Man pages for epi-sam/SamsElves
Helper functions for the data science at IHME
| aggregate_from_children_to_parents | Aggregate from children to parents using a hierarchy |
| apply_comma_string_to_list | Convert atomic list elements to comma strings |
| assert_git_diff | Stop progress if user has uncommitted changes |
| assert_git_hash | Assert that daughter scripts share a common code state with... |
| assert_list_elements_and_types | Assert that a list contains all the element from a _named_... |
| assert_named_list | Assert that an object is a list, and that all top level items... |
| assert_no_na | Assert no NA values in select columns |
| assert_no_null_arguments | Assert function arguments are not null. |
| assert_scalar | Ensure an element is atomic and length 1 |
| assert_square | Assert a data.table is square by id_varnames |
| assert_x_in_y | Assert all elements of x are in y |
| break_for_failed_jobs | Helper function for wait_on_slurm_job_id - how do you want... |
| build_metadata_shell | Build metadata from a template |
| children_of_parents | Get child locations given parent IDs from IHME hierarchies |
| comma_string_to_vec | Convert a comma-separated string to a vector |
| datetime_stamp | Current Date-Time Stamp |
| extract_command_string | Search a cluster submitted command string for some pattern |
| extract_cores | Extract number of interactive user cores |
| extract_script_path | Extract the path to the current script |
| extract_sessionInfo | Extract key pieces of session info to avoid metadata bloat |
| extract_submission_commands | Find a string in a user's recent Slurm squeue |
| find_file_extension | Find the file extension from a full path |
| get_latest_output_date_index | get the latest index for given an output dir and a date |
| get_latest_output_dir | Find the latest output directory with format YYYY_MM_DD.VV |
| get_new_output_dir | Increment a new output folder date-version |
| get_new_output_dv | Increment a new output folder date-version |
| increment_file_version | If a file exists, get a new path with 'v1', 'v2', etc.... |
| is_child_of_parent | Helper function for children_of_parents. |
| is_cli_null | Check if an element would be empty when passed as a CLI... |
| is_empty | Check that a vector/element is not empty |
| is_sequential_int_vec | Are all elements of a vector contiguous integers? |
| job_finder | Find cluster jobs for a user |
| make_directory | Convenience 'dir.create' wrapper with desired defaults |
| make_new_output_dir | Make a date-versioned output directory for output results. |
| make_versioned_dir | Get output directory for results to save in |
| msg_multiline | Print a message with multiple lines |
| msg_prt | Control how user-defined messages submit to std_err or... |
| parent_of_child | parent_of_child |
| parents_of_children | parents_of_children |
| parse_all_named_cli_args | Parse command-line arguments to global environment |
| prep_windows_path_for_unix | Convert windows file paths |
| prt_multiline | Paste data.frame output for a message |
| query_git_diff | Record uncommitted git changes |
| read_file | Read a file of an arbitrary type |
| save_file | Save file I/O with overwrite and message control |
| submit_job | Submit a script as a job to the Slurm cluster |
| validate_children_of_parents_inputs | Helper function for children_of_parents. |
| validate_parents_of_children_inputs | Helper function to validate inputs to function |
| vec_to_comma_string | Convert a vector to a comma-separated string |
| wait_on_jobs | Given string pattern matching job name, wait while jobs are... |
| wait_on_slurm_job_id | Wait for a Slurm job to finish (find 'RUNNING|PENDING' State... |
