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NAMESPACE
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NAMESPACE
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# Generated by roxygen2: do not edit by hand
export("%>%")
export(check_alignment)
export(check_alignment_params)
export(check_alignment_params_names)
export(check_beast2_installed)
export(check_candidates_save_to_same_files)
export(check_error_fun)
export(check_error_measure_params)
export(check_experiment)
export(check_experiments)
export(check_experiments_all_inference_models_are_unique)
export(check_experiments_candidates_have_same_mcmcs)
export(check_gen_and_cand_exps_save_to_different_files)
export(check_inference_conditions)
export(check_inference_model_type_names)
export(check_inference_model_weights)
export(check_init_pir_params)
export(check_is_ns_beast2_pkg_installed)
export(check_model_type)
export(check_mutation_rate)
export(check_pir_out)
export(check_pir_out_errors_above_zero)
export(check_pir_out_names)
export(check_pir_params)
export(check_pir_params_data_types)
export(check_pir_params_names)
export(check_pir_paramses)
export(check_reconstructed_phylogeny)
export(check_root_sequence)
export(check_sim_tral_fun)
export(check_sim_twal_fun)
export(check_sim_twin_tree_fun)
export(check_tree_and_model)
export(check_tree_and_model_errors)
export(check_tree_and_models)
export(check_tree_type)
export(check_tree_types)
export(check_twin_phylogeny)
export(check_twinning_params)
export(check_twinning_params_names)
export(collapse_tree_and_model)
export(collect_pir_outs)
export(combine_brts_and_topology)
export(combine_models)
export(complete_treelog_filename)
export(convert_pir_out_to_long)
export(convert_tree2brts)
export(copy_true_alignment)
export(count_n_mutations)
export(create_alignment_params)
export(create_all_bd_experiments)
export(create_all_coal_experiments)
export(create_all_experiments)
export(create_bd_tree)
export(create_blocked_dna)
export(create_cand_experiment)
export(create_copy_twtr_from_true_fun)
export(create_error_measure_params)
export(create_exemplary_dd_tree)
export(create_exemplary_dd_tree_giappo)
export(create_experiment)
export(create_gen_experiment)
export(create_inference_conditions)
export(create_mono_nuc_dna)
export(create_pir_params)
export(create_sim_yule_twin_tree_fun)
export(create_standard_mutation_rate)
export(create_std_pir_params)
export(create_std_pir_paramses)
export(create_test_alignment_params)
export(create_test_cand_experiment)
export(create_test_experiment)
export(create_test_gen_experiment)
export(create_test_marg_liks)
export(create_test_phylogeny)
export(create_test_pir_params)
export(create_test_pir_params_setup)
export(create_test_pir_run_output)
export(create_test_pir_run_output2)
export(create_tral_file)
export(create_tree_and_model_errors_from_folder)
export(create_tree_and_model_errors_from_folders)
export(create_true_alignment)
export(create_twal_file)
export(create_twin_branching_times)
export(create_twin_tree)
export(create_twinning_params)
export(create_yule_tree)
export(delete_beast2_state_files)
export(errorses_to_data_frame)
export(est_evidences)
export(get_alignment_n_taxa)
export(get_alignment_sequence_length)
export(get_alignment_sequences)
export(get_copy_tral_fun)
export(get_experiment_filenames)
export(get_experiments_filenames)
export(get_gamma_error_fun)
export(get_model_selections)
export(get_model_type_names)
export(get_nltt_error_fun)
export(get_pir_params_filenames)
export(get_pir_plot_fill_colors)
export(get_pir_plot_line_colors)
export(get_pir_plot_theme)
export(get_pir_plot_tree_and_model_descriptions)
export(get_remove_hex_twin_fun)
export(get_sim_bd_twin_tree_fun)
export(get_sim_tral_with_lns_nsm_fun)
export(get_sim_tral_with_std_nsm_fun)
export(get_sim_tral_with_uns_nsm_fun)
export(get_sim_twal_same_n_muts_fun)
export(get_sim_twal_with_std_nsm_fun)
export(get_sim_yule_twin_tree_fun)
export(get_temp_errors_filename)
export(get_temp_evidence_filename)
export(get_temp_fasta_filename)
export(get_temp_tree_filename)
export(get_test_alignment)
export(get_tree_and_model_descriptions)
export(get_tree_and_model_values)
export(get_tree_types)
export(get_twin_methods)
export(get_twin_models)
export(has_candidate_experiments)
export(has_twinning)
export(init_experiment)
export(init_pir_params)
export(is_best_candidate)
export(is_dna_seq)
export(is_pir_params)
export(phylo_to_errors)
export(pir_plot)
export(pir_plot_from_file)
export(pir_plot_from_long)
export(pir_plots)
export(pir_rename)
export(pir_rename_to_std)
export(pir_run)
export(pir_run_distribution)
export(pir_run_true_tree)
export(pir_run_twin_tree)
export(pir_runs)
export(pir_save)
export(pir_to_pics)
export(pir_to_tables)
export(plot_alignment_from_file)
export(read_errors_csv)
export(relevel_inference_model)
export(relevel_tree_and_model)
export(renum_rng_seeds)
export(replicate_pir_params)
export(rm_pir_param_files)
export(select_candidate_evidences)
export(select_experiments)
export(shorten_experiments)
export(shorten_pir_params)
export(shorten_pir_paramses)
export(sim_alignment_with_n_mutations)
export(sim_alignment_with_std_nsm)
export(sim_alignment_with_std_nsm_from_params)
export(sim_bd_twin_tree)
export(sim_tral_with_lns_nsm)
export(sim_tral_with_std_nsm)
export(sim_tral_with_uns_nsm)
export(sim_true_alignment)
export(sim_twal_with_lns_nsm)
export(sim_twal_with_same_n_mutation)
export(sim_twal_with_std_nsm)
export(sim_twal_with_uns_nsm)
export(sim_twin_alignment)
export(sim_yule_twin_tree)
export(to_evidence_filename)
export(to_twin_filename)
export(to_twin_filenames)
export(will_measure_evidence)
importFrom(magrittr,"%>%")