Getting up to date with Sage - Bionetworks Develop

R/data.R

@@ -7,6 +7,109 @@
 #' @source \url{https://www.synapse.org/#!Synapse:syn10146135/wiki/448409}
 "guanlab_nn_weights"
 
+#' Accelerometer sensor measurements
+#' 
+#' @format An 990 x 4 data frame with column names \code{t}, \code{x},
+#' \code{y}, \code{z} containing accelerometer measurements. \code{t} is
+#' the timestamp of each measurement, and \code{x}, \code{y} and \code{z}
+#' are linear acceleration measurements along the respective axis. 
+"accelerometer_data"
+
+#' Gyroscope sensor measurements
+#' 
+#' @format An 990 x 4 data frame with column names \code{t}, \code{x},
+#' \code{y}, \code{z} containing accelerometer measurements. \code{t} is
+#' the timestamp of each measurement, and \code{x}, \code{y} and \code{z}
+#' are linear velocity measurements along the respective axis. 
+"gyroscope_data"
+
+#' Gravity sensor measurements
+#' 
+#' @format An 990 x 4 data frame with column names \code{t}, \code{x},
+#' \code{y}, \code{z} containing acceleration measurements due to gravity. 
+#' \code{t} is the timestamp of each measurement, and \code{x}, \code{y}
+#' and \code{z} are linear gravity measurements along the respective axis. 
+"gravity_data"
+
+#' Device-Motion data from a performed balance assay
+#' 
+#' The balance assay entails participants standing still for 30 seconds
+#' with the mobile device in their pocket or in a bag.
+#' 
+#' @format A 3002 x 6 data frame with column names \code{attitude},
+#' \code{timestamp}, \code{rotationRate}, \code{userAcceleration},
+#' \code{gravity}, and \code{magneticField}. The column names correspond
+#' to the measurements returned by a
+#' [CMDeviceMotion](https://developer.apple.com/documentation/coremotion/cmdevicemotion)
+#' object as described in Apple's developer documentation. \code{rotationRate},
+#' \code{userAcceleration},\code{gravity} are each 3002 x 3 data frames with column names
+#' \code{x}, \code{y}, \code{z} containing axial measurements for their respective sensor.
+#' \code{magneticField} has an additional column \code{accuracy} specifying
+#' the calibration accuracy of the magnetic field estimate. \code{attitude}
+#' columns are quaternion coefficients. 
+"balance_data"
+
+#' Device-Motion data from a performed walk assay
+#' 
+#' The walk assay entails participants walking in a straight line for
+#' approximately 20 steps with the mobile device in their pocket or in a bag.
+#' 
+#' @format A 3002 x 6 data frame with column names \code{attitude},
+#' \code{timestamp}, \code{rotationRate}, \code{userAcceleration},
+#' \code{gravity}, and \code{magneticField}. The column names correspond
+#' to the measurements returned by a
+#' [CMDeviceMotion](https://developer.apple.com/documentation/coremotion/cmdevicemotion)
+#' object as described in Apple's developer documentation. \code{rotationRate},
+#' \code{userAcceleration},\code{gravity} are each 3002 x 3 data frames with column names
+#' \code{x}, \code{y}, \code{z} containing axial measurements for their respective sensor.
+#' \code{magneticField} has an additional column \code{accuracy} specifying
+#' the calibration accuracy of the magnetic field estimate. \code{attitude}
+#' columns are quaternion coefficients. 
+"walk_data"
+
+#' Device-Motion data from a performed resting tremor assay
+#' 
+#' The resting tremor assay entails participants holding the mobile device
+#' in their hand (either right or left) while resting that hand in their lap
+#' for approximately 10 seconds.
+#' 
+#' @format A 3002 x 6 data frame with column names \code{attitude},
+#' \code{timestamp}, \code{rotationRate}, \code{userAcceleration},
+#' \code{gravity}, and \code{magneticField}. The column names correspond
+#' to the measurements returned by a
+#' [CMDeviceMotion](https://developer.apple.com/documentation/coremotion/cmdevicemotion)
+#' object as described in Apple's developer documentation. \code{rotationRate},
+#' \code{userAcceleration},\code{gravity} are each 3002 x 3 data frames with column names
+#' \code{x}, \code{y}, \code{z} containing axial measurements for their respective sensor.
+#' \code{magneticField} has an additional column \code{accuracy} specifying
+#' the calibration accuracy of the magnetic field estimate. \code{attitude}
+#' columns are quaternion coefficients. 
+"rest_tremor_data"
+
+#' Device-Motion data from a performed kinetic tremor assay
+#' 
+#' The kinetic tremor assay (also known as the finger/hand to nose test)
+#' entails participants holding the mobile device
+#' in their hand (either right or left) with both the mobile device and the
+#' participants elbow at nose level. The participant then moves the mobile device
+#' away from the nose, with both mobile device and elbow parallel to the ground
+#' and the elbow joint acting as an axis of rotation. When the arm is fully extended,
+#' the participant moves the mobile device back to the nose. This happens in a 
+#' continuous motion and the motion is repeated for approximately 10 seconds.
+#' 
+#' @format A 3002 x 6 data frame with column names \code{attitude},
+#' \code{timestamp}, \code{rotationRate}, \code{userAcceleration},
+#' \code{gravity}, and \code{magneticField}. The column names correspond
+#' to the measurements returned by a
+#' [CMDeviceMotion](https://developer.apple.com/documentation/coremotion/cmdevicemotion)
+#' object as described in Apple's developer documentation. \code{rotationRate},
+#' \code{userAcceleration},\code{gravity} are each 3002 x 3 data frames with column names
+#' \code{x}, \code{y}, \code{z} containing axial measurements for their respective sensor.
+#' \code{magneticField} has an additional column \code{accuracy} specifying
+#' the calibration accuracy of the magnetic field estimate. \code{attitude}
+#' columns are quaternion coefficients. 
+"kinetic_tremor_data"
+
 #' Sample heartrate data from a smartphone camera
 #' 
 #' A dataframe containing sample JSON output format of the heartrate data,
@@ -50,4 +153,4 @@
 #'   'TappedButtonNone' indicating that at that time the left, right or No 
 #'   button was tapped respectively}
 #' }
-"tap_data"
+"tap_data"

R/get_balance_features.R

@@ -1,8 +1,9 @@
 #' Preprocess and extract interpretable features from balance assay.
 #' 
-#' A convenience wrapper for extracting
-#' interpretable features from the balance assay measured using smartphone raw 
-#' accelerometer and gyroscope sensors.
+#' A convenience wrapper for extracting interpretable features from the
+#' balance assay measured using smartphone raw accelerometer and gyroscope
+#' sensors.The balance assay entails participants standing still for 30 seconds
+#' with the mobile device in their pocket or in a bag.
 #' 
 #' @param accelerometer_data An \code{n} x 4 data frame with columns \code{t}, \code{x},
 #' \code{y}, \code{z} containing accelerometer measurements. Here \code{n} is the

R/get_kinetic_tremor_features.R

@@ -4,6 +4,15 @@
 #' kinetic tremor assay measured using smartphone raw accelerometer
 #' and gyroscope sensors.
 #' 
+#' The kinetic tremor assay (also known as the finger/hand to nose test)
+#' entails participants holding the mobile device
+#' in their hand (either right or left) with both the mobile device and the
+#' participants elbow at nose level. The participant then moves the mobile device
+#' away from the nose, with both mobile device and elbow parallel to the ground
+#' and the elbow joint acting as an axis of rotation. When the arm is fully extended,
+#' the participant moves the mobile device back to the nose. This happens in a 
+#' continuous motion and the motion is repeated for approximately 10 seconds.
+#' 
 #' @param accelerometer_data An \code{n} x 4 data frame with columns \code{t}, \code{x},
 #' \code{y}, \code{z} containing accelerometer measurements. Here \code{n} is the
 #' total number of measurements, \code{t} is the timestamp of each measurement, and

R/get_tremor_features.R

@@ -4,6 +4,15 @@
 #' and postural tremor assays measured using smartphone raw accelerometer
 #' and gyroscope sensors.
 #' 
+#' The resting tremor assay entails participants holding the mobile device
+#' in their hand (either right or left) while resting that hand in their lap
+#' for approximately 10 seconds.
+#' 
+#' The postural tremor assay entails participants holding the mobile device
+#' in their hand (either right or left) while keeping their arm extended --
+#' the arm parallel to the ground and perpindicular to the front of the body --
+#' for approximately 10 seconds.
+#' 
 #' @param accelerometer_data An \code{n} x 4 data frame with columns \code{t}, \code{x},
 #' \code{y}, \code{z} containing accelerometer measurements. Here \code{n} is the
 #' total number of measurements, \code{t} is the timestamp of each measurement, and

R/get_walk_features.R

@@ -2,6 +2,8 @@
 #' 
 #' A convenience wrapper for extracting interpretable features from the
 #' walk assay measured using smartphone raw accelerometer and gyroscope sensors.
+#' The walk assay entails participants walking in a straight line for
+#' approximately 20 steps with the mobile device in their pocket or in a bag.
 #' 
 #' @param accelerometer_data An \code{n} x 4 data frame with columns \code{t}, \code{x},
 #' \code{y}, \code{z} containing accelerometer measurements. Here \code{n} is the