Man pages for metrumresearchgroup/bbr
R package for bbi
| add_log_impl | Add columns to log df |
| add_model_status | Add model status to a run log |
| add_na_filter | Adjust filters to retain NA values for relevant columns |
| add_param_shrinkage | Add shrinkage details to param table |
| add_run_id_col | add run col to bbi_log_df |
| add_to_path_message | Helper to message user about adding the bbi directory to... |
| adjust_estimation_options | Parse model files and overwrite estimation iterations |
| apply_indices | Add parameter indices to a label tibble |
| assert_bbi_version | Check that bbi satisfies a version constraint |
| assert_nm_table_format | Check if a 'NONMEM' table file contains one or more tables in... |
| assert_record_type | Helper for checking if a specified record type is valid. |
| as_summary_list | Convert object to 'bbi_summary_list' |
| BBI_ARGS | List of valid arguments bbi arguments |
| bbi_current_release | Get version number of bbi current release |
| bbi_dry_run | Creates a 'bbi_process' object with all the required keys,... |
| bbi_exec | Execute call to bbi |
| bbi_help | Executes ('bbi –help') and prints the output string |
| bbi_init | Initialize bbi |
| bbi_nonmem_model_status | Return status of a model |
| bbi_version | Get version of installed bbi |
| bbr | bbr |
| build_bbi_install_path | Build default path to install bbi to |
| build_bbi_param_list | Group models for bbi submission |
| build_matrix_indices | Builds matrix indices labels |
| build_new_model_path | Private helper to build absolute path for... |
| build_path_from_model | Build path to output file |
| check_bbi_args | Checks that all passed NONMEM command line args are valid and... |
| check_bbi_exe | Check that bbi is installed |
| check_bbi_run_log_df_object | Private helper to check if an object inherits a run log class... |
| check_cor_threshold | Check for high correlations |
| check_file | Check an output file |
| check_for_existing_model | Private helper to look for existing model and overwrite if... |
| check_lst_file | Private helper function to look for .lst function in a... |
| check_mode_argument | Private helper to check if '.mode' arg to 'submit_model()' is... |
| check_model_for_sim | Check that a 'bbr' model can be used for simulation |
| check_model_object | Private helper to check if an object inherits a model class... |
| check_model_object_list | Private helper to check if a list of objects all inherit a... |
| check_nonmem_table_bbi | Private helper to pull a NONMEM table from a model |
| check_nonmem_table_output | Check NONMEM output files |
| check_os | Check what operating system R is running on |
| check_output_dir | Check output directory |
| check_record_val | Check if a record option matches a specific value |
| check_run_times | Check estimation time for models run with various threads... |
| check_status_code | Checks status code from processx process |
| check_up_to_date | Check model and data up to date with outputs |
| check_up_to_date_nonmem | Private implementation to check that NONMEM model is... |
| clean_ctl | Parse control stream to a named list of the blocks |
| cleanup_bootstrap_run | Cleanup bootstrap run directory |
| collapse_to_string | Collapse list column to a character column |
| color_model_type | Format and color the model type of a model |
| color_status | Function to color the status. Green for finished; red... |
| combine_list_objects | Combines two named lists. By default, shared keys are... |
| config_log | Parse bbi configs to log |
| config_log_entry | Parse a bbi config file |
| config_log_impl | Build config log |
| config_log_make_entry | Prepare a model-specific config log entry |
| copy_control_stream | Copy a NONMEM control stream file |
| copy_model_from | Create new model by copying existing model |
| copy_model_from_impl | Copy model from an existing model |
| cov_cor | NONMEM Covariance and Correlation Matrices |
| create_bbi_object | Create bbi object |
| create_model_hook | Perform model-type specific setup |
| current_release_url | Private helper function to most recent release version from... |
| delete_models | Remove model files associated with the specified tags |
| dev_error | Construct error message that users shouldn't see |
| download_bbi | Download bbi executable to the specified path. |
| download_with_retry | Call 'utils::download.file()', retrying once on failure. |
| drop_dups | Drop duplicate columns to prepare for join |
| execute_nmtran | Execute 'NM-TRAN' in a given directory |
| extract_from_summary | Extract from summary object |
| file_matches | Compare a file to an MD5 sum |
| file_matches_string | Compare a file to a string |
| filter_nm_data | Filter 'NONMEM' input data based on 'IGNORE' and 'ACCEPT'... |
| find_models | Search for model YAML files and read them |
| find_nonmem_model_file_path | Find the path to a NONMEM model file |
| fmt_record_num | Get record number of initial estimates |
| format_cmd_args | Formats command line args from a named list to a string as it... |
| format_matrix | Format vector into matrix using positional vector |
| format_model_type | Format the model type for use in 'model_tree()' |
| get_based_on | Get based_on from bbi object |
| get_boot_spec | Read in and format the bootstrap specification file. |
| get_data_path | Get path to data file |
| get_model_id | Get model identifier |
| get_model_working_directory | Get the working directory of a model object |
| get_msf_path | Get path to 'MSF' file path |
| get_next_integer | Check directory for model files with integer names and return... |
| get_omega | Return a formatted object for a given parameter |
| get_param | Return a formatted object for a given parameter |
| get_path_from_log_df | Private helper function to extract paths from bbi_log_df |
| get_path_from_object | Get path from bbi object |
| get_sim_replicate_record | Determine whether 'NONMEM' control stream is using a $PRED or... |
| get_sim_spec | Read in and format the simulation specification file. |
| get_spec_path | Get the relevant specification file path |
| get_theta_inits | Helper function for getting the initial theta values,... |
| highlight_cell | Highlight cell in kable table |
| inherit_param_estimates | Inherit parameter estimates |
| initial_estimates | Retrieve and format initial parameter estimates |
| install_menu | Private implementation function for installing bbi with... |
| invert_operator | Function to invert 'R' operators in filter expressions |
| is_diag | Check if diagonal index or not |
| is_valid_nonmem_extension | Private helper to check if file has a valid NONMEM control... |
| is_valid_yaml_extension | Private helper to check if file has a valid YAML extension |
| make_boot_run | Set up a single bootstrap model run |
| make_boot_spec | Store bootstrap run details before submission |
| make_tree_data | Construct dataset for use in 'model_tree' |
| map_list_recursive | Recursively apply a function to each list element |
| model_diff | Compare model files between models |
| model_diff_get_comp | Private helper to get a valid comparison model |
| model_diff_impl | Private helper to diff two model files |
| model_status | Check the status of 'NONMEM' run(s) |
| model_summaries | Summarize multiple models in batch |
| model_summary | Summarize model outputs |
| model_tree | Create a tree diagram of a modeling directory |
| model_tree_png | Save an interactive 'model_tree()' as a PNG and load in... |
| modify_based_on | Modify based_on field in a model object |
| modify_bbi_args | Modify bbi_args on a model object |
| modify_description | Modify description on a model object |
| modify_model_field | Modify field in model object |
| modify_model_field_lgl | Adds or removes boolean attribute from model object and YAML |
| modify_notes | Modify notes on a model object |
| modify_records | Modify or retrieve options and records from a 'NONMEM'... |
| modify_star | Modify star attribute on a model object |
| modify_tags | Modify tags on a model object |
| mod_list_setup | Coerce model object to a list of models for use in... |
| na_to_null | Convert an object containing entirely NA's to NULL |
| new_bootstrap_run | Create a bootstrap run from an existing model |
| new_ext | Change file extension |
| new_model | Create new model object |
| new_sim_model | Create a simulation model object from an existing model |
| nm_file | Read NONMEM files |
| nm_file_impl | Implementation function for reading NONMEM files |
| nm_file_multi_tab | Read in table file with multiple 'NONMEM' tables. |
| nm_join | Return a single data frame with model output and input data |
| nm_join_impl | Implementation function for 'nm_join()' |
| nm_join_sim | Join simulation and input data |
| nm_tables | Read all tables and input data |
| nmtran_setup | Sets up 'NM-TRAN' to run by identifying an 'NM-TRAN'... |
| nonmem_summary | Run bbi nonmem summary and parse the output to a list |
| open_model_file | Open main model definition file in text editor |
| param_estimates | Parses parameter estimates table |
| param_estimates_batch | Batch Processing of Parameter Estimates |
| param_estimates_compare | Compare parameter estimates |
| param_labels | Extract parameter labels for report tables, etc. |
| parse_args_list | Combines NONMEM args that were passed into the function call... |
| parse_cov_cor_full_file | Helper to pull full matrix from final estimation method from... |
| parse_ctl_to_list | Parses NONMEM control stream to a list of $ blocks. Adapted... |
| parse_nmtran_args | Parse '.bbi_args' and return the three expected... |
| parse_param_comment | Parse parameter labels |
| pipe | Pipe operator |
| plot_nonmem_table_df | Plot NONMEM output files |
| print_bbi | Print methods for bbr objects |
| print_bbi_args | Print valid .bbi_args |
| print_model_files | Print a list of files. |
| read_bbi_path | Set the path to the bbi executable |
| read_model | Creates a model object from a YAML model file |
| register_model_type | Register a model type to class mapping |
| remove_dup_cols | Removes duplicate col names |
| req_tree_pkgs | Required packages for running 'model_tree()' |
| resolve_nonmem_version | Determine the NONMEM version used |
| run_log | Create tibble summarizing all model runs |
| run_log_entry | Create a run log row from a bbi_{.model_type}_model object |
| run_nmtran | Interface for running 'NM-TRAN' on model objects |
| safe_based_on | Checks for yaml files relative to a starting location |
| safe_read_model | Read in model with error handling |
| sanitize_file_extension | Private helper to remove file extensions to match expected... |
| save_model_yaml | Saves a model object to a yaml file |
| set_bbi_null | Replace BBI_NULL_NUM and BBI_NULL_STR with NA_real_ |
| setup_bootstrap_run | Set up a bootstrap model run |
| setup_sim_run | Set up 'NONMEM' simulation |
| sig | Format digits |
| simulate | Simulate a 'bbi_nonmem_model' object |
| skip_if_not_ci_or_metworx | Skip test if not on Metworx or in CI |
| skip_if_old_bbi | Skip test if current bbi version is below specified one. |
| skip_if_old_nmrec | Skip test if current nmrec version is below specified one. |
| skip_if_over_rate_limit | Skip test if over Github API rate limit |
| skip_long_tests | Skip long-running tests |
| stop_get_fail_msg | Build error message and throw error for generic failure fo... |
| stop_get_scalar_msg | Build error message and throw error for passing character... |
| strict_mode_error | Raise error in strict mode |
| style_html | Helper for coloring text and applying other styles |
| submit_model | Submit a model to be run |
| submit_models | Submit models to be run in batch |
| submit_nonmem_model | Submit a NONMEM model via bbi |
| summarize_bootstrap | Summarize a bootstrap run |
| summary_log | Create a tibble from 'model_summaries()' data |
| summary_log_impl | Build summary log |
| suppressSpecificWarning | Suppress a warning that matches '.regexpr' |
| tags_diff | Compare tags between models |
| test_nmrec_version | Check that nmrec satisfies a version constraint |
| test_threads | Takes a model object and runs it with various threads values |
| translate_nm_expr | Translate 'NONMEM' 'IGNORE' and 'ACCEPT' expressions into... |
| translate_nm_operator | Function to translate 'NONMEM' operators to 'R' operators |
| tweak_initial_estimates | Tweak the initial parameter estimates |
| tweak_thetas | Tweak theta estimates while respecting bounds |
| unquote_filename | Unquote file paths for inclusion within a NONMEM control file |
| update_model_id | Update model ID (run number) in the control stream |
| use_bbi | Installs most current release of bbi |
| using_old_priors | Check if _non-specific_ priors are being used. |
| validate_parent_mod | Confirm parent model path is valid, and error informatively... |
| verbose_msg | Prints message(s) if 'isTRUE(getOption("bbr.verbose"))' |
| verify_model_yaml_integrity | Verify YAML file integrity |
| version_message | Private helper to construct version comparison message |
