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How to Install and Load menstrualcycleR

To install and load the menstrualcycleR package, follow these steps:

  1. Install the remotes package (if not already installed): install.packages("remotes")

  2. Install menstrualcycleR from GitHub

remotes::install_github("eisenlohrmoullab/menstrualcycleR", build_vignettes = TRUE)

  1. Load the package

library(menstrualcycleR)

Quick start

pacts_scaling() is the main function: give it a long-format diary (one row per person-day) with menses and ovulation markers, and it returns the same data with continuous, phase-aligned cycle-time columns added.

library(menstrualcycleR)

# cycledata is a small example dataset bundled with the package
scaled <- pacts_scaling(
  cycledata,
  id      = id,
  date    = daterated,
  menses  = menses,
  ovtoday = ovtoday
)

# cyclic_time / cyclic_time_impute / cyclic_time_ov / cyclic_time_imp_ov are the
# columns to model -- see ?pacts_scaling for what each one covers
head(scaled[, c("id", "daterated", "cyclic_time", "cyclic_time_impute")])

For the full workflow, including GAMM modeling of the resulting cycle-time variables, see the vignette (vignette("menstrualcycleR-overview") once installed with build_vignettes = TRUE above, or the hosted copy linked below) or ?menstrualcycleR for an overview of every exported function.

To utilize the shinyapp, visit: https://menstrualcycledata.shinyapps.io/shiny/

For a tutorial on using menstrualcycleR visit: https://eisenlohrmoullab.github.io/menstrualcycleR/articles/menstrualcycleR-overview.html

For a visual explainer of how PACTS works — why cycle-day counting misaligns hormones and how PACTS realigns them — visit: https://eisenlohrmoullab.github.io/menstrualcycleR/pacts-explainer.html

To browse an auto-generated, annotated bibliography of papers that cite, apply, or extend menstrualcycleR and PACTS, visit: https://menstrualcycler.base44.app

For a history of changes by version, see the changelog: https://eisenlohrmoullab.github.io/menstrualcycleR/news/index.html

How to cite

If you use menstrualcycleR in your research, please cite:

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. https://doi.org/10.1016/j.psyneuen.2025.107584

You can also run citation("menstrualcycleR") in R to get the citation in plain-text and BibTeX form.