/general_pipeline

General pipeline to calculate classical summary indicators of cortisol dynamics in the STRESS-EU database

Primary LanguageRMIT LicenseMIT

General pipeline to calculate classical summary indicators of cortisol dynamics in the STRESS-EU database (www.stressdatabase.eu)

  • Authors: Milou Sep, Laura de Nooij and Jonathan Posthuma
  • contact: m.s.c.sep(at)amsterdamumc.nl

Index

  • README.md: an overview of the project
  • data: folder for raw data files
  • r: folder with r-scripts
  • processed_data: folder for processed data files

R-script stresseu_summary_indicators_cortisol_dynamics.r contains:

  • Input: data/participants.csv and data/studies.csv (see www.stressdatabase.eu for the data access procedure)

  • Output: processed_data/df_sum_cort.rds

  • Baseline correction:

    • Timepoints: values between 20 minutes before and 2 minutes after stressor onset are considered baseline
    • for studies with multiple baseline values: replace baseline values by average
    • for studies without baseline values: makes NA explicit on T0

  • Calculation of classical summary indicators of cortisol dynamics:

    • Timepoints: values more then 2h after stressor onset are excluded, peak values are determined between 15 and 50 minutes after stressor onset
    • Peak reactivity: peak - baseline
    • Slope reactivity: slope baseline to peak
    • Slope recovery: slope peak to last value
    • Area under the curve with respect to ground (AUCg)
    • Area under the curve with respect to increase (AUCi)

References

For background and formula's for the summary cortisol indicators see Khoury, 2015 and Pruessner, 2003.