jranaraki/jaeger_analysis

Code to clean data from Jaeger Metabolic cart based on the paper "Methods used to process data from indirect calorimetry and their application to V02 max" Robert A Robergs and Angus F Burnett. Journal of Exercise Physiology. 6(2), 2003. https://www.asep.org/asep/asep/Robergs3.pdf

Authors

• Javad Rahimipour Anaraki
• Daniel Fuller

Introduction

Code to clean data from Jaeger Oxycon Pro metabolic cart based on the paper "Methods Used to Process Data from Indirect Calorimetry and Their Application to VO2MAX" Robert A Robergs and Angus F Burnett. Journal of Exercise Physiology. 6(2), 2003.

Preliminaries

Place the code next to the participants folder which contain a file called timing.csv and a CSV data file generated by Jaeger.

• data
  • Jaeger
    • 301
      • timing.csv
      • JaegerDataFile.csv
    • 302
      • timing.csv
      • JaegerDataFile.csv
    • ...
  • intervals.csv

The timing.csv should contain the following columns:

• Task name stores the task done by participant
• Start time is start date and time (in ####-##-## ##:##:## format)
• End time is end date and time (in ####-##-## ##:##:## format)

The data folder also contains a file called intervals.csv which stores information about each participants as follows:

• herox stores participants alias names
• kit is the package number
• phone is phone id
• watch is Apple watch id
• fitbit is Fitbit id
• geneactiv is GENEActiv id
• snesedoc is SenseDoc id
• start is start date and time (in ####-##-## ##:##:## format)
• end is end date and time (in ####-##-## ##:##:## format)
• userid is a unique id for each participant
• wrist is 1 if Apple Watch and GENEActiv are on the same wrist, otherwise 0
• age, gender, weight and height are demographic data
• street, city, postal are address information for each participant.

Note: This file should be kept updated throughout the experiment.

Steps to run the code as in the follows:

1. Modifying required variables

• Modify path and intrPath, the Jaeger participants folder and intervals.csv, respectively
• Change the uid (e.g. 301) for choose which participant data should be processed
• Modify the timeZone variable to your local timezone

Info: More information on setting the timezone can be found here.

2. Run the code

Select all the code and run it using Ctrl + Enter.

3. Results

Based on the interpolation and spline cure fitting six plots are generated. For VO2, VCO2 and RER the generated curve and Bland-Altman figures are plotted and saved in each participant folder. Also, a CSV file to check the validity of the collected Jaeger data is generated and placed next to the plots.