PEG3 data entry tracking

Author

Yufan Gong

Published

November 5, 2025

1 Introduction

This document aims to track the data entry process for PEG3 study. Currently, I focus on the data entry tracking for the following forms [i.e., GDS, MoCA, and UPDRS(if case), Medical checklist, timeline, and life history questionnaire] among participants who 1) have screeningstatus; or 2) have blood sample; 3) have stool sample; 4) have phys_apptdate_status (for cases).

Notes:

The following code is assuming that you are using Windows OS on a HIPAA compliant device.

Make sure you have read this post before you run the code.
If you are using Mac OS, please check this link for .accdb connection, and please make sure the .accdb file doesn’t have a password if you are using Mac OS.
Alternatively, you can also connect to the database using pyodbc package if you prefer using Python.
For other database types, please refer to this blog.

2 Visualizing

2.1 Stool sample collection tracking

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2.2 Entry progress tracking

Definition:

Entry completed: Both entry initial and entry date are completed
In old database: Both entry initial and entry date are null and participant is not in PEG3
Entry initial needed: Entry initial is null and entry date is completed
Entry date needed: Entry initial is completed and entry date is null
Partially completed: For timeline forms, if one of the forms (either occupation or residence) is completed, it is considered partially completed
Entry needed: Both entry initial and entry date are null and RA status indicated completed
Cannot complete: Entry initial and entry date are null and RA status indicated Deceased, Too ill, Do not contact, Ineligible, Withdrew / can use information or peg3status1 is not null
Cannot collect: screeningstatus contains Deceased, Institutionalized, or Too ill
Pending: All circumstances not covered by the above categories (i.e., haven’t been collected/RA checklist status not updated and haven’t been entered)