Package index • bbr

Model management

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

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

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
add_dofv(): Calculate change in objective function value of models in a run log
model_tree(): Create a tree diagram of a modeling directory

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

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() deprecated: 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() deprecated: Plot NONMEM output files
reconcile_yaml() check_yaml_in_sync(): Verify YAML file integrity
suppressSpecificWarning(): Suppress a warning that matches .regexpr