Package 'asleep'

Run asleep Model on Data

Description

Run asleep Model on Data

Run asleep with Python

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
)

py_asleep(
  ...,
  pyenv_function = function() {
     asleep::py_require_asleep()
 },
  show = FALSE
)

Arguments

file	accelerometry file to process, including CSV, CWA, GT3X, and GENEActiv bin files
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 sl_download_models()
...	arguments to pass to asleep
pyenv_function	function that loads the forest Python package. By default, it uses reticulate::py_import("asleep") to import the package. If this function has an args argument, the output of pyenv_function will be re-assigned to args.
show	Logical, whether to show the standard output on the screen while the child process is running, passed to callr::r()

Value

A list of outputs, including summaries, paths, and dataframes.

Examples

asleep_check_result = function() {
  res = try({suppressWarnings(asleep_check())})
  if (inherits(res, "try-error")) {
    res = FALSE
  }
  res
}

  file = system.file("extdata/example_sleep.csv.gz", package = "asleep")
  stopifnot(file.exists(file))
  if (asleep_check_result()) {
    out = try({asleep(file = file, verbose = 2L)})
    if (inherits(out, "try-error")) {
      message(out)
      if (interactive()) {
        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_result()) {
    out = try({asleep(file = df)})
    if (inherits(out, "try-error")) {
      message(out)
    } else {
      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()
  }

---

Command for py_require for asleep

Description

Command for py_require for asleep

Usage

py_require_asleep(...)

Arguments

...	arguments to pass to reticulate::py_require()

Value

A logical value indicating whether the package is available.

---

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 model_path

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 NULL to disable. Defaults to "uniform".
keep_pandas	do not convert the data to a data.frame and keep as a pandas data.frame

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 data.frame of raw accelerometry
path	path to the CSV output file

Value

A data.frame of renamed columns

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