Package index • FlyDreamR

Metadata & Data Import

Functions to 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

Functions to load DAM activity data, link it with metadata, and calculate normalized activity and phases.

HMMDataPrep(): Prepare DAM Activity Data for HMM Analysis

HMM Analysis

The core functions for running Hidden Markov Models to infer sleep/wake states.

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

Visualization

Tools for visualizing inferred states using heatmaps, faceted plots, or individual 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 Metrics

Functions to calculate standard sleep metrics (immobility bouts) for comparison with HMM results.

calcTradSleep(): Calculate Comprehensive Sleep Metrics from Activity Data

Interactive Analysis

Functions to launch the graphical user interface (Shiny App).

runFlyDreamRApp(): Launch the FlyDreamR Shiny App