stepwedgepower

stepwedgepower refactors a one-off academic R script into a reusable R package for:

• physician-level data cleaning,
• specialty-level binomial modeling,
• stepped-wedge simulation, and
• simulation-based power / type I error estimation.

Project background

This package is based on a PhD biostatistics rotation project on statistical methods for stepped wedge clinical trial designs. According to the rotation evaluation, the project involved:

• research of published literature,
• summarizing literature in slides/presentations, and
• building well-organized, well-documented R software.

The software was also used to provide sample size calculations for a study under development. In the permission email shown in the screenshots, Prof. Florin Vaida approved publishing the software to GitHub.

What was changed from the original script

The original file mixed together:

1. raw CSV imports,
2. one-off data cleaning,
3. model fitting,
4. ad hoc probability extraction, and
5. repeated simulation loops.

This package reorganizes those steps into exported functions:

• prepare_physician_data()
• summarize_by_specialty()
• fit_specialty_rate_model()
• estimate_specialty_rates()
• analyze_lpa_outcomes()
• simulate_stepwedge_trial()
• run_stepwedge_analysis()
• estimate_power()
• estimate_type1_error()

Installation

# install.packages("remotes")
remotes::install_github("AmandaLinLi/stepwedgepower")

Minimal workflow

library(stepwedgepower)

dat0 <- read.csv("data_pseudo_homeDPT.csv")
dat <- prepare_physician_data(dat0)

summary_tbl <- summarize_by_specialty(
  dat,
  vars = c("n_total_pat", "n_ldl_pat")
)

results <- analyze_lpa_outcomes(dat)

results$overall$logit$glm_rates
results$overall$logit$glmer_rates

power_out <- estimate_power(
  n_simulations = 500,
  effect_size_or = 2.11,
  n_providers_per_specialty = c(40, 40, 40, 40) * 0.25,
  tau_provider = 1.21,
  base_probs = c(0.05, 0.05, 0.05, 0.05),
  pts_per_step = 50 / 5,
  seed = 2026
)

power_out$power

Example data

A small synthetic dataset is included for quick testing:

ex_dat <- read_example_physician_data()
head(ex_dat)

Repository structure

stepwedgepower/
  DESCRIPTION
  NAMESPACE
  R/
  man/
  inst/extdata/
  inst/scripts/
  tests/
  .github/workflows/

Notes

• The package is structured to be GitHub-ready.
• I assumed an MIT license for convenience; you can change that before publishing.
• The original external CSV files are not bundled here, so the package ships with synthetic example data only.
• Because the current environment does not have an R runtime, this package scaffold was prepared carefully but not executed with R CMD check inside the container.

Suggested next steps before publishing

1. Open the package locally in RStudio.
2. Run devtools::document().
3. Run devtools::check().
4. Replace YOUR_GITHUB_USERNAME in README.md.
5. Replace the maintainer email placeholder in DESCRIPTION.
6. Commit and push to GitHub.