Read in the example actigraphy data, specify column names for Date, Time and Activity | screening actigraphy data to check minumum wearing days and continuous wearing | apply consinor fitting | apply circacp algorithm | plot estimated cosinor fitting and circadian cycles | plot estimated cosinor fitting and slee-wake cycles | Non-parametric metrics for circadian rhythsm | Extract all sleep and circadian rhythm related metrics
Package: CircaCP 0.1.2
CircaCP: Sleep and Circadian Metrics Estimation from Actigraphy Data
A generic sleep–wake cycle detection algorithm for analyzing unlabeled actigraphy data. The algorithm has been validated against event markers using data from the Multi-Ethnic Study of Atherosclerosis (MESA) Sleep study, and its methodological details are described in Chen and Sun (2024) <doi:10.1098/rsos.231468>. The package provides functions to estimate sleep metrics (e.g., sleep and wake onset times) and circadian rhythm metrics (e.g., mesor, phasor, interdaily stability, intradaily variability), as well as tools for screening actigraphy quality, fitting cosinor models, and performing parametric change point detection. The workflow can also be used to segment long actigraphy sequences into regularized structures for physical activity research.
Authors:
CircaCP_0.1.2.tar.gz
CircaCP_0.1.2.zip(r-4.7-any)CircaCP_0.1.2.zip(r-4.6-any)CircaCP_0.1.2.zip(r-4.5-any)
CircaCP_0.1.2.tgz(r-4.6-any)CircaCP_0.1.2.tgz(r-4.5-any)
CircaCP_0.1.2.tar.gz(r-4.7-any)CircaCP_0.1.2.tar.gz(r-4.6-any)
CircaCP_0.1.2.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
CircaCP/json (API)
| # Install 'CircaCP' in R: |
| install.packages('CircaCP', repos = c('https://shanshanchen-biostat.r-universe.dev', 'https://cloud.r-project.org')) |
Datasets:
- actigraphy - Example Actigraphy Dataset
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated from:5906fe87bd. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel | OK | 126 | ||
| source / vignettes | OK | 160 | ||
| linux-release | OK | 115 | ||
| macos-release | OK | 169 | ||
| macos-oldrel | OK | 208 | ||
| windows-devel | OK | 82 | ||
| windows-release | OK | 76 | ||
| windows-oldrel | OK | 78 | ||
| wasm-release | OK | 110 |
Exports:cp_detectextract_nonparametric_metricsextract_sleep_metricsextract_sw_periodimport_acti_filescreen_wearsleep_cossleep_detection
Dependencies:clidata.tablegluelifecyclemagrittrpillarpkgconfigpracmarlangtibbleutf8vctrs
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Example Actigraphy Dataset | actigraphy |
| Detect a single change point (parametric methods) | cp_detect |
| Nonparametric circadian metrics (RA, IS, IV, L5, M10) | extract_nonparametric_metrics |
| Extract metrics related to sleep and circadian rhythm after using CircaCP algorithm | extract_sleep_metrics |
| Extract contiguous sleep or wake periods from a labeled minute series | extract_sw_period |
| Import actigraphy with header stripping and harmonized 'Activity' | import_acti_file |
| Screen wear and extract the longest valid minute-level segment | screen_wear |
| Estimates circadian cycle by cosinor fit of minute-level activity (period = 1440) | sleep_cos |
| Estimate precise sleep_wake cycles using CircaCP algorithm | sleep_detection |