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sleepcycles: Detect and Visualize Sleep Cycles from Hypnograms

The sleepcycles package provides tools for detecting, analyzing, and visualizing sleep cycles from hypnogram data using density-based and rule-based (Feinberg) algorithms. It supports both single- and multi-subject hypnograms, enabling users to extract and explore Non-REM (NREMP) and REM (REMP) periods with flexible parameter settings. The package includes an interactive Shiny application, a suite of visualization functions and utilities validating sleep staging data.

📌 Designed for sleep researchers, clinicians, and data scientists, sleepcycles helps uncover the underlying dynamics of sleep architecture and assess the impact of sleep patterns in healthy and clinical populations.

📦 Installation

You can install the development version from GitHub using remotes:

# Install remotes if not installed
install.packages("remotes")

# Install sleepcycles from GitHub
remotes::install_github("jasondude16/sleepcycles")

🚀 Quick Start Guide

1️⃣ Load the Package

2️⃣ Load Example Data

sleepcycles contains two example datasets: hypnogram_single and hypnogram_grouped, which contain single- and multi-subject hypnograms, respectively. We will load the multi-subject hypnogram for this example.

data("hypnogram_grouped", package = "sleepcycles")

sleepcycles requires a hypnogram (in the format of a data frame) with two variables: one of the epoch, and one of the sleep stage; if there are multiple subjects, an ID variable is also required.

head(hypnogram_grouped)
#>   epoch stage id
#> 1     1     W  1
#> 2     2     W  1
#> 3     3     W  1
#> 4     4     W  1
#> 5     5     W  1
#> 6     6     W  1

3️⃣ Detect Sleep Cycles 

sleepcycle_obj <- sleepcycles_from_hypnogram(
  hypnogram_grouped, 
  epoch_col = "epoch", 
  stage_col = "stage", 
  id_col = "id",
  verbose = FALSE
)

4️⃣ Visualize Sleep Cycles 

plot_cycles(sleepcycle_obj, id = "1")

plot_hypnogram(sleepcycle_obj, id = "1")

5️⃣ Run the Interactive Shiny App 

if (interactive()) {
  run_sleepcycles_app(sleepcycle_obj)
}

📊 Features

  • ✔ Sleep Cycle Detection: Supports Feinberg (Rule-Based) algorithm and a novel density-based algorithm
  • ✔ Interactive Visualization: Generate hypnograms, density plots, and cycle summaries
  • ✔ Shiny App: Modify and explore cycle detection parameters interactively
  • ✔ Preprocessing & Validation: Built-in data validation tools
  • ✔ Single and Grouped Data Support: Works with individual and multi-subject hypnogram datasets

📖 Available Functions

Function Description
sleepcycles_from_hypnogram() Detects sleep cycles using DUDE or Feinberg method
plot_hypnogram() Generates a hypnogram plot
plot_densities() Plots hypnogram stage densities
plot_cycles() Visualizes detected sleep cycles
plot_summary() Provides a combined visualization of sleep cycles and hypnogram
run_sleepcycles_app() An interactive Shiny app for sleep cycle parameter exploration
check_hypnogram() Validates hypnogram data for errors

📌 Contributing

We welcome contributions! If you find a bug, please open an issue.

📜 License

This package is licensed under the MIT License.