Man pages for metrumresearchgroup/rbabylon
R package for babylon

apply_indicesAdd parameter indices to a label tibble
as_modelConvert object to bbi_{.model_type}_model
bbi_current_releaseGet version number of babylon current release
bbi_dry_runCreates a 'babylon_process' object with all the required...
bbi_execExecute call to bbi
bbi_helpExecutes ('bbi –help') and prints the output string
bbi_initInitialize babylon
bbi_versionGet version number of babylon installed on system
build_bbi_param_listBuilds list of unique parameter sets for multiple model bbi...
build_matrix_indicesBuilds matrix indices labels
build_path_from_mod_objBuilds the absolute path to a file in the output directory...
check_bbi_exeChecks that a bbi binary is present at the path passed to...
check_bbi_version_constraintCheck if bbi_version is below minimum allowed version
check_fileCheck an output file
check_lst_filePrivate helper function to look for .lst function in a...
check_model_objectPrivate helper to check if an object inherits a model class...
check_model_object_listPrivate helper to check if a list of objects all inherit a...
check_nonmem_argsChecks that all passed NONMEM command line args are valid and...
check_nonmem_table_outputCheck NONMEM output files
check_output_dirCheck output directory
check_status_codeChecks status code from processx process
clean_ctlParse control stream to a named list of the blocks
combine_directory_pathBuild absolute path from a directory and path
combine_list_objectsCombines two named lists. By default, shared keys are...
config_logParse babylon configs to log
copy_control_streamCopy a NONMEM control stream file
copy_model_fromCreate new model by copying existing model
copy_nonmem_model_fromCopy model from an existing NONMEM model
create_bbi_objectCreate bbi object
current_releasePrivate helper function to most recent release version from...
enforce_lengthPrivate helper to enforce length of a list element
find_config_file_pathPrivate helper to search for babylon.yaml config files
find_model_file_pathPrivate helper to find valid model file and return...
find_yaml_file_pathPrivate helper to find valid yaml file
format_cmd_argsFormats command line args from a named list to a string as it...
get_based_onGet based_on from bbi object
get_model_directoryGet or set global model directory option
get_model_idGet model identifier
get_path_from_objectGet path from bbi object
install_menuPrivate implementation function for installing bbi with...
is_diagCheck if diagonal index or not
is_valid_nonmem_extensionPrivate helper to check if file has a valid NONMEM control...
is_valid_yaml_extensionPrivate helper to check if file has a valid YAML extension
linux_install_commandsPrivate helper function for building commands to install bbi...
model_summarySummarize model outputs
modify_model_fieldModify field in model object
new_extChange file extension
new_modelCreate new model object
nonmem_summaryRun bbi nonmem summary and parse the output to a list
param_estimatesParses parameter estimates table
param_labelsExtract parameter labels for report tables, etc.
parse_args_listCombines NONMEM args that were passed into the function call...
parse_param_commentParse parameter labels
pipePipe operator
plot_nonmem_table_dfPlot NONMEM output files
print_nonmem_argsPrint valid .bbi_args
rbabylonRBabylon
read_modelCreates a model object from a YAML model file
run_logCreate tibble summarizing all model runs
run_log_entryCreate a run log row from a bbi_{.model_type}_model object
safe_based_onChecks for yaml files relative to a starting location
safe_read_modelRead in model YAML with error handling
save_model_yamlSaves a model model object to a yaml file
stop_get_fail_msgBuild error message and throw error for generic failure fo...
stop_get_scalar_msgBuild error message and throw error for passing character...
strict_mode_errorRaise error in strict mode
submit_modelSubmit a model to be run
submit_modelsSubmit models to be run in batch
submit_nonmem_modelSubmit a NONMEM model via babylon
submit_nonmem_modelsSubmit multiple NONMEM models in batch via babylon
suppressSpecificWarningSuppress a warning that matches '.regexpr'
use_bbiInstalls most current release of bbi
verify_model_yaml_integrityVerify YAML file integrity
version_messagePrivate helper to construct version comparison message
metrumresearchgroup/rbabylon documentation built on June 29, 2020, 5:04 a.m.