Function reference • bbr

Model management
`new_model()`	Create new model object
`read_model()`	Creates a model object from a YAML model file
`copy_model_from()`	Create new model by copying existing model
`inherit_param_estimates()`	Inherit parameter estimates
`tweak_initial_estimates()`	Tweak the initial parameter estimates
`update_model_id()`	Update model ID (run number) in the control stream
`model_diff()`	Compare model files between models
`tags_diff()` `add_tags_diff()`	Compare tags between models
`check_up_to_date()`	Check model and data up to date with outputs
Model submission
`submit_model()`	Submit a model to be run
`submit_models()`	Submit models to be run in batch
`run_nmtran()`	Interface for running `NM-TRAN` on model objects
`print_bbi_args()`	Print valid .bbi_args
Model summary and outputs
`model_summary()`	Summarize model outputs
`model_summaries()`	Summarize multiple models in batch
`param_estimates()`	Parses parameter estimates table
`nm_join()`	Return a single data frame with model output and input data
`nm_tables()` `nm_table_files()`	Read all tables and input data
`nm_file()` `nm_grd()` `nm_tab()` `nm_par_tab()` `nm_data()`	Read NONMEM files
`nm_file_multi_tab()`	Read in table file with multiple `NONMEM` tables.
`get_omega()` `get_sigma()` `get_theta()`	Return a formatted object for a given parameter
`cov_cor()`	NONMEM Covariance and Correlation Matrices
`check_cor_threshold()`	Check for high correlations
`as_summary_list()`	Convert object to `bbi_summary_list`
`param_labels()`	Extract parameter labels for report tables, etc.
`apply_indices()` `block()`	Add parameter indices to a label tibble
Bootstrap and Simulation
`add_simulation()` `has_simulation()` `get_simulation()`	Simulate a `bbi_nonmem_model` object
`nm_join_sim()`	Join simulation and input data
`new_bootstrap_run()`	Create a bootstrap run from an existing model
`setup_bootstrap_run()`	Set up a bootstrap model run
`summarize_bootstrap_run()` `bootstrap_estimates()` `get_boot_models()`	Summarize a bootstrap run
`cleanup_bootstrap_run()`	Cleanup bootstrap run directory
`param_estimates_batch()`	Batch Processing of Parameter Estimates
`param_estimates_compare()`	Compare parameter estimates
Summary log tables
`run_log()`	Create tibble summarizing all model runs
`summary_log()` `add_summary()`	Create a tibble from `model_summaries()` data
`config_log()` `add_config()`	Parse bbi configs to log
`model_tree()`	Create a tree diagram of a modeling directory
Model object interactions
`add_tags()` `replace_tag()` `replace_all_tags()` `remove_tags()`	Modify tags on a model object
`add_notes()` `replace_note()` `replace_all_notes()` `remove_notes()`	Modify notes on a model object
`add_based_on()` `replace_all_based_on()` `remove_based_on()`	Modify based_on field in a model object
`add_description()` `replace_description()`	Modify description on a model object
`add_star()` `remove_star()`	Modify star attribute on a model object
`add_bbi_args()` `replace_all_bbi_args()`	Modify bbi_args on a model object
`modify_model_field()` `replace_model_field()`	Modify field in model object
`build_path_from_model()`	Build path to output file
`get_based_on()` `get_model_ancestry()`	Get based_on from bbi object
`get_model_id()`	Get model identifier
`get_model_path()` `get_output_dir()` `get_yaml_path()` `get_config_path()`	Get path from bbi object
`get_data_path()`	Get path to data file
`print(<bbi_process>)` `print(<bbi_model>)` `print(<bbi_nonmem_summary>)` `print(<bbi_nmboot_summary>)` `print(<nmtran_process>)` `print(<model_tree_static>)`	Print methods for bbr objects
`initial_estimates()`	Retrieve and format initial parameter estimates
bbi configuration
`use_bbi()`	Installs most current release of bbi
`bbi_init()`	Initialize bbi
`bbi_version()`	Get version of installed bbi
`bbi_current_release()`	Get version number of bbi current release
`bbi_help()`	Executes (`bbi --help`) and prints the output string
Assorted helpers
`test_threads()`	Takes a model object and runs it with various threads values
`check_run_times()`	Check estimation time for models run with various threads values
`delete_models()`	Remove model files associated with the specified tags
`check_nonmem_finished()` `get_model_status()` `wait_for_nonmem()`	Check the status of `NONMEM` run(s)
`check_file()` `tail_output()` `tail_lst()`	Check an output file
`collapse_to_string()`	Collapse list column to a character column
`check_nonmem_table_output()` `check_grd()` `check_ext()`	Check NONMEM output files
`check_output_dir()`	Check output directory
`check_status_code()`	Checks status code from processx process
`format_cmd_args()`	Formats command line args from a named list to a string as it would be passed on the command line
`new_ext()` `ctl_ext()` `mod_ext()` `yaml_ext()`	Change file extension
`open_model_file()`	Open main model definition file in text editor
`plot_nonmem_table_df()` `plot_grd()` `plot_ext()`	Plot NONMEM output files
`reconcile_yaml()` `check_yaml_in_sync()`	Verify YAML file integrity
`suppressSpecificWarning()`	Suppress a warning that matches `.regexpr`

Reference

Model management

Model submission

Model summary and outputs

Bootstrap and Simulation

Summary log tables

Model object interactions

bbi configuration

Assorted helpers