| Title: | Estimate Sleep from 'Accelerometry' Data |
| Version: | 0.1.0 |
| Description: | Interfaces the 'asleep' python module https://github.com/OxWearables/asleep from Yuan (2024) <doi:10.1038/s41746-024-01148-y> to estimate sleep from 'accelerometry' data. |
| License: | MIT + file LICENSE |
| Encoding: | UTF-8 |
| Imports: | assertthat, curl, lubridate, magrittr, readr, reticulate (≥ 1.42.0) |
| Suggests: | tidyr, dplyr, ggplot2, testthat (≥ 3.0.0) |
| Config/testthat/edition: | 3 |
| URL: | https://github.com/jhuwit/asleep, https://jhuwit.github.io/asleep/ |
| BugReports: | https://github.com/jhuwit/asleep/issues |
| Config/roxygen2/version: | 8.0.0 |
| NeedsCompilation: | no |
| Packaged: | 2026-07-24 20:53:38 UTC; johnmuschelli |
| Author: | John Muschelli 
[aut, cre] |
| Maintainer: | John Muschelli <muschellij2@gmail.com> |
| Repository: | CRAN |
| Date/Publication: | 2026-08-04 13:50:08 UTC |
Pipe operator
Description
See magrittr::%>% for details.
Usage
lhs %>% rhs
Arguments
lhs |
A value or the magrittr placeholder. |
rhs |
A function call using the magrittr semantics. |
Value
The result of calling rhs(lhs).
Run asleep Model on Data
Description
Run asleep Model on Data
Usage
asleep(
file,
outdir = NULL,
min_wear_hours = 22L,
time_shift = "0",
report_light_and_temp = FALSE,
pytorch_device = c("cpu", "cuda:0"),
sample_rate = NULL,
verbose = TRUE,
force_download = FALSE
)
Arguments
file |
accelerometry file to process, including CSV,
CWA, GT3X, and |
outdir |
output directory for CSVs and outputs |
min_wear_hours |
Min wear time in hours to be eligible for summary statistics computation. The sleepnet paper uses 22 |
time_shift |
The number hours to shift forward or backward from the current device time. e.g. +1 or -1 |
report_light_and_temp |
If true, it adds mean temp, and light columns to the predictions |
pytorch_device |
device to use for prediction for PyTorch. |
sample_rate |
Sample rate for the data, currently not used. |
verbose |
print diagnostic messages |
force_download |
force a download of the model, passed to |
Value
A list of outputs, including summaries, paths, and dataframes.
Examples
file = system.file("extdata/example_sleep.csv.gz", package = "asleep")
stopifnot(file.exists(file))
if (asleep_check()) {
sl_download_models()
out = try({asleep(file = file, verbose = 2L)})
if (inherits(out, "try-error")) {
message(out)
reticulate::py_last_error()
} else {
pred = out$predictions
}
}
file = system.file("extdata/example_sleep.csv.gz", package = "asleep")
df = readr::read_csv(file)
if (asleep_check()) {
out = asleep(file = df)
st = out$predictions
if (requireNamespace("ggplot2", quietly = TRUE) &&
requireNamespace("tidyr", quietly = TRUE) &&
requireNamespace("dplyr", quietly = TRUE)) {
d = st[1:250,] %>%
dplyr::mutate(
time = lubridate::as_datetime(time),
time_end = dplyr::lead(time)
) %>%
dplyr::filter(!is.na(time_end))
raw = df %>% dplyr::filter(time >= min(d$time) & time <= max(d$time))
dat = raw %>%
tidyr::gather(axis, value, -time)
d = d %>% dplyr::mutate(activity_y = as.numeric(sleep_wake == "sleep"))
dat %>%
ggplot2::ggplot(ggplot2::aes(x = time, y = value, colour = axis)) +
ggplot2::geom_step() +
ggplot2::geom_segment(
data = d,
ggplot2::aes(
x = time, xend = time_end,
y = activity_y, yend = activity_y,
linetype = sleep_wake
),
colour = "black", linewidth = 1, inherit.aes = FALSE
) +
ggplot2::labs(linetype = "Sleep/wake")
}
}
Get SSL Net -
Description
Get SSL Net -
Usage
get_sslnet()
sl_get_sslnet()
Value
A keras model representing the SSL Net.
Check the asleep Python Module
Description
Check the asleep Python Module
Usage
have_asleep()
asleep_check(...)
asleep_version(...)
Arguments
... |
additional arguments to pass to reticulate::py_list_packages |
Value
A logical value indicating whether the asleep Python module is available.
Examples
if (have_asleep()) {
asleep_version()
}
Download asleep models to Cache
Description
Download asleep models to Cache
Usage
sl_download_models(force_download = FALSE)
Arguments
force_download |
force a download of the model, even if it already exists at |
Value
A model from Python. sl_download_model returns a model file path.
Load asleep Model for Sleep Window Detector
Description
Load asleep Model for Sleep Window Detector
Usage
sl_load_model(model_path = NULL, force_download = FALSE, as_python = TRUE)
sl_download_model(model_path, ...)
Arguments
model_path |
the file path to the model. If on disk, this can be
re-used and not re-downloaded. If |
force_download |
force a download of the model, even if it already exists at |
as_python |
Keep model object as a python object |
... |
for |
Value
A model from Python. sl_download_model returns a model file path.
Read a Data Set for asleep
Description
Read a Data Set for asleep
Usage
sl_read(file, resample_hz = "uniform", keep_pandas = FALSE)
Arguments
file |
path to the file for reading |
resample_hz |
Target frequency (Hz) to resample the signal. If
"uniform", use the implied frequency (use this option to fix any device
sampling errors). Pass |
keep_pandas |
do not convert the data to a |
Value
A list of the data and information about the data
Note
The data P30_wrist100 is from
https://ora.ox.ac.uk/objects/uuid:19d3cb34-e2b3-4177-91b6-1bad0e0163e7,
where we took the first 180,000 rows, the first 30 minutes of data
from that participant as an example.
Examples
file = system.file("extdata/example_sleep.csv.gz", package = "asleep")
if (asleep_check()) {
out = sl_read(file, resample_hz = FALSE)
}
Rename data for asleep
Description
Rename data for asleep
Usage
sl_rename_data(data)
sl_write_csv(data, path = tempfile(fileext = ".csv"))
Arguments
data |
a |
path |
path to the CSV output file |
Value
A data.frame of renamed columns