file.Rd man/read_errors_csv.Rd man/relevel_inference_model.Rd man/relevel_tree_and_model.Rd man/renum_rng_seeds.Rd man/replicate_pir_params.Rd man/rm_pir_param_files.Rd man/select_candidate_evidences.Rd man/select_experiments.Rd man/shorten_experiments.Rd man/shorten_pir_params.Rd man/shorten_pir_paramses.Rd man/sim_alignment_with_n_mutations.Rd man/sim_alignment_with_std_nsm.Rd man/sim_alignment_with_std_nsm_from_params.Rd man/sim_bd_twin_tree.Rd man/sim_tral_with_lns_nsm.Rd man/sim_tral_with_std_nsm.Rd man/sim_tral_with_uns_nsm.Rd man/sim_true_alignment.Rd man/sim_twal_with_lns_nsm.Rd man/sim_twal_with_same_n_mutation.Rd man/sim_twal_with_std_nsm.Rd man/sim_twal_with_uns_nsm.Rd man/sim_twin_alignment.Rd man/sim_yule_twin_tree.Rd man/to_evidence_filename.Rd man/to_twin_filename.Rd man/to_twin_filenames.Rd man/will_measure_evidence.Rd

mlc_config.json

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pirouette.Rproj

scripts/.gitignore

scripts/README.md

scripts/build_cran.sh

scripts/clean.sh

scripts/create_fig_bd.R scripts/create_test_pir_params_gen_twin.R scripts/create_workflow_pics.R scripts/find_ideal_tree.R scripts/find_ideal_tree_by_max_clade_cred_error.R

scripts/install_beast2_and_ns.sh

scripts/install_pir_deps.sh

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scripts/issue_323.R scripts/montelbano_strikes.R scripts/pir_params_modifiers.R scripts/pir_plot_from_files.R

scripts/run_r_script.sh

scripts/uninstall_beast2_and_ns.sh

tests/testthat.R

tests/testthat/.gitignore

tests/testthat/test-alignment_params_to_posterior_trees.R tests/testthat/test-check_alignment.R tests/testthat/test-check_alignment_params.R tests/testthat/test-check_candidates_save_to_same_files.R tests/testthat/test-check_error_fun.R tests/testthat/test-check_error_measure_params.R tests/testthat/test-check_experiment.R tests/testthat/test-check_experiments.R tests/testthat/test-check_inference_conditions.R tests/testthat/test-check_inference_model_type_names.R tests/testthat/test-check_init_pir_params.R tests/testthat/test-check_is_ns_beast2_pkg_installed.R tests/testthat/test-check_mutation_rate.R tests/testthat/test-check_pir_out.R tests/testthat/test-check_pir_params.R tests/testthat/test-check_pir_paramses.R tests/testthat/test-check_reconstructed_phylogeny.R tests/testthat/test-check_root_sequence.R tests/testthat/test-check_sim_tral_fun.R tests/testthat/test-check_sim_twal_fun.R tests/testthat/test-check_sim_twin_tree_fun.R tests/testthat/test-check_tree_and_model.R tests/testthat/test-check_tree_and_model_errors.R tests/testthat/test-check_tree_and_models.R tests/testthat/test-check_tree_types.R tests/testthat/test-check_twin_phylogeny.R tests/testthat/test-check_twinning_params.R tests/testthat/test-collapse_tree_and_model.R tests/testthat/test-collect_pir_outs.R tests/testthat/test-combine_brts_and_topology.R tests/testthat/test-combine_models.R tests/testthat/test-complete_treelog_filename.R tests/testthat/test-convert_pir_out_to_long.R tests/testthat/test-copy_true_alignment.R tests/testthat/test-count_n_mutations.R tests/testthat/test-create_alignment_params.R tests/testthat/test-create_alignment_with_linked_node_sub_site_model.R tests/testthat/test-create_all_bd_experiments.R tests/testthat/test-create_all_coal_experiments.R tests/testthat/test-create_all_experiments.R tests/testthat/test-create_blocked_dna.R tests/testthat/test-create_error_measure_params.R tests/testthat/test-create_exemplary_dd_tree.R tests/testthat/test-create_experiment.R tests/testthat/test-create_generative_trees.R tests/testthat/test-create_inference_conditions.R tests/testthat/test-create_mono_nuc_dna.R tests/testthat/test-create_pir_out_from_folder.R tests/testthat/test-create_pir_outs_from_folders.R tests/testthat/test-create_pir_params.R tests/testthat/test-create_pir_run_test_output.R tests/testthat/test-create_rate_matrix.R tests/testthat/test-create_standard_mutation_rate.R tests/testthat/test-create_std_pir_params.R tests/testthat/test-create_std_pir_paramses.R tests/testthat/test-create_test_marg_liks.R tests/testthat/test-create_test_phylogeny.R tests/testthat/test-create_test_pir_params_setup.R tests/testthat/test-create_tral_file.R tests/testthat/test-create_tree_and_model_errors_from_folder.R tests/testthat/test-create_tree_and_model_errors_from_folders.R tests/testthat/test-create_true_alignment.R tests/testthat/test-create_twal_file.R tests/testthat/test-create_twal_with_std_nsm.R tests/testthat/test-create_twin_branching_times.R tests/testthat/test-create_twin_tree.R tests/testthat/test-create_twinning_params.R tests/testthat/test-delete_beast2_state_files.R tests/testthat/test-errorses_to_data_frame.R tests/testthat/test-est_evidences.R tests/testthat/test-get_alignment_n_taxa.R tests/testthat/test-get_alignment_sequence_length.R tests/testthat/test-get_alignment_sequences.R tests/testthat/test-get_experiment_filenames.R tests/testthat/test-get_experiments_filenames.R tests/testthat/test-get_gamma_error_fun.R tests/testthat/test-get_model_selections.R tests/testthat/test-get_nltt_error_fun.R tests/testthat/test-get_pir_params_filenames.R tests/testthat/test-get_pir_plot_fill_colors.R tests/testthat/test-get_pir_plot_line_colors.R tests/testthat/test-get_pir_plot_theme.R tests/testthat/test-get_pir_plot_tree_and_model_descriptions.R tests/testthat/test-get_remove_hex_twin_fun.R tests/testthat/test-get_sim_tral_with_linked_node_sub_site_model_fun.R tests/testthat/test-get_sim_tral_with_std_nsm_fun.R tests/testthat/test-get_sim_tral_with_unlinked_node_sub_site_model_fun.R tests/testthat/test-get_sim_twal_with_same_n_mutation_fun.R tests/testthat/test-get_sim_twal_with_std_nsm_fun.R tests/testthat/test-get_temp_errors_filename.R tests/testthat/test-get_temp_evidence_filename.R tests/testthat/test-get_temp_fasta_filename.R tests/testthat/test-get_temp_tree_filename.R tests/testthat/test-get_test_alignment.R tests/testthat/test-get_tree_and_model_descriptions.R tests/testthat/test-get_twin_models.R tests/testthat/test-has_candidate_experiments.R tests/testthat/test-has_twinning.R tests/testthat/test-init_experiment.R tests/testthat/test-init_pir_params.R tests/testthat/test-is_best_candidate.R tests/testthat/test-is_dna_seq.R tests/testthat/test-is_pir_params.R tests/testthat/test-phylo_to_errors.R tests/testthat/test-pir_plot.R tests/testthat/test-pir_plot_from_file.R tests/testthat/test-pir_plot_from_folder.R tests/testthat/test-pir_plot_from_long.R tests/testthat/test-pir_plots.R tests/testthat/test-pir_rename.R tests/testthat/test-pir_rename_to_std.R tests/testthat/test-pir_run.R tests/testthat/test-pir_run_distribution.R tests/testthat/test-pir_runs.R tests/testthat/test-pir_save.R tests/testthat/test-pir_to_pics.R tests/testthat/test-pir_to_tables.R tests/testthat/test-plot_alignment_from_file.R tests/testthat/test-read_errors_csv.R tests/testthat/test-relevel_inference_model.R tests/testthat/test-relevel_tree_and_model.R tests/testthat/test-renum_rng_seeds.R tests/testthat/test-replicate_pir_params.R tests/testthat/test-rm_pir_param_files.R tests/testthat/test-select_candidate_evidences.R tests/testthat/test-select_experiments.R tests/testthat/test-shorten_experiments.R tests/testthat/test-shorten_pir_params.R tests/testthat/test-shorten_pir_paramses.R tests/testthat/test-sim_alignment_with_n_mutations.R tests/testthat/test-sim_alignment_with_std_nsm.R tests/testthat/test-sim_alignment_with_std_nsm_from_params.R tests/testthat/test-sim_bd_twin_tree.R tests/testthat/test-sim_tral_with_lns_site_model.R tests/testthat/test-sim_tral_with_std_nsm.R tests/testthat/test-sim_tral_with_unlinked_node_sub_site_model.R tests/testthat/test-sim_true_alignment.R tests/testthat/test-sim_twal_with_lns_nsm.R tests/testthat/test-sim_twal_with_same_n_mutation.R tests/testthat/test-sim_twal_with_uns_nsm.R tests/testthat/test-sim_twin_alignment.R tests/testthat/test-sim_yule_twin_tree.R tests/testthat/test-to_evidence_filename.R tests/testthat/test-to_twin_filename.R tests/testthat/test-to_twin_filenames.R tests/testthat/test-utils.R tests/testthat/test-will_measure_evidence.R

vignettes/.gitignore

vignettes/create_twin_tree.Rmd vignettes/demo.Rmd vignettes/experiment.Rmd vignettes/partial_function_evaluation.Rmd vignettes/tutorial.Rmd vignettes/twinning.Rmd

richelbilderbeek/pirouette documentation built on Oct. 18, 2023, 3:09 p.m.