| %>% |
Man page
|
| alignment_params_to_posterior_trees |
Source code
|
| calc_base_freq |
Source code
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| check_alignment |
Man page
Source code
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| check_alignment_params |
Man page
Source code
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| check_alignment_params_names |
Man page
Source code
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| check_beast2_installed |
Man page
Source code
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| check_candidates_save_to_same_files |
Man page
Source code
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| check_error_fun |
Man page
Source code
|
| check_error_measure_params |
Man page
Source code
|
| check_experiment |
Man page
Source code
|
| check_experiments |
Man page
Source code
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| check_experiments_all_inference_models_are_unique |
Man page
Source code
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| check_experiments_candidates_have_same_mcmcs |
Man page
Source code
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| check_gen_and_cand_exps_save_to_different_files |
Man page
Source code
|
| check_inference_conditions |
Man page
Source code
|
| check_inference_model_type_names |
Man page
Source code
|
| check_inference_model_weights |
Man page
Source code
|
| check_init_pir_params |
Man page
Source code
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| check_is_ns_beast2_pkg_installed |
Man page
Source code
|
| check_model_type |
Man page
Source code
|
| check_mutation_rate |
Man page
Source code
|
| check_pir_out |
Man page
Source code
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| check_pir_out_errors_above_zero |
Man page
Source code
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| check_pir_out_names |
Man page
Source code
|
| check_pir_params |
Man page
Source code
|
| check_pir_params_data_types |
Man page
Source code
|
| check_pir_params_names |
Man page
Source code
|
| check_pir_paramses |
Man page
Source code
|
| check_reconstructed_phylogeny |
Man page
Source code
|
| check_root_sequence |
Man page
Source code
|
| check_sim_tral_fun |
Man page
Source code
|
| check_sim_twal_fun |
Man page
Source code
|
| check_sim_twin_tree_fun |
Man page
Source code
|
| check_tree_and_model |
Man page
Source code
|
| check_tree_and_model_errors |
Man page
Source code
|
| check_tree_and_models |
Man page
Source code
|
| check_tree_type |
Man page
Source code
|
| check_tree_types |
Man page
Source code
|
| check_twin_phylogeny |
Man page
Source code
|
| check_twinning_params |
Man page
Source code
|
| check_twinning_params_names |
Man page
Source code
|
| collapse_tree_and_model |
Man page
Source code
|
| collect_pir_outs |
Man page
Source code
|
| combine_brts_and_topology |
Man page
Source code
|
| combine_models |
Man page
Source code
|
| complete_treelog_filename |
Man page
Source code
|
| convert_pir_out_to_long |
Man page
Source code
|
| convert_tree2brts |
Man page
Source code
|
| copy_true_alignment |
Man page
Source code
|
| count_n_mutations |
Man page
Source code
|
| create_alignment_params |
Man page
Source code
|
| create_all_bd_experiments |
Man page
Source code
|
| create_all_coal_experiments |
Man page
Source code
|
| create_all_experiments |
Man page
Source code
|
| create_bd_tree |
Man page
Source code
|
| create_blocked_dna |
Man page
Source code
|
| create_cand_experiment |
Man page
Source code
|
| create_copy_twtr_from_true_fun |
Man page
Source code
|
| create_error_measure_params |
Man page
Source code
|
| create_exemplary_dd_tree |
Man page
Source code
|
| create_exemplary_dd_tree_giappo |
Man page
Source code
|
| create_experiment |
Man page
Source code
|
| create_gen_experiment |
Man page
Source code
|
| create_inference_conditions |
Man page
Source code
|
| create_mono_nuc_dna |
Man page
Source code
|
| create_pir_params |
Man page
Source code
|
| create_rate_matrix |
Source code
|
| create_sim_yule_twin_tree_fun |
Man page
Source code
|
| create_standard_mutation_rate |
Man page
Source code
|
| create_std_pir_params |
Man page
Source code
|
| create_std_pir_paramses |
Man page
Source code
|
| create_test_alignment_params |
Man page
Source code
|
| create_test_cand_experiment |
Man page
Source code
|
| create_test_experiment |
Man page
Source code
|
| create_test_gen_experiment |
Man page
Source code
|
| create_test_marg_liks |
Man page
Source code
|
| create_test_phylogeny |
Man page
Source code
|
| create_test_pir_params |
Man page
Source code
|
| create_test_pir_params_setup |
Man page
Source code
|
| create_test_pir_run_output |
Man page
Source code
|
| create_test_pir_run_output2 |
Man page
Source code
|
| create_tral_file |
Man page
Source code
|
| create_tree_and_model_errors_from_folder |
Man page
Source code
|
| create_tree_and_model_errors_from_folders |
Man page
Source code
|
| create_true_alignment |
Man page
Source code
|
| create_twal_file |
Man page
Source code
|
| create_twin_branching_times |
Man page
Source code
|
| create_twin_tree |
Man page
Source code
|
| create_twinning_params |
Man page
Source code
|
| create_yule_tree |
Man page
Source code
|
| default_params_doc |
Man page
Source code
|
| delete_beast2_state_files |
Man page
Source code
|
| errorses_to_data_frame |
Man page
Source code
|
| est_evidences |
Man page
Source code
|
| get_alignment_n_taxa |
Man page
Source code
|
| get_alignment_sequence_length |
Man page
Source code
|
| get_alignment_sequences |
Man page
Source code
|
| get_copy_tral_fun |
Man page
Source code
|
| get_experiment_filenames |
Man page
Source code
|
| get_experiments_filenames |
Man page
Source code
|
| get_gamma_error_fun |
Man page
Source code
|
| get_model_selections |
Man page
Source code
|
| get_model_type_names |
Man page
Source code
|
| get_nltt_error_fun |
Man page
Source code
|
| get_pir_params_filenames |
Man page
Source code
|
| get_pir_plot_fill_colors |
Man page
Source code
|
| get_pir_plot_line_colors |
Man page
Source code
|
| get_pir_plot_theme |
Man page
Source code
|
| get_pir_plot_tree_and_model_descriptions |
Man page
Source code
|
| get_remove_hex_twin_fun |
Man page
Source code
|
| get_sim_bd_twin_tree_fun |
Man page
Source code
|
| get_sim_tral_with_lns_nsm_fun |
Man page
Source code
|
| get_sim_tral_with_std_nsm_fun |
Man page
Source code
|
| get_sim_tral_with_uns_nsm_fun |
Man page
Source code
|
| get_sim_twal_same_n_muts_fun |
Man page
Source code
|
| get_sim_twal_with_std_nsm_fun |
Man page
Source code
|
| get_sim_yule_twin_tree_fun |
Man page
Source code
|
| get_temp_errors_filename |
Man page
Source code
|
| get_temp_evidence_filename |
Man page
Source code
|
| get_temp_fasta_filename |
Man page
Source code
|
| get_temp_tree_filename |
Man page
Source code
|
| get_test_alignment |
Man page
Source code
|
| get_tree_and_model_descriptions |
Man page
Source code
|
| get_tree_and_model_values |
Man page
Source code
|
| get_tree_types |
Man page
Source code
|
| get_twin_methods |
Man page
Source code
|
| get_twin_models |
Man page
Source code
|
| has_candidate_experiments |
Man page
Source code
|
| has_twinning |
Man page
Source code
|
| init_experiment |
Man page
Source code
|
| init_pir_params |
Man page
Source code
|
| is_best_candidate |
Man page
Source code
|
| is_dna_seq |
Man page
Source code
|
| is_pir_params |
Man page
Source code
|
| phylo_to_errors |
Man page
Source code
|
| pir_plot |
Man page
Source code
|
| pir_plot_from_file |
Man page
Source code
|
| pir_plot_from_long |
Man page
Source code
|
| pir_plots |
Man page
Source code
|
| pir_rename |
Man page
Source code
|
| pir_rename_to_std |
Man page
Source code
|
| pir_run |
Man page
Source code
|
| pir_run_distribution |
Man page
Source code
|
| pir_run_true_tree |
Man page
Source code
|
| pir_run_twin_tree |
Man page
Source code
|
| pir_runs |
Man page
Source code
|
| pir_save |
Man page
Source code
|
| pir_to_pics |
Man page
Source code
|
| pir_to_pics_twin |
Source code
|
| pir_to_tables |
Man page
Source code
|
| pirouette |
Man page
|
| pirouette-package |
Man page
|
| plot_alignment_from_file |
Man page
Source code
|
| read_errors_csv |
Man page
Source code
|
| relevel_inference_model |
Man page
Source code
|
| relevel_tree_and_model |
Man page
Source code
|
| renum_rng_seeds |
Man page
Source code
|
| replicate_pir_params |
Man page
Source code
|
| rm_pir_param_files |
Man page
Source code
|
| select_candidate_evidences |
Man page
Source code
|
| select_experiments |
Man page
Source code
|
| shorten_experiments |
Man page
Source code
|
| shorten_pir_params |
Man page
Source code
|
| shorten_pir_paramses |
Man page
Source code
|
| sim_alignment_with_n_mutations |
Man page
Source code
|
| sim_alignment_with_std_nsm |
Man page
Source code
|
| sim_alignment_with_std_nsm_from_params |
Man page
Source code
|
| sim_bd_twin_tree |
Man page
Source code
|
| sim_tral_with_lns_nsm |
Man page
Source code
|
| sim_tral_with_std_nsm |
Man page
Source code
|
| sim_tral_with_uns_nsm |
Man page
Source code
|
| sim_true_alignment |
Man page
Source code
|
| sim_twal_with_lns_nsm |
Man page
Source code
|
| sim_twal_with_same_n_mutation |
Man page
Source code
|
| sim_twal_with_std_nsm |
Man page
Source code
|
| sim_twal_with_uns_nsm |
Man page
Source code
|
| sim_twin_alignment |
Man page
Source code
|
| sim_yule_twin_tree |
Man page
Source code
|
| to_evidence_filename |
Man page
Source code
|
| to_twin_filename |
Man page
Source code
|
| to_twin_filenames |
Man page
Source code
|
| will_measure_evidence |
Man page
Source code
|
