carwatch-analysis

A python project for the analysis of data from the CARWatch study, aimed to assess the influence of the inner clock on the Cortisol Awakening Response.

This package contains various helper functions to work with the dataset (including tpcp Dataset representations) and to process data. Additionally, it contains different analysis experiments performed with the dataset.

Repository Structure

The repository is structured as follows:

├── carwatch_analysis/                                      # `carwatch-analysis` Python package with helper functions
└── experiments/                                            # Folder with conducted analysis experiments; each experiment has its own subfolder
    ├── 00_general/                                         # General analysis of the dataset
    │   ├── exports/                                        # Processed data and extracted parameters
    │   ├── notebooks/                                      # Notebooks for data processing, analysis, plotting, etc. in subfolder
    │   └── results/                                        # results of analysis
    ├── 2021_car_inner_clock_bhi/                           # Analysis for the 2021 BHI Conference Paper (see below)
    │   ├── exports/
    │   ├── notebooks/
    │   │   ├── analysis/
    │   │   ├── classification/
    │   │   ├── data_cleaning/
    │   │   ├── pipeline_visualization/
    │   │   └── paper_path.json                             # json file with path to paper folder as 'pather_path' argument. used to export figures and latex tables
    │   └── results/
    │   │   ├── plots/
    │   │   └── statistics/
    └── 2023_car_sampling_pnec/                             # Analysis for the 2023 PNEC Paper (see below)
        ├── exports/
        ├── notebooks/
        │   ├── analysis/
        │   ├── data_cleaning/
        │   ├── data_processing/
        │   ├── plotting/
        │   └── paper_path.json                             # json file with path to paper folder as 'pather_path' argument. used to export figures and latex tables
        └── results/
            ├── plots/
            ├── statistics/
            └── ...

Installation

Dataset

In order to run the code, first download the CARWatch Dataset, e.g. from OSF. Then, create a file named config.json in the /experiments folder with the following content:

{
    "base_path": "<path-to-dataset>"
}

This config file is parsed by all notebooks to extract the path to the dataset.
NOTE: This file is ignored by git because the path to the dataset depends on the local configuration!

Code

If you want to use this package to reproduce the analysis results then clone the repository and install the package via poetry. For that, open a terminal and run the following commands:

git clone [email protected]:mad-lab-fau/carwatch-analysis.git
cd carwatch-analysis
poetry install # alternative: pip install .

This creates a new python venv in the carwatch-analysis/.venv folder. Next, register a new IPython kernel for the venv:

cd carwatch-analysis
poetry run poe register_ipykernel

Finally, go to the experiments folder and run the Jupyter Notebooks for the specific experiment you want to reproduce (see below).

Experiments

General (00_general)

This "experiment" contains general data processing, cleaning, and feature extraction.

Folder Structure

It consists of the following subfolders:

• notebooks:
  • data_processing: Notebooks to process data and extract relevant features:
    • IMU_Feature_Extraction_Pipeline.ipynb: Notebook for IMU feature extraction and sleep endpoint computation. Results are exported as per-subject files in the subject-specific folders of the dataset (sleep/<subject_id>/processed).
    • Questionnaire_Processing.ipynb: Notebook for extracting relevant information from questionnaire data, such as chronotype (assessed by MEQ), ideal bedtime range, and self-reported sleep endpoints (bedtime, sleep onset, wake onset, etc.).
    • Saliva_Processing.ipynb: Notebook for cleaning and processing saliva data, as well as computing saliva features (area under the curve, slope, maximum increase, etc.).
    • Sleep_IMU_Questionnaire_Merge.ipynb: Notebook for merging sleep endpoints (from IMU data) with chronotype and self-assessed sleep endpoints (from questionnaire data). Missing sleep endpoints (due to missing or corrupted IMU data) will be imputed by self-assessed sleep endpoints. Also, the notebook computes whether subjects went to bed within the ideal bedtime according to their chronotype (by computing whether the sensor-assessed bedtime lies within the questionnaire-assessed ideal bedtime range). The results are saved in the CARWatch dataset.
  • data_cleaning: Notebooks to clean processed data:
    • IMU_Cleaning.ipynb: Cleaning of sleep endpoints and static moment features.
      Note: For cleaning saliva data information from the merged sleep information (../exports/sleep_information_merged.csv) are required.
      Outputs:
      • ../exports/imu_sleep_endpoints_cleaned.csv: Sleep endpoints computed from IMU data, such as:
        • Sleep and Wake Onset (sleep_onset, wake_onset)
        • Total Sleep Time (total_sleep_time)
        • Bed Interval Start and End (major_rest_period_start, major_rest_period_end)
        • Sleep Efficiency (sleep_efficiency)
        • Sleep Onset and Getup Latency (sleep_onset_latency, getup_latency)
        • Wake Time after Sleep Onset (wake_after_sleep_onset)
        • Number of Wake Bouts (number_wake_bouts)
      • ../exports/imu_static_moment_features_cleaned.csv: IMU features characterizing pre-awakening movement. All features listed here are computed for two different ways of assessing wakeup time: imu and selfreport as well as for two different time intervals: for the whole night (total), the last hour before awakening (last_hour), and the last 30min before awakening (last_30min).
        • Number of static moments (larger than 60s) (ss_max, ss_max_60)
        • Position of the largest static moment relative to night (ss_max_position)
        • Mean duration of static moments (larger than 60s) (ss_mean, ss_mean_60)
        • Median duration of static moments (larger than 60s) (ss_median, ss_median_60)
        • Total number of static moments (larger than 60s) (ss_number, ss_number_60)
        • Skewness of static moments (larger than 60s) (ss_skewness, ss_skewness_60)
        • Standard deviation of static moments (larger than 60s) (ss_std, ss_std_60)
    • Saliva_Cleaning.ipynb: Cleaning of saliva features.
      Note: For cleaning saliva data information from the merged sleep information (../exports/sleep_information_merged.csv) are required.
      Outputs:
      • ../exports/cortisol_samples_cleaned.csv: Raw cortisol values after cleaning
      • ../exports/cortisol_features_cleaned.csv: Cortisol features after cleaning
  • analysis: Notebooks for statistical analysis of saliva and IMU/sleep data
  • classification: Notebooks for classification experiments, in particular for the attempt to predict the chronotype based on IMU patterns during sleep (Chronotype_Classification.ipynb)
• exports: Files exported from data processing and cleaning steps:
  • cortisol_samples_cleaned.csv
  • cortisol_features_cleaned.csv
  • imu_sleep_endpoints_cleaned.csv
  • imu_static_moment_features_cleaned.csv
• results: Plots and statistical results from the analysis steps

Notebook Processing Order

To run the data processing and analysis pipeline, we recommend the following order:

1. data_processing: IMU_Feature_Extraction_Pipeline.ipynb | Questionnaire_Processing.ipynb | Saliva_Processing.ipynb (no specific order)
2. data_merge: Sleep_IMU_Questionnaire_Merge.ipynb (Sleep_IMU_Questionnaire_Merge.ipynb requires exports from the notebooks in the data_processing step, so it needs to be run afterwards)
3. data_cleaning: IMU_Cleaning.ipynb | Saliva_Cleaning.ipynb (no specific order)
4. analysis: General_Information.ipynb | IMU_Analysis.ipynb | Saliva_Analysis.ipynb (no specific order)

2021 BHI Paper (2021_car_inner_clock_bhi)

This analysis was performed for the paper: Richer, R., Küderle, A., Dörr, J., Rohleder, N., & Eskofier, B. M. (2021, July). Assessing the Influence of the Inner Clock on the Cortisol Awakening Response and Pre-Awakening Movement. In 2021 IEEE EMBS International Conference on Biomedical and Health Informatics (BHI) (pp. 1-4). IEEE.

Folder Structure

This experiment contains the following subfolders:

• notebooks:
  • data_cleaning: Notebooks for cleaning saliva and IMU/sleep data
  • analysis: Notebooks for statistical analysis of saliva and IMU/sleep data
  • pipeline_visualization: Notebooks for creating plots illustrating the single data processing steps
• exports: Files exported from data processing and cleaning steps (Note: These results are the same as in the General analysis, but included here for consistency):
  • cortisol_samples_cleaned.csv
  • cortisol_features_cleaned.csv
  • imu_sleep_endpoints_cleaned.csv
  • imu_static_moment_features_cleaned.csv
• results: Plots and statistical results from the analysis steps

Notebook Processing Order

To run the data processing and analysis pipeline, we recommend the following order:

0. general data_processing: First, run the data processing (data_processing) and data merge (data_merge) notebook of the general data processing and analysis pipeline (folder 00_general) to create the export files that are used for further cleaning and processing
1. data_cleaning: IMU_Cleaning.ipynb | Saliva_Cleaning.ipynb (no specific order)
2. analysis: BHI2021_IMU.ipynb | BHI2021_Saliva.ipynb (no specific order)

2023 PNEC Paper (2023_car_sampling_pnec)

This analysis was performed for the paper: Richer, R., Abel, L., Küderle, A., Eskofier, B. M., Rohleder, N. (2023). CARWatch – A smartphone application for improving the accuracy of cortisol awakening response sampling. Psychoneuroendocrinology, 151, 106073.

Folder Structure

This experiment contains the following subfolders:

• notebooks:
  • data_processing:
    • Saliva_Processing_All_Reporting_Types.ipynb: Notebook computing relevant saliva features for the different reporting types (naive, self-report, app, etc.)
  • data_cleaning:
    • Cortisol_Cleaning.ipynb: Notebook for cleaning data from missing data, outlier, etc.
  • analysis: Notebooks for statistical analysis of sampling time and saliva data
    • General_Information.ipynb: General information about the dataset reported in the paper (demographics, descriptive information, etc.)
    • Sample_Time_Analysis.ipynb: Analysis of sampling and awakening times for different reporting types
    • Time_Unit_Digit_Analysis.ipynb: Analysis of time unit digits for different reporting types
    • Cortisol_Analysis.ipynb: Analysis of differences in derived CAR measures for different reporting types
  • plotting: Notebooks to create plots used in presentations, graphical abstracts, etc.
• exports: Files exported from data processing and cleaning steps (Note: These results are the same as in the General analysis, but included here for consistency):
  • cortisol_samples_cleaned.csv
  • cortisol_samples_processed_all_reporting_types.csv
  • cortisol_features_cleaned.csv
  • cortisol_features_processed_all_reporting_types.csv
• results: Plots and statistical results from the analysis steps

Notebook Processing Order

To run the data processing and analysis pipeline, we recommend the following order:

0. general data_processing: First, run the data processing (data_processing) and data merge (data_merge) notebook of the general data processing and analysis pipeline (folder 00_general) to create the export files that are used for further cleaning and processing
1. data_processing: Saliva_Processing_All_Reporting_Types.ipynb
2. data_cleaning: Cortisol_Cleaning.ipynb
3. analysis: General_Information.ipynb | Sample_Time_Analysis.ipynb | Time_Unit_Digits_Analysis.ipynb | Cortisol_Analysis.ipynb (no specific order)