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.