PPMI_Data_Wrangling

Overview

Gets raw PPMI data -> outputs processed/cleaned versions

Required Libraries (& Versions)

R: 4.2.1 (2022-06-23)
library(tidyr): 1.2.1
library(dplyr): 1.1.0
library(reshape2): 1.4.4
library(hablar): 0.3.1
library(data.table): 1.14.6
library(stringr): 1.5.0

Steps

Step 1: Createa new folder & put the following 12 or 13 files/scripts inside it

1. PPMI_Wide_to_Cleaned.R
2. PPMI_Wide_to_Cleaned_Imaging.R
3. PPMI_Cleaned_to_Processed.R
4. PPMI_Wide_to_Processed_Bio.R
5. PPMI_Cleaned_to_Processed_Imaging.R
6. PPMI_Wrapper.R
7. PPMI_AllMeasure_Merge.R
8. PPMI_Raw_to_Wide.R
9. UPSIT_to_percentile.R
10. UPSIT_Normative_Values_female.csv
11. UPSIT_Normative_Values_male.csv
12. PPMI_LEDD_Drug_Categories.csv
13. OPTIONAL: PPMI_CNO.csv
    13.1 if you want to add CNO, create a file with unique patient IDs as column 1 and CNO numbers as column 2
    13.2 if CNO is not needed, comment the "Add CNOs" section out in the PPMI_Cleaned_to_Processed.R file

Step 2: Run PPMI_Wrapper.R

Final Useful Files

Complete dataset (Behavioral + Imaging + Bio)

PPMI_Merged_AllMeasures_AllVisits_FINAL.csv
PPMI_Merged_AllMeasures_AllVisits_FINAL_vMATLAB.csv (has NAN instead of NA for easier import to MATLAB)

Behavioral

PPMI_allVisits_cleaned_processed.csv
PPMI_extraVisits_cleaned_processed.csv
PPMI_regularVisits_cleaned_processed.csv
NOTE: Regular Visit include BL and Uxx visits. Extra Visit included everything in All Visit except the regular Visit ones.

Imaging

PPMI_Imaging_All_cleaned_processed.csv
PPMI_Imaging_Main_cleaned_processed.csv
NOTE: "PPMI_Imaging_Main_cleaned_processed.csv" has the imaging information that is used in "Merged_Final" files"

Bio

PPMI_Bio_cleaned_processed.csv