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menstrualcycleR: Phase-Aligned Cycle Time Scaling (PACTS)

Source: R/menstrualcycleR-package.R
menstrualcycleR-package.Rd

Tools for standardizing menstrual cycle data onto a continuous, phase-aligned timeline (PACTS), so cycle-time predictors can be modeled the same way across participants and cycles despite variability in cycle length and ovulation timing.

Where to start

pacts_scaling is the main entry point – it takes a long-format diary (one row per person-day) with menses and ovulation markers and returns the same data with cyclic_time, cyclic_time_impute, cyclic_time_ov, and cyclic_time_imp_ov added (see ?pacts_scaling's @return for what each means and which to use). For a full worked example, including GAMM modeling of the resulting cycle-time variables, see the "Getting Started" vignette: vignette("menstrualcycleR-overview", package = "menstrualcycleR"), or the hosted copy at https://eisenlohrmoullab.github.io/menstrualcycleR/articles/menstrualcycleR-overview.html – installing via remotes::install_github() does not build vignettes locally unless you pass build_vignettes = TRUE.

For a visual explainer of why PACTS realigns cycles the way it does, see https://eisenlohrmoullab.github.io/menstrualcycleR/pacts-explainer.html.

Other exported functions

  • cycledata_check: summarize per-symptom, per-phase data availability before scaling.

  • summary_ovulation: summarize confirmed-vs-imputed ovulation rates after scaling.

  • cycle_plot / cycle_plot_individual: visualize a symptom across phase-aligned cycle time, across the whole sample or for one individual.

  • launch_app: an interactive Shiny app covering the same workflow (requires the shinyjs and cpass packages, installed separately – see ?launch_app).

References

Nagpal, A., Schmalenberger, K. M., Barone, J. C., Mulligan, E., Stumper, A., Knol, L., Failenschmid, J., Kiesner, J., Peters, J. R., & Eisenlohr-Moul, T. A. (2025). Studying the Menstrual Cycle as a Continuous Variable: Implementing Phase-Aligned Cycle Time Scaling (PACTS) with the menstrualcycleR package. Psychoneuroendocrinology, 107584. doi:10.1016/j.psyneuen.2025.107584

See also

Useful links:

Author

Maintainer: Tory Eisenlohr-Moul temo@uchicago.edu (ORCID)

Authors: