Package index • zeitR

Import

Read raw actigraphy files into R.

read_actigraphy(): Read an actigraphy file into a zeitr_recording object
read_actigraphy_dir(): Read all actigraphy files in a directory
read_acttrust(): Read a Condor Instruments ActTrust actigraphy file
read_axivity(): Read an Axivity AX3/AX6 .cwa file into a zeitR-standard epoch tibble

Prepare recordings for analysis and check data quality.

Off-wrist, sleep period, and epoch-level scoring algorithms.

detect_offwrist_bimodal(): Off-wrist detection using the Condor bimodal activity/temperature model
detect_sleep_crespo(): Detect main sleep periods using the Crespo algorithm
detect_naps_crespo(): Detect secondary sleep periods (naps) using the Crespo nap algorithm
score_epochs_cole_kripke(): Score actigraphy epochs as wake or sleep using the Cole-Kripke algorithm
compute_waso(): Compute WASO and nightly sleep statistics

Non-parametric circadian rhythm variables.

Summarise results across multiple participants.

study_summary(): Summarise a zeitr_study across participants
study_sleep_metrics(): Batch sleep-timing and chronotype metrics across a study

Run the full analysis pipeline on one file or a directory.

run_pipeline(): Run the full actigraphy sleep analysis pipeline
run_pipeline_batch(): Run the pipeline on all files in a directory
acttrust_params(): ActTrust device parameter preset
run_pipeline_native(): Run the Vallim native actigraphy sleep analysis pipeline
run_pipeline_native_batch(): Run the native pipeline on all files in a directory
extract_sleep_episodes(): Extract sleep episodes from a CSPD-scored epoch table
classify_sleep_episodes(): Classify sleep episodes as main or secondary (native pipeline)

Summarise sleep across nights and compute chronobiological phenotype metrics.

Locomotor Inactivity During Sleep – ultradian sleep-cycle dynamics from actigraphy.

lids_transform(): Apply the LIDS (Locomotor Inactivity During Sleep) transform
fit_lids(): Fit a sloped cosine to a LIDS profile, scanning candidate periods
detect_lids_bouts(): Detect nighttime sleep bouts via the Roenneberg relative-immobility method
compute_lids(): Compute LIDS ultradian-rhythm parameters for every sleep bout
study_lids_metrics(): Batch LIDS ultradian-rhythm summary across a study

Convert raw triaxial acceleration into epoch-level activity counts.

compute_activity_counts(): Compute PIM, TAT, and ZCM activity counts from raw triaxial acceleration

Estimate energy expenditure and classify PA intensity from activity counts.

pa_equations(): Published activity-count equations for estimating METs and PA intensity
estimate_ee(): Estimate energy expenditure (METs) from activity counts
classify_pa_intensity(): Classify physical activity intensity from METs
classify_pa_counts(): Classify physical activity intensity directly from activity counts

Actogram and raster display of actigraphy recordings.

plot_actogram(): Plot a single-column actogram
plot_actogram_double(): Plot a double-plotted actogram
plot_actogram_activity(): Plot a double-plotted actogram with activity bars
actogram_colours(): Default state colour palette for actogram plots

Helper functions for working with pipeline output.

label_states(): Convert integer epoch states to a labelled factor
export_hypnogram(): Export a zeitR pipeline result as a hypnoR-compatible hypnogram
circ_mean_h(): Circular mean of clock times in decimal hours
circ_sd_h(): Circular standard deviation of clock times in decimal hours

Package-level documentation.