Package 'ActiSleep'

Accelerometry Data

Description

A dataset containing accelerometry data for a single subject in 1-minute epochs, includes vector magnitude and other measurements.

• date: Time and date of a single measurement.

• axis1: X-axis movement.

• axis2: Y-axis movement.

• axis3: Z-axis movement.

• steps: Steps taken by the subject.

• lux: Amount of light present, measured in lux.

• inclineOff: Incline off.

• inclineStanding: Incline standing.

• inclineSitting: Incline sitting.

• inclineLying: Incline lying.

• VM: Vector magnitude, calculated from x-, y-, and z-axis measurements.

Usage

data("AccelData")

Format

A data frame with 1351 rows and 11 variables.

---

Aggregate Accelerometer Data

Description

Obtain table from raw accelerometer table in 1-min intervals

Usage

aggregate_dat(datain, cutnum = 1, unit = c("min", "sec"), tz = "GMT")

Arguments

datain	raw ActiGraph GT3X data
cutnum	quantity of unit to serve as interval, default is 1
unit	time unit to use
tz	timezone, default is GMT

Value

data frame of accelerometer data aggregated by intervals

---

Calculate Mean Index

Description

Calculate the mean index of a segment

Usage

cal_mean_idx(i, datain, idx_start, idx_end)

Arguments

i	segment index
datain	activity data, must be a data frame
idx_start	array of segment start indices
idx_end	array of segment end indices

Value

mean value of segment indices

---

Reformat Time Variable

Description

Reformat the time variable to match analysis-ready format

Usage

ChangeTimeVar(datain, col_idx, format = "%Y-%m-%d %H:%M:%S")

Arguments

datain	input dataset, must be a data frame
col_idx	index of column to convert to date object
format	format of input date data, default is YYYY-MM-DD HH:MM:SS

Value

dataframe with formatted time values

Examples

data("SleepDiary1Week")

ChangeTimeVar(
SleepDiary1Week,
col_idx = c(5:18),
format = "%Y-%m-%d %H:%M:%S")

---

Diary In/Out-bed Times

Description

Obtain table of in-bed and out-bed times from sleep diary data

Usage

GetDiary_subj(datain, subj_idx, idx_bed, idx_wake, tz = "GMT")

Arguments

datain	input dataset, must be a data frame
subj_idx	index indicating subject
idx_bed	array specifying indices for in-bed time data
idx_wake	array specifying indices for out-bed time data
tz	timezone, default is GMT

Value

dataframe with in-bed and out-bed times

Examples

data("SleepDiary1Week")

SleepDiary1Week <-
ChangeTimeVar(SleepDiary1Week, c(5:18), format = "%m/%d/%Y %H:%M")

colIdx_diary_bed <- c(1:7) * 2 - 2 + 5
colIdx_diary_wake <- c(1:7) * 2 - 1 + 5

GetDiary_subj(
SleepDiary1Week,
1,
colIdx_diary_bed,
colIdx_diary_wake,
tz = "GMT")

---

Estimated sleep interval

Description

Obtain in-bed and out-bed times from diary data

Usage

GetEstSleepInterval_subj(
  datain,
  bed = "22:00:00",
  wake = "8:00:00",
  tz = "GMT"
)

Arguments

datain	diary data
bed	default in-bed time
wake	default out-bed time
tz	timezone, default is GMT

Value

data frame containing in-bed and out-bed times based on sleep diary

---

Read in AGD filedata

Description

Obtain a list of AGD filenames and data

Usage

read_agd(file, tz = "GMT", sec = 10)

Arguments

file	AGD data file
tz	timezone, default is GMT
sec	time interval used to set date

Value

list of AGD filenames and data

---

Find specific sleep segment

Description

Obtain specific sleep segment based on day, indices, etc.

Usage

SearchSleepSeg(
  date,
  Y,
  idx_start,
  idx_end,
  NoPA_cut = 0.7,
  sleep_mins = 30,
  SI_i,
  tz = "GMT"
)

Arguments

date	date of interest
Y	vector containing validated sleep counts
idx_start	start index of sleep segment
idx_end	end index of sleep segment
NoPA_cut	percent of 0 counts to define NoPA segments
sleep_mins	threshold number of minutes to define sleep segment
SI_i	estimated sleep intervals based on sleep diary data
tz	timezone, default is GMT

Value

list of validated sleep segments

---

This code was written by Alice Cleynen, Guillem Rigaill, and Michel Koskas as part of the Segmentor3IsBack package, which is no longer in CRAN. It has been imported into the ActiSleep package to ensure this package's longevity.

Description

This code was written by Alice Cleynen, Guillem Rigaill, and Michel Koskas as part of the Segmentor3IsBack package, which is no longer in CRAN. It has been imported into the ActiSleep package to ensure this package's longevity.

---

Sleep Diary 1-Day Data

Description

A small dataset containing sleep diary data for a single day and single subject

• bed. time at which the subject reported going to sleep on day 1

• wake. time at which the subject reported waking up on day 1

Usage

data("SleepDiary1Day")

Format

a data frame with 1 row and 2 variables

---

Sleep Diary 1-Week Data

Description

A small dataset containing sleep diary data for a single week and single subject

• FOLIOCC. unique subject id

• etapa.

• stage.

• start_day. first day of measurement

• time_bed1. time at which the subject reported going to sleep on day 1

• time_wake1. time at which the subject reported waking up on day 1

• time_bed2. time at which the subject reported going to sleep on day 2

• time_wake2. time at which the subject reported waking up on day 2

• time_bed3. time at which the subject reported going to sleep on day 3

• time_wake3. time at which the subject reported waking up on day 3

• time_bed4. time at which the subject reported going to sleep on day 4

• time_wake4. time at which the subject reported waking up on day 4

• time_bed5. time at which the subject reported going to sleep on day 5

• time_wake5. time at which the subject reported waking up on day 5

• time_bed6. time at which the subject reported going to sleep on day 6

• time_wake6. time at which the subject reported waking up on day 6

• time_bed7. time at which the subject reported going to sleep on day 7

• time_wake7. time at which the subject reported waking up on day 7

Usage

data("SleepDiary1Week")

Format

a data frame with 1 row and 18 variables

---

Daily sleep estimate

Description

Obtain sleep data from accelerometer data

Usage

SleepEstEachDay(
  datain,
  f = 1,
  id = NA,
  Y_name = "max_count",
  T = 0.4,
  nonwear_detect = FALSE,
  wear_mins = 120,
  S = 3,
  NoPA_cut = 0.7,
  sleep_mins = 20,
  wake_mins = 180,
  nap_mins = 20,
  UseDiary = FALSE,
  diary_data = c(),
  CommonBedTime = "22:00:00",
  CommonWakeTime = "8:00:00",
  tz = "GMT"
)

Arguments

datain	input accelerometry dataset, must be tibble, data frame, etc.
f	cost function indicator
id	subject id
Y_name	column name of the activity count data to be used in analysis, for example max count of x, y, z axes or vector magnitude
T	threshold percentile of activity level
nonwear_detect	flag indicating use of nonwear detection algorithm, default is FALSE
wear_mins	threshold number of minutes to define wear segment
S	number of segments per hour
NoPA_cut	percent of 0 counts to define NoPA segments
sleep_mins	threshold number of minutes to define sleep segment
wake_mins	threshold number of minutes to define wake segment
nap_mins	threshold number of minutes to define nap segment
UseDiary	flag indicating if diary data to be used, default is FALSE
diary_data	diary data, must be a data frame
CommonBedTime	in-bed time if no diary data, default is "22:00:00"
CommonWakeTime	out-bed time if no diary data, default is "8:00:00"
tz	timezone, default is GMT

Value

list containing a data frame of summary sleep data

Examples

data("AccelData")

AccelData <-
ChangeTimeVar(AccelData, col_idx = 1, format = "%m/%d/%Y %H:%M")

SleepEstEachDay(AccelData, Y_name = "VM")

data("AccelData")

AccelData <-
ChangeTimeVar(AccelData, col_idx = 1, format = "%m/%d/%Y %H:%M")

SleepEstEachDay(AccelData, Y_name = "VM", nonwear_detect = TRUE)

data("AccelData")
data("SleepDiary1Day")

SleepDiary1Day <-
ChangeTimeVar(
SleepDiary1Day,
col_idx = c(1,2),
format = "%m/%d/%Y %H:%M")

AccelData <-
ChangeTimeVar(AccelData, col_idx = 1, format = "%m/%d/%Y %H:%M")

SleepEstEachDay(
AccelData,
f = 2,
Y_name = "VM",
T = 0,
nonwear_detect = TRUE,
S = 2,
NoPA_cut = 0.45,
sleep_mins = 5,
UseDiary = TRUE,
diary_data = SleepDiary1Day
)

---