Function reference • PROMISE.data

Functions available for use Only these functions are loaded when using PROMISE.data. All the other functions are internal, but have documentation to describe them.
`PROMISE`	The final, master dataset for the PROMISE cohort
`export()`	This is just a thin wrapper around readr::write_excel_csv.
`view_manual()`	View the various PROMISE manuals.
`combine_datasets()`	Combine multiple datasets together into one, merged dataset. Merges based on SID and VN columns.
Package description
`PROMISE-package`	`PROMISE.data` contains the code, manuals, and data for the PROMISE cohort.
Internal functions: Generating Rda datasets Save individual datasets as accessible Rda objects and merging them into a single dataset.
`merge_datasets()`	Merge datasets together
`generate_datasets()`	(Re-)Generate the individual datasets from PROMISE.
`generate_promise()`	Cleans, adds to, and processes the combined dataset into the final saved PROMISE dataset.
Internal functions: Wrangling individual datasets Prepare and clean the individual datasets into tidy dataframes. These functions are used before saving the dataset as an accessible Rda object.
`clean_bia()`	Imports raw BIA data and wrangles it into a tidy format.
`clean_bloodwork()`	Import raw bloodwork data and wrangle it into a tidy format.
`clean_canoe()`	Imports raw Canoe data and wrangles it into tidy format
`clean_dhq()`	Import DHQ data and wrangle it into a tidy format.
`clean_diabetes_status()`	Import raw diabetes status data and wrangling into tidy format.
`clean_dxa()`	Imports the raw DXA data and wrangles into a tidy format.
`clean_fattyacids()`	Import fatty acid raw datafiles and wrangle it into a tidy format
`clean_form010()`	Import screening data from Form 1.0 (form010) and wrangle it into a tidy format
`clean_form012dx()`	Import family history of disease data from Form 1.2 (form012dx) and wrangle it into a tidy format
`clean_form012e()`	Import medical history and anthropometric data from Form 1.2 (form012e) and wrangle it into a tidy format
`clean_form012()`	Merge form012dx and form012e datasets
`clean_form014()`	Import raw data from Form 1.4 (form014) and wrangle into a tidy format.
`clean_form015()`	Import bloodwork data from Form 1.5 (form015) and wrangle it into a tidy format.
`clean_homa2()`	Homa2-IR, HOMA %B (beta cell function) and HOMA %S (insulin sensitivity) values for subjects with fasting insulin and glucose measures (n=1749). Calculated using HOMA2 excel spreadsheet available online.
`clean_meds()` `meds_general_types()` `clean_meds_usage()` `clean_meds_lipids_chol()` `clean_meds_blood_pressure()` `clean_meds_blood_glucose()` `clean_meds_diabetes()`	Convert medication data into tidy format.
`clean_msd()`	Merge all MSD protein data (adiponectin, TNFa, IL6, and YKL40). Code extracts and cleans raw data from files.
`clean_ogtt()`	Imports raw OGTT data and wrangles it into a tidy format.
`clean_phys_act()`	Calculates the MET (metabolic equivalents) from the physical activity questionnaire.
`clean_udbp()`	Imports raw UDBP data and wrangles it into a tidy format.
`clean_vitamin_d()`	Imports raw vitamin D data and wrangles it into a tidy format.
`clean_wbc()`	Imports raw WBC data and wrangles it into a tidy format.
`months_from_baseline()`	Calculate months and years from baseline visit.
`visit_info()`	Visit date, drop reason, visit comments.
Internal functions: Calculating measures These functions are used to calculate various measures such as MET (physical activity) and age.
`add_single_variable()` `add_age()` `add_dysglycemia()` `add_outcomes_ir()` `add_outcomes_bcf()` `add_outcomes_ic()` `add_total_fa()` `add_metabolic_syndrome()` `add_ethnicity()` `add_bmi()` `add_map()`	Add variables to the merged dataset.
`calc_job_met()`	Calculate job-base MET.
`calc_pa_met()`	Calculate general (life) physical activity MET.
`calc_total_met()`	Calculate total MET (metabolic equivalents) for physical activity.
`calculate_age()`	Calculate age from birth date to visit date.
Internal functions: Minor fixer functions
`fix_job_times()`	Fix job working times that are almost impossible.
`tidy_msd()`	Clean up the imported raw MSD datasets and keep what is important (there is a lot of unnecessary data inside the MSD raw files).
Internal functions: Importing specific datasets These functions import specific raw datasets that need special wrangling not available from the PROMISE.scrub package, such as from the MSD machine.
`import_csv_msd()`	Import the raw datasets obtained from the MSD analyzers for the various proteins.
`import_dxa()`	Import raw DXA data files.
`import_fattyacid()`	General function for fatty acid datasets only.
`import_txt_cd163()`	Import one dataset from the CD163 measurement (it's in a tab delimited format).
`import_txt_multiple_cd163()`	Import multiple CD163 datasets and clean them up (kind of necessary to clean up at the same time as importing).
Internal functions: Incomplete functions
`dhqextra()`	Import DHQ additional milk and cheese data from raw scanned forms and wrangle it into a tidy format
`cd163_signals()`	Export 450nm and 570nm output from CD163 runs.

Reference

Functions available for use

Package description

Internal functions: Generating Rda datasets

Internal functions: Wrangling individual datasets

Internal functions: Calculating measures

Internal functions: Minor fixer functions

Internal functions: Importing specific datasets

Internal functions: Incomplete functions