Phase-Aligned Cycle Time Scaling (PACTS) and Menstrual Cycle Analysis

Implements Phase-Aligned Cycle Time Scaling (PACTS) for menstrual cycle data, placing observations from cycles of differing length onto a common continuous timeline that accounts for variability in ovulation timing. Provides cycle time variables anchored on either menses onset or ovulation, summaries of how ovulation was determined in each cycle, and plotting functions for cycle-aligned outcomes. Methods are described in Nagpal et al. (2025) .

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")])

One default worth knowing before you interpret results. The 21–35 day lower_cyclength_bound / upper_cyclength_bound gate ovulation imputation, not which cycles get scaled: a cycle with a confirmed ovulation is scaled whatever its length, gated by its phase lengths instead. This differs from how Nagpal et al. (2025) Section 2.1.1 describes it. summary_ovulation() reports how many of your cycles fall outside 21–35 days, and ?pacts_scaling explains the behavior in full.

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://menstrualcycler.clearlabresearch.com/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://menstrualcycler.clearlabresearch.com/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://menstrualcycler.clearlabresearch.com/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.

Use of AI coding tools

menstrualcycleR was created by Anisha Nagpal and Tory Eisenlohr-Moul, and the PACTS method is theirs and their co-authors'. No AI coding tool was used in the package's initial development, which began in January 2025 and produced the scaling engine, the exported functions, and the original documentation.

Anisha Nagpal's contributions predate all AI tool use. Her final commit is dated 18 March 2026. The first AI-assisted commit is dated 30 May 2026.

The decision to use AI coding tools was made by Dr. Tory Eisenlohr-Moul, the package maintainer, and it applies only to work after that date: debugging, documentation, and release preparation. Two tools appear in the history, each marked in the commits it touched — GitHub Copilot's coding agent, which updated the citation files in May 2026, and Claude Code, used from June 2026 onward and carrying a Co-Authored-By trailer.

Neither tool is an author, and neither is listed in Authors@R. Dr. Eisenlohr-Moul reviewed and approved every AI-assisted change and is responsible for the code and for every claim in the documentation.