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Getting started with hypnoR

Source: vignettes/getting-started.Rmd
getting-started.Rmd

Overview

hypnoR is the hypnogram layer of the Circadia Lab R ecosystem. It accepts staged hypnograms from two upstream sources:

  • mrpheus — full AASM staging: W / N1 / N2 / N3 / REM
  • zeitR — coarse actigraphy-derived staging: W / Sleep / Quiet sleep

All metric functions are resolution-agnostic: they compute what is possible given the available stages and document which outputs require full AASM staging.

Installation 

# install.packages("remotes")
remotes::install_github("circadia-bio/hypnoR")

Basic workflow 

library(hypnoR)

# 1. Read a hypnogram
hyp <- read_hypnogram("path/to/hypnogram.csv")

# 2. Compute sleep architecture metrics
arch <- compute_sleep_architecture(hyp)

# 3. Detect NREM/REM cycles (full AASM only)
cyc <- compute_cycles(hyp)

# 4. Stage-transition analysis
trans <- compute_transitions(hyp)

# 5. Plot
plot_hypnogram(hyp)
plot_architecture(arch)
plot_transition_matrix(trans$matrix)

Supported input formats

read_hypnogram() currently handles:

Format Argument
Generic CSV (epoch, stage columns) "csv"
EDF+ annotations "edf_annotations"
YASA output "yasa"
Compumedics Profusion "compumedics"
Nox Medical "nox"

Pass format = "auto" (the default) to infer the format from the file header and extension.

Staging resolution

hypnoR detects resolution automatically from the stage labels present in the hypnogram. Metrics that require full AASM staging (REM latency, SWS latency, cycle detection, N1/N2/N3 percentages) return NA with an informative message for coarse hypnograms.