Package index • FlyDreamR

Metadata & Data Import

Convert raw master files into the metadata format required to link experimental conditions with monitor files.

convMasterToMeta(): Convert Master File to FlyDreamR Metadata Format
convMasterToMetaBatch(): Batch Convert Multiple Master Files to FlyDreamR Metadata Format

Data Preparation

Load DAM activity data, link it with metadata, and calculate normalized activity, day number, and light/dark phase.

HMMDataPrep(): Prepare DAM Activity Data for HMM Analysis

HMM Analysis

Fit hidden Markov models to infer sleep and wake states from activity counts, serially or in parallel.

HMMbehavr(): Infer Sleep States Using Hidden Markov Model
HMMbehavrFast(): Parallel Hidden Markov Model for Sleep State Inference

Visualization

Plot inferred states as heatmap hypnograms, faceted group profiles, or individual daily profiles.

HMMplot(): Plot HMM Inferred Sleep States as Tile Heatmap
HMMFacetedPlot(): Create Faceted Plot of HMM Inferred States
HMMSinglePlot(): Save Individual HMM State Plots to Disk

Traditional Sleep Metrics

Calculate standard immobility-based sleep metrics for comparison with HMM results.

calcTradSleep(): Calculate Comprehensive Sleep Metrics from Activity Data

Shiny App

Launch the interactive GUI for point-and-click analysis.

runFlyDreamRApp(): Launch the FlyDreamR Shiny App