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