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pirouette  

Create a Bayesian Posterior from a Phylogeny
View on CRAN: Click here


Download and install pirouette package within the R console
Install from CRAN:
install.packages("pirouette")

Install from Github:
library("remotes")
install_github("cran/pirouette")

Install by package version:
library("remotes")
install_version("pirouette", "1.6.9")



Attach the package and use:
library("pirouette")
Maintained by
Richel Bilderbeek
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2022-10-06
Latest Update: 2023-01-20
Description:
Theoretical biologists are interested in measuring the extent at which we can measure the truth. This package allows to create a Bayesian posterior from a phylogeny that depicts the true evolutionary relationships. The given and true phylogeny can than be compared to the posterior phylogenies. Rich
How to cite:
Richel Bilderbeek (2022). pirouette: Create a Bayesian Posterior from a Phylogeny. R package version 1.6.9, https://cran.r-project.org/web/packages/pirouette
Previous versions and publish date:
1.6.4 (2022-10-06 18:30), 1.6.5 (2022-10-18 09:20), 1.6.6 (2023-01-20 17:00), 1.6.7 (2023-09-27 12:10), 1.6.8 (2023-09-29 15:42), 1.6.9 (2023-10-07 09:20)
Other packages that cited pirouette R package
View pirouette citation profile
Other R packages that pirouette depends, imports, suggests or enhances
Functions, R codes and Examples using the pirouette R package
Some associated functions: check_alignment . check_alignment_params . check_alignment_params_names . check_beast2_installed . check_candidates_save_to_same_files . check_error_fun . check_error_measure_params . check_experiment . check_experiments . check_experiments_all_inference_models_are_unique . check_experiments_candidates_have_same_mcmcs . check_gen_and_cand_exps_save_to_different_files . check_inference_conditions . check_inference_model_type_names . check_inference_model_weights . check_init_pir_params . check_is_ns_beast2_pkg_installed . check_model_type . check_mutation_rate . check_pir_out . check_pir_out_errors_above_zero . check_pir_out_names . check_pir_params . check_pir_params_data_types . check_pir_params_names . check_pir_paramses . check_reconstructed_phylogeny . check_root_sequence . check_sim_tral_fun . check_sim_twal_fun . check_sim_twin_tree_fun . check_tree_and_model . check_tree_and_model_errors . check_tree_and_models . check_tree_type . check_tree_types . check_twin_phylogeny . check_twinning_params . check_twinning_params_names . collapse_tree_and_model . collect_pir_outs . combine_brts_and_topology . combine_models . complete_treelog_filename . convert_pir_out_to_long . convert_tree2brts . copy_true_alignment . count_n_mutations . create_alignment_params . create_all_bd_experiments . create_all_coal_experiments . create_all_experiments . create_bd_tree . create_blocked_dna . create_cand_experiment . create_copy_twtr_from_true_fun . create_error_measure_params . create_exemplary_dd_tree . create_exemplary_dd_tree_giappo . create_experiment . create_gen_experiment . create_inference_conditions . create_mono_nuc_dna . create_pir_params . create_sim_yule_twin_tree_fun . create_standard_mutation_rate . create_std_pir_params . create_std_pir_paramses . create_test_alignment_params . create_test_cand_experiment . create_test_experiment . create_test_gen_experiment . create_test_marg_liks . create_test_phylogeny . create_test_pir_params . create_test_pir_params_setup . create_test_pir_run_output . create_test_pir_run_output2 . create_tral_file . create_tree_and_model_errors_from_folder . create_tree_and_model_errors_from_folders . create_true_alignment . create_twal_file . create_twin_branching_times . create_twin_tree . create_twinning_params . create_yule_tree . default_params_doc . delete_beast2_state_files . errorses_to_data_frame . est_evidences . get_alignment_n_taxa . get_alignment_sequence_length . get_alignment_sequences . get_copy_tral_fun . get_experiment_filenames . get_experiments_filenames . get_gamma_error_fun . get_model_selections . get_model_type_names . get_nltt_error_fun . get_pir_params_filenames . get_pir_plot_fill_colors . get_pir_plot_line_colors . get_pir_plot_theme . get_pir_plot_tree_and_model_descriptions . get_remove_hex_twin_fun . get_sim_bd_twin_tree_fun . get_sim_tral_with_lns_nsm_fun . get_sim_tral_with_std_nsm_fun . get_sim_tral_with_uns_nsm_fun . get_sim_twal_same_n_muts_fun . get_sim_twal_with_std_nsm_fun . get_sim_yule_twin_tree_fun . get_temp_errors_filename . get_temp_evidence_filename . get_temp_fasta_filename . get_temp_tree_filename . get_test_alignment . get_tree_and_model_descriptions . get_tree_and_model_values . get_tree_types . get_twin_methods . get_twin_models . has_candidate_experiments . has_twinning . init_experiment . init_pir_params . is_best_candidate . is_dna_seq . is_pir_params . phylo_to_errors . pipe . pir_plot . pir_plot_from_file . pir_plot_from_long . pir_plots . pir_rename . pir_rename_to_std . pir_run . pir_run_distribution . pir_run_true_tree . pir_run_twin_tree . pir_runs . pir_save . pir_to_pics . pir_to_tables . pirouette . plot_alignment_from_file . read_errors_csv . relevel_inference_model . relevel_tree_and_model . renum_rng_seeds . replicate_pir_params . rm_pir_param_files . select_candidate_evidences . select_experiments . shorten_experiments . shorten_pir_params . shorten_pir_paramses . sim_alignment_with_n_mutations . sim_alignment_with_std_nsm . sim_alignment_with_std_nsm_from_params . sim_bd_twin_tree . sim_tral_with_lns_nsm . sim_tral_with_std_nsm . sim_tral_with_uns_nsm . sim_true_alignment . sim_twal_with_lns_nsm . sim_twal_with_same_n_mutation . sim_twal_with_std_nsm . sim_twal_with_uns_nsm . sim_twin_alignment . sim_yule_twin_tree . to_evidence_filename . to_twin_filename . to_twin_filenames . will_measure_evidence . 
Some associated R codes: alignment_params_to_posterior_trees.R . check_alignment.R . check_alignment_params.R . check_beast2_installed.R . check_error_fun.R . check_error_measure_params.R . check_experiment.R . check_experiments.R . check_experiments_all_inference_models_are_unique.R . check_experiments_candidates_have_same_beast2_files.R . check_experiments_candidates_have_same_mcmcs.R . check_gen_and_cand_save_to_different_files.R . check_inference_conditions.R . check_inference_model_type_names.R . check_inference_model_weights.R . check_init_pir_params.R . check_is_ns_beast2_pkg_installed.R . check_model_type.R . check_mutation_rate.R . check_pir_out.R . check_pir_out_errors_above_zero.R . check_pir_params.R . check_pir_paramses.R . check_reconstructed_phylogeny.R . check_root_sequence.R . check_sim_tral_fun.R . check_sim_twal_fun.R . check_sim_twin_tree_fun.R . check_tree_and_model.R . check_tree_and_model_errors.R . check_tree_and_models.R . check_tree_type.R . check_tree_types.R . check_twin_phylogeny.R . check_twinning_params.R . check_twinning_params_names.R . collapse_tree_and_model.R . collect_pir_outs.R . combine_brts_and_topology.R . combine_models.R . complete_treelog_filename.R . convert_pir_out_to_long.R . copy_true_alignment.R . count_n_mutations.R . create_alignment_params.R . create_all_bd_experiments.R . create_all_coal_experiments.R . create_all_experiments.R . create_blocked_dna.R . create_cand_experiment.R . create_copy_twin_tree_from_true_fun.R . create_error_measure_params.R . create_exemplary_dd_tree.R . create_exemplary_dd_tree_giappo.R . create_experiment.R . create_gen_experiment.R . create_generative_trees.R . create_inference_conditions.R . create_mono_nuc_dna.R . create_pir_params.R . create_rate_matrix.R . create_sim_yule_twin_tree_fun.R . create_standard_mutation_rate.R . create_std_pir_params.R . create_std_pir_paramses.R . create_test_cand_experiment.R . create_test_experiment.R . create_test_gen_experiment.R . create_test_marg_liks.R . create_test_phylogeny.R . create_test_pir_params_setup.R . create_test_pir_run_output.R . create_tral_file.R . create_tree_and_model_errors_from_folder.R . create_tree_and_model_errors_from_folders.R . create_true_alignment.R . create_twal_file.R . create_twin_branching_times.R . create_twin_tree.R . create_twinning_params.R . default_params_doc.R . delete_beast2_state_files.R . errorses_to_data_frame.R . est_evidences.R . get_alignment_n_taxa.R . get_alignment_sequence_length.R . get_alignment_sequences.R . get_copy_tral_fun.R . get_experiment_filenames.R . get_experiments_filenames.R . get_gamma_error_fun.R . get_model_selections.R . get_nltt_error_fun.R . get_pir_params_filenames.R . get_pir_plot_fill_colors.R . get_pir_plot_line_colors.R . get_pir_plot_theme.R . get_pir_plot_tree_and_model_descriptions.R . get_remove_hex_twin_fun.R . get_sim_bd_twin_tree_fun.R . get_sim_tral_with_lns_site_model_fun.R . get_sim_tral_with_std_nsm_fun.R . get_sim_tral_with_uns_site_model_fun.R . get_sim_twal_with_same_n_mutation_fun.R . get_sim_twal_with_std_nsm_fun.R . get_sim_yule_twin_tree_fun.R . get_temp_errors_filename.R . get_temp_evidence_filename.R . get_temp_fasta_filename.R . get_temp_tree_filename.R . get_test_alignment.R . get_tree_and_model_descriptions.R . get_tree_and_model_values.R . has_candidate_experiments.R . has_twinning.R . init_experiment.R . init_pir_params.R . is_best_candidate.R . is_dna_seq.R . is_pir_params.R . phylo_to_errors.R . pir_plot.R . pir_plot_from_file.R . pir_plot_from_long.R . pir_plots.R . pir_rename.R . pir_rename_to_std.R . pir_run.R . pir_run_distribution.R . pir_run_true_tree.R . pir_run_twin_tree.R . pir_runs.R . pir_save.R . pir_to_pics.R . pir_to_tables.R . pirouette.R . plot_alignment_from_file.R . read_errors_csv.R . relevel_inference_model.R . relevel_tree_and_model.R . renum_rng_seeds.R . replicate_pir_params.R . rm_pir_param_files.R . select_candidate_evidences.R . select_experiments.R . shorten_experiments.R . shorten_pir_params.R . shorten_pir_paramses.R . sim_alignment_with_n_mutations.R . sim_alignment_with_std_nsm.R . sim_alignment_with_std_nsm_from_params.R . sim_bd_twin_tree.R . sim_tral_with_lns_site_model.R . sim_tral_with_nsm.R . sim_tral_with_uns_site_model.R . sim_true_alignment.R . sim_twal_with_lns_site_model.R . sim_twal_with_nsm.R . sim_twal_with_same_n_mutation.R . sim_twal_with_uns_site_model.R . sim_twin_alignment.R . to_evidence_filename.R . to_twin_filename.R . to_twin_filenames.R . twin_to_yule_tree.R . utils-pipe.R . utils.R . will_measure_evidence.R .  Full pirouette package functions and examples
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