check_alignment         Check if the alignment is of the right type
check_alignment_params
                        Checks if the argument is a valid alignment
                        parameters structure, as created by
                        create_alignment_params. Will stop if not.
check_alignment_params_names
                        Checks if the list elements' names match that
                        of a valid 'alignment_params'
check_beast2_installed
                        Checks if BEAST2 is installed
check_candidates_save_to_same_files
                        Check if all experiments save to the same files
check_error_fun         Check that the 'error_fun' is valid.
check_error_measure_params
                        Checks if the argument is a valid error_measure
                        parameters structure, as created by
                        create_error_measure_params. Will stop if not.
check_experiment        Checks if the argument is a valid pirouette
                        experiment.
check_experiments       Checks if the argument is a list of one or more
                        pirouette experiments.
check_experiments_all_inference_models_are_unique
                        Check if all experiments have unique inference
                        models.
check_experiments_candidates_have_same_mcmcs
                        Check that the candidate experiments have a
                        same MCMC
check_gen_and_cand_exps_save_to_different_files
                        Check that generative and candidate experiments
                        save to different files.
check_inference_conditions
                        Checks if inference conditions are valid as
                        created by create_inference_conditions. Will
                        stop if not.
check_inference_model_type_names
                        Check the model type names
check_inference_model_weights
                        Check the one or more inference model's weights
check_init_pir_params   Check if the 'pir_params' is initialized
check_is_ns_beast2_pkg_installed
                        Checks if the 'NS' BEAST2 package is installed.
check_model_type        Checks if model type is valid Will stop if not.
check_mutation_rate     Check if the mutation rate is valid
check_pir_out           Checks if the argument is a valid pirouette
                        parameter set.
check_pir_out_errors_above_zero
                        Checks that 'pir_out' errors all are more than
                        zero
check_pir_out_names     Checks if the 'pir_out' has elements with the
                        names needed.
check_pir_params        Checks if the argument is a valid pirouette
                        parameter set.
check_pir_params_data_types
                        Checks if the 'pir_params' elements are all of
                        the right data type.
check_pir_params_names
                        Checks if the 'pir_params' has all the named
                        elements needed
check_pir_paramses      Check if all elements in the list of
                        'pir_params' are valid.
check_reconstructed_phylogeny
                        Check if the phylogeny is a reconstructed
                        phylogeny.
check_root_sequence     Check if the root sequence is valid
check_sim_tral_fun      Check if the function to create a true
                        alignment with (from the true phylogeny) is
                        valid.
check_sim_twal_fun      Check if the function to create a twin
                        alignment with (from a true phylogeny and a
                        true alignment) is valid.
check_sim_twin_tree_fun
                        Check if the 'sim_twin_tree_fun' is valid
check_tree_and_model    Check if the 'tree_and_model' is valid
check_tree_and_model_errors
                        Check if the 'tree_and_model_errors' is valid.
check_tree_and_models   Check if the 'tree_and_model' is valid
check_tree_type         Checks if tree type is valid Will stop if not.
check_tree_types        Checks if the tree types are valid Will stop if
                        not.
check_twin_phylogeny    Check if a twin phylogeny is a valid phylogeny
check_twinning_params   Checks if the argument is a valid twinning
                        parameters structure.
check_twinning_params_names
                        Check that the 'twinning_params' has all the
                        list elements' names
collapse_tree_and_model
                        Internal function
collect_pir_outs        Collect the results of multiple pirouette runs
combine_brts_and_topology
                        Substitute branching times keeping the topology
combine_models          Combine a combination of site models, clock
                        models and tree priors into a collection of
                        inference models.
complete_treelog_filename
                        Complete a treelog's filename
convert_pir_out_to_long
                        Convert a 'pir_out' to its long form
convert_tree2brts       Convert a tree into branching times
copy_true_alignment     Adapter function to create a twin alignment by
                        simply copying the true alignment
count_n_mutations       Count mutations
create_alignment_params
                        Create the parameters for the alignment
                        simulation.
create_all_bd_experiments
                        Create all pirouette experiments that have a
                        tree prior that follows a birth-death model.
create_all_coal_experiments
                        Create all pirouette experiments that have a
                        tree prior that follows a coalescent model.
create_all_experiments
                        Create all pirouette experiments.
create_bd_tree          Create a (constant-rate) birth-death (BD) tree
create_blocked_dna      Create a 'blocked' DNA sequence, which is a
                        sequence with four equal-sized nucleotide
                        sections
create_cand_experiment
                        Create a valid testing pirouette candidate
                        experiment.
create_copy_twtr_from_true_fun
                        Create a function that can simulate the twin
                        tree from the true tree, by just copying the
                        true tree
create_error_measure_params
                        Create the parameters to specify how the error
                        between the given phylogeny and the Bayesian
                        posterior trees is measured.
create_exemplary_dd_tree
                        Create an exemplary diversity-dependent (DD)
                        birth-death tree.
create_exemplary_dd_tree_giappo
                        Create an exemplary diversity-dependent (DD)
                        birth-death tree.
create_experiment       Create a valid pirouette experiment.
create_gen_experiment   Create a valid testing pirouette generative
                        experiment.
create_inference_conditions
                        Create the inference conditions
create_mono_nuc_dna     Create a 'blocked' DNA sequence, which is a
                        sequence with four equal-sized nucleotide
                        sections
create_pir_params       Create the parameters for pirouette
create_sim_yule_twin_tree_fun
                        Create a partially evaluated function to to
                        sim_yule_twin_tree.
create_standard_mutation_rate
                        Create the parameters for the mutation rate
create_std_pir_params   Create a standard 'pir_params'
create_std_pir_paramses
                        Create a number of standard 'pir_params'
create_test_alignment_params
                        Create testing parameters for the alignment
                        simulation.
create_test_cand_experiment
                        Create a valid testing pirouette candidate
                        experiment.
create_test_experiment
                        Create a valid testing pirouette experiment.
create_test_gen_experiment
                        Create a valid testing pirouette generative
                        experiment.
create_test_marg_liks   Create a testing marginal likelihoods data
                        frame.
create_test_phylogeny   Create a testing phylogeny with 3 taxa and a
                        crown age of 3
create_test_pir_params
                        Create a set of testing parameters for
                        pirouette
create_test_pir_params_setup
                        Create a 'pir_params' that follows a specific
                        setup
create_test_pir_run_output
                        Create the same output of pir_run to be used
                        for testing
create_test_pir_run_output2
                        Create the same output of pir_run to be used
                        for testing, but with more data
create_tral_file        Simulates a DNA alignment and saves it to a
                        FASTA file.
create_tree_and_model_errors_from_folder
                        Internal function to create a
                        'tree_and_model_errors' from the files in a
                        folder
create_tree_and_model_errors_from_folders
                        Internal function to create a
                        'tree_and_model_errors' from the files in one
                        or more folders
create_true_alignment   Create the true alignment from the true/given
                        phylogeny.
create_twal_file        Simulates a twin DNA alignment and saves it to
                        a FASTA file.
create_twin_branching_times
                        Generate twin branching times given estimated
                        lambda and mu and the original tree
create_twin_tree        Create a twin tree
create_twinning_params
                        Create the parameters for the twinning
                        simulation
create_yule_tree        Create a Yule tree.
default_params_doc      This function does nothing. It is intended to
                        inherit is parameters' documentation.
delete_beast2_state_files
                        Delete the BEAST2 state files, if present.
errorses_to_data_frame
                        Convert the collect of errors to a data frame
est_evidences           Estimate the evidences
get_alignment_n_taxa    Get the number of taxa of an alignment
get_alignment_sequence_length
                        Get the sequence length of an alignment
get_alignment_sequences
                        Get the sequences from an alignment
get_copy_tral_fun       Get a function to 'simulate' a twin alignment
                        by simply copying the true alignment.
get_experiment_filenames
                        Extract the filenames from an experiment
get_experiments_filenames
                        Extract the filesnames in the experiments
get_gamma_error_fun     Get an error function that uses the difference
                        in gamma statistic.
get_model_selections    Get the possible ways to select an inference
                        model
get_model_type_names    Get the names of the model types
get_nltt_error_fun      Get an error function that uses the nLTT
                        statistic
get_pir_params_filenames
                        Extract the filenames from a 'pir_params'
get_pir_plot_fill_colors
                        Internal function to get the fill colors for
                        pir_plot
get_pir_plot_line_colors
                        Internal function to get the line colors for
                        pir_plot
get_pir_plot_theme      Get the pir_plot theme
get_pir_plot_tree_and_model_descriptions
                        Internal function to obtain the pir_plot legend
                        labels
get_remove_hex_twin_fun
                        Get a function that removes the hex string from
                        filenames.
get_sim_bd_twin_tree_fun
                        Create a partially evaluated function to to
                        sim_bd_twin_tree.
get_sim_tral_with_lns_nsm_fun
                        Get a partially evaluated function to simulate
                        a true alignment with a linked node
                        substitution site model.
get_sim_tral_with_std_nsm_fun
                        Get a function to simulate the true alignment
                        with, that uses a standard site model.
get_sim_tral_with_uns_nsm_fun
                        Get a partially evaluated function to simulate
                        a true alignment with an unlinked node
                        substitution site model.
get_sim_twal_same_n_muts_fun
                        of mutations as the true alignment has.
get_sim_twal_with_std_nsm_fun
                        Get a function to simulate a twin alignment
                        which uses a standard site model
get_sim_yule_twin_tree_fun
                        Create a partially evaluated function to to
                        sim_yule_twin_tree.
get_temp_errors_filename
                        Get the name for a temporary file to store
                        inference errors.
get_temp_evidence_filename
                        Get the name for a temporary file to store the
                        evidences (aka marginal likelihoods) as a
                        comma-separated file
get_temp_fasta_filename
                        Get the name for a temporary file to store an
                        alignment in the FASTA format
get_temp_tree_filename
                        Get the name for a temporary file to store a
                        tree in Newick format
get_test_alignment      Get an alignment for testing.
get_tree_and_model_descriptions
                        Internal function to create a mapping from a
                        'tree_and_model' to a description
get_tree_and_model_values
                        Get the valid 'tree_and_model' values
get_tree_types          Get the names of the tree types
get_twin_methods        Twin methods
get_twin_models         Twin models
has_candidate_experiments
                        Detect if there is at least one candidate model
                        among the set of experiments.
has_twinning            Determine if these 'pir_params' use twinning
init_experiment         Initialize the 'experiment'.
init_pir_params         Initialize the 'pir_params'.
is_best_candidate       Is the experiment the one with the most
                        evidence?
is_dna_seq              Determine if the string is a lowercase DNA
                        sequence of at least one base pair
is_pir_params           Determine if the 'pir_params' is valid.
phylo_to_errors         Measure the error BEAST2 makes from a true
                        phylogeny.
pir_plot                Plot the error 'BEAST2' makes from a known
                        phylogeny
pir_plot_from_file      Plot the error BEAST2 make from the known
                        phylogeny
pir_plot_from_long      Plot the error 'BEAST2' makes from a known
                        phylogeny from tidy data
pir_plots               Plot the output of pir_runs.
pir_rename              Rename the filenames in a 'pir_params' using a
                        rename function.
pir_rename_to_std       Rename the 'pir_params' filenames to follow a
                        standard naming scheme.
pir_run                 Measure the error BEAST2 makes from a known
                        phylogeny.
pir_run_distribution    Do multiple pirouette runs off a distribition
                        of phylogenies
pir_run_true_tree       Measure the error BEAST2 makes from a phylogeny
pir_run_twin_tree       Measure the error BEAST2 makes from a phylogeny
pir_runs                Do multiple pirouette runs
pir_save                Save all output from pir_run
pir_to_pics             Create all pictures created by the pirouette
                        pipeline
pir_to_tables           Create all tables to checks pirouette pipeline
pirouette               pirouette: A package to estimate the error
                        BEAST2 makes in inferring a phylogeny.
plot_alignment_from_file
                        Plot an alignment stored as a file
read_errors_csv         Read the errors from a '.csv' file
relevel_inference_model
                        Internal function
relevel_tree_and_model
                        Internal function
renum_rng_seeds         Renumber the RNG seeds
replicate_pir_params    Replicate pir_params assigning new names to
                        each file
rm_pir_param_files      Deletes all files
select_candidate_evidences
                        Select the evidences for candidate experiments
select_experiments      Select the experiments to do a Bayesian
                        inference with.
shorten_experiments     Shorten the experiments' runtime
shorten_pir_params      Shorten the 'pir_params'
shorten_pir_paramses    Shorten the list of 'pir_params'
sim_alignment_with_n_mutations
                        Converts a phylogeny to a random DNA alignment
sim_alignment_with_std_nsm
                        Create an alignment with a standard site model
                        using a raw interface
sim_alignment_with_std_nsm_from_params
                        Create an alignment with a standard site model
sim_bd_twin_tree        Simulate a Birth-Death (BD) twin tree from the
                        true phylogeny
sim_tral_with_lns_nsm   Create an alignment with the 'lns' site model
sim_tral_with_std_nsm   Adapter function to simulate a twin alignment
                        using a standard site model
sim_tral_with_uns_nsm   Adapter function to simulate an alignment with
                        the 'linked_node_sub' (lns) site model.
sim_true_alignment      Simulate the true alignment from the true
                        phylogeny
sim_twal_with_lns_nsm   Adapter function to simulate the twin alignment
                        using the 'lns' site model
sim_twal_with_same_n_mutation
                        Simulate a twin alignment using a standard site
                        model
sim_twal_with_std_nsm   Simulate a twin alignment using a standard site
                        model
sim_twal_with_uns_nsm   Adapter function to simulate an alignment with
                        the 'linked_node_sub' (lns) site model.
sim_twin_alignment      Creates a twin alignment.
sim_yule_twin_tree      Create a twin tree from a phylogeny using a
                        Yule process
to_evidence_filename    Converts a filename to an evidence filename
to_twin_filename        Converts true tree filenames to twin tree
                        filenames
to_twin_filenames       Convert multiple filenames to their twin
                        equivalent
will_measure_evidence   Determine if there is an experiment in which
                        the evidence will be measured.
