Package 'activityCounts'

Title: Generate ActiLife Counts
Description: ActiLife software generates activity counts from data collected by Actigraph accelerometers <https://s3.amazonaws.com/actigraphcorp.com/wp-content/uploads/2017/11/26205758/ActiGraph-White-Paper_What-is-a-Count_.pdf>. Actigraph is one of the most common research-grade accelerometers. There is considerable research validating and developing algorithms for human activity using ActiLife counts. Unfortunately, ActiLife counts are proprietary and difficult to implement if researchers use different accelerometer brands. The code creates ActiLife counts from raw acceleration data for different accelerometer brands and it is developed based on the study done by Brond and others (2017) <doi:10.1249/MSS.0000000000001344>.
Authors: Ruben Brondeel [aut], Javad Rahimipour Anaraki [aut], Daniel Fuller [aut, cph, cre], SeyedJavad KhataeiPour [aut], Beap Lab [cph]
Maintainer: Daniel Fuller <[email protected]>
License: GPL-3
Version: 0.2.1
Built: 2026-05-21 07:16:04 UTC
Source: https://github.com/walkabillylab/activitycounts

Help Index

counts

Description

Calculates ActiLife counts based on raw accelerometer data

Usage

counts(
  data,
  hertz = -1,
  x_axis = 2,
  y_axis = 3,
  z_axis = 4,
  time_column = -1,
  start_time = -1
)

Arguments

data

Accelerometer data, Must have at least three columns.
hertz

Sampling frequency in Hz
x_axis

Indicates the column number which has the accel data for x direction, the default is 2
y_axis

Indicates the column number which has the accel data for y direction, the default is 3
z_axis

Indicates the column number which has the accel data for z direction, the default is 4
time_column

Optional. Indicates the column number which has the date and time. The first row will be considered as the start time of the study. You can use the "start_time" argument to provide the start time explicitly.
start_time

Optional. Use this to define the start time of the experiment. You can use this argument if the data does not contain a time column.

Value

Returns a data.table with four columns:

Time

The start time of the measurement

x

the number of counts for X axis

y

the number of counts for Y axis

z

the number of counts for Z axis

See Also

sampleXYZ raw accelerometer data for testing counts() function.

sampleCounts counts calculated by activityCounts and ActiLife

Examples

# for tha sampleXYZ dataset, sampling frequency is 100 Hz
counts(data = sampleXYZ, hertz = 100)

# when start time is given explicitly
study_start_time <- "2017-08-22 12:30:10"
counts(data = sampleXYZ, hertz = 100 , start_time = study_start_time)

# the data has a time column, which is the first column
counts(data = sampleXYZ, hertz = 100 , time_column = 1)

# explicitly specify the X, Y and Z axis columns.
counts(data = sampleXYZ, hertz = 100 , x_axis = 2,y_axis = 3, z_axis = 4)

pptrunc

Description

pptrunc

Usage

pptrunc(data, max_value)

Arguments

data

The variable that will be truncated
max_value

The upper bound ( -max_value is the lower bound)

Value

the highest(or the lowest) value of "data" and "max_value"

runsum

Description

runsum

Usage

runsum(data, len, threshold)

Arguments

data

input data
len

the length
threshold

the threshold

Value

returns a

The counts calculated by activityCounts and ActiLife based on included raw accelerometer data

Description

A simple data.table which its first row is measurement time. Then for each time step, counts are calculated by activityCounts and the ActiLife software. The counts are calculated based on included sampleXYZ dataset, which its sampling frequency is 100H.

Usage

sampleCounts

Format

A data.table with nine columns:

Time

Date and time

activityCounts_x_counts

counts calculated by counts() function in X direction

activityCounts_y_counts

counts calculated by counts() function in Y direction

activityCounts_z_counts

counts calculated by counts() function in Z direction

ActiLife_x_counts

counts calculated by ActiLife software in X direction

ActiLife_y_counts

counts calculated by ActiLife software in Y direction

ActiLife_z_counts

counts calculated by ActiLife software in Z direction

See Also

counts to see how to produce counts.

sampleXYZ raw accelerometer data for testing counts() function.

Raw accelerometer data for the activityCounts package

Description

A simple data.table that contains raw accelerometer data for testing the counts function. Sampling frequency of this data.table is 100Hz, therefore pass 100 as the second argument when using the counts function.

Usage

sampleXYZ

Format

A data.table with four columns:

Time

Timestamp

accelerometer_X

accelerometer data in X direction

accelerometer_Y

accelerometer data in Y direction

accelerometer_Z

accelerometer data in Z direction

See Also

counts to see how to produce counts.

sampleCounts counts calculated by activityCounts and ActiLife

trunc

Description

trunc

Usage

trunc(data, min_value)

Arguments

data

The input variable which will be altered if less than the threshold
min_value

the threshold which the input below it will be set to zero

Value

returns zero if the "data" is less than the "mean_value" otherwise returns the "data"