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.

list_manuals

View the various PROMISE manuals.

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 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.