Analyzing Sleep States with FlyDreamR

FlyDreamR is an R package for analyzing Drosophila Activity Monitor (DAM) data, with workflows for:

• Preparing DAM master/monitor files for downstream analyses
• Traditional sleep metrics (sleep time, bout statistics, activity indices, brief awakenings)
• Hidden Markov Models (HMMs) to infer discrete behavioral states and visualize state dynamics
• An optional Shiny app for interactive analysis

This vignette gives a short roadmap and points you to the more focused vignettes included with the package.

What to read next

• Getting data into FlyDreamR: vignette("data-prep", package = "FlyDreamR")
• Traditional sleep analyses: vignette("traditional-sleep", package = "FlyDreamR")
• HMM fitting and visualization: vignette("hmm-workflow", package = "FlyDreamR")
• Running the Shiny app: vignette("shiny-app", package = "FlyDreamR")

Installation (typical options)

From GitHub (recommended)

# Install from GitHub (devtools or remotes)
install.packages(c('devtools','remotes'), repos='https://cloud.r-project.org')
remotes::install_github('orijitghosh/FlyDreamR', upgrade = 'never')

Then load the package:

library(FlyDreamR)

Getting help

• Check documentation: ?HMMbehavr
• View examples: example(HMMplot)

Citation

If you use FlyDreamR in your research, please cite:

Ghosh A, Harbison ST. Inferring the genetic basis of sleep states in Drosophila melanogaster using hidden Markov models. bioRxiv. 2026: 2026.2001.2014.699526.