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Getting and Cleaning Data

Data source variables

Original data and experiment description

The experiments have been carried out with a group of 30 volunteers within an age bracket of 19-48 years. Each person performed six activities (WALKING, WALKING_UPSTAIRS, WALKING_DOWNSTAIRS, SITTING, STANDING, LAYING) wearing a smartphone (Samsung Galaxy S II) on the waist. Using its embedded accelerometer and gyroscope, we captured 3-axial linear acceleration and 3-axial angular velocity at a constant rate of 50Hz. The experiments have been video-recorded to label the data manually. The obtained dataset has been randomly partitioned into two sets, where 70% of the volunteers was selected for generating the training data and 30% the test data.

The sensor signals (accelerometer and gyroscope) were pre-processed by applying noise filters and then sampled in fixed-width sliding windows of 2.56 sec and 50% overlap (128 readings/window). The sensor acceleration signal, which has gravitational and body motion components, was separated using a Butterworth low-pass filter into body acceleration and gravity. The gravitational force is assumed to have only low frequency components, therefore a filter with 0.3 Hz cutoff frequency was used. From each window, a vector of features was obtained by calculating variables from the time and frequency domain.

Aim of our analysis is to normalize and clean data, only focusing on mean and standard deviation measurements

Study design : Data collecting process, transformations

First, we're getting data from Human Activity Recognition Using Smartphones Data Set

  • it is copied and unzipped in ./data directory

Original dataset is split into 2 distinct datasets (one for training (70% of original data), the other for testing (30% remaining))

Our process consists in:

  • Getting data
    • This step takes several minutes
    • First of all
      • subject_train.txt and subject_train.txt : Individuals participating in tests (represented by a number)
        • File is CSV fixed with columns (containing 561 measure columns)
      • y_train.txt and y_test.txt : Performed and measured activities
        • Single column CSV file
      • X_train.txt and X_test.txt : Measurements
        • Single column CSV file
  • Merging dataset
    • Traning and Test datasets have been merged for all 3 type of files
    • At this step, we join 3 data frame into a single one
  • Only keeping mean and standard deviation
    • Columns are then analyzed and filter to only have a data frame containing subject, activity, and all mean and standard deviation measurements
  • Creating a factor for measured activities to ease dataset exploration
    • activity feature is then converted to a factor containing label of all 6 activities
      • Factor levels: "WALKING", "WALKING_UPSTAIRS", "WALKING_DOWNSTAIRS", "SITTING", "STANDING", "LAYING"
  • Labelize all features
    • All 68 features are labelized for easy understanding of data
  • Generate final tidydata
    • Grouped by subject and activity
    • Get average values for each mean and standard deviation measurements

For step by step and scripts description, please consult our README.md file

CodeBook : Tidy dataset description - Features

Tidydata

The tidydata set is a text csv file (generated through write.table() function)

  • Filename: tidydata.txt
    • File contains header
    • ';' separated file
    • '"' quote charater
  • Columns : 68 variables - subject, activity, and all 66 mean or standard deviation for each measurement
  • Rows : 180 observations (plus header line)

Features

  • 'subject'
    • Subject (individual) participating to study.
    • Field does not contain real name but an Id to preserve anonymous
      • Its range is from 1 to 30
    • Type : integer
    • Unit : NA, identifier
  • 'activity'
    • Measured activity
    • Type : Factor
    • Factor levels:
      • "WALKING"
      • "WALKING_UPSTAIRS"
      • "WALKING_DOWNSTAIRS"
      • "SITTING"
      • "STANDING"
      • "LAYING"
    • Unit : String factor
  • 'tBodyAccMeanX'
    • Body Acceleration mean - X axis
    • Unit : 'g' gravity, acceleration
  • 'tBodyAccMeanY'
    • Body Acceleration mean - Y axis
    • Unit : 'g' gravity, acceleration
  • 'tBodyAccMeanZ'
    • Body Acceleration mean - Z axis
    • Unit : 'g' gravity, acceleration
  • 'tBodyAccStdX'
    • Body acceleration standard deviation - X axis
    • Unit : 'g' gravity, acceleration
  • 'tBodyAccStdY'
    • Body acceleration standard deviation - Y axis
    • Unit : 'g' gravity, acceleration
  • 'tBodyAccStdZ'
    • Body acceleration standard deviation - Z axis
    • Unit : 'g' gravity, acceleration
  • 'tGravityAccMeanX'
    • Gravity acceleration mean - X axis
    • Unit : 'g' gravity, acceleration
  • 'tGravityAccMeanY'
    • Gravity acceleration mean - Y axis
    • Unit : 'g' gravity, acceleration
  • 'tGravityAccMeanZ'
    • Gravity acceleration mean - Z axis
    • Unit : 'g' gravity, acceleration
  • 'tGravityAccStdX'
    • Gravity acceleration standard deviation - X axis
    • Unit : 'g' gravity, acceleration
  • 'tGravityAccStdY'
    • Gravity acceleration standard deviation - Y axis
    • Unit : 'g' gravity, acceleration
  • 'tGravityAccStdZ'
    • Gravity acceleration standard deviation - Z axis
    • Unit : 'g' gravity, acceleration
  • 'tBodyAccJerkMeanX'
    • Body acceleration jerk mean - X axis
    • Unit : 'g' gravity, acceleration
  • 'tBodyAccJerkMeanY'
    • Body acceleration jerk mean - Y axis
    • Unit : 'g' gravity, acceleration
  • 'tBodyAccJerkMeanZ'
    • Body acceleration jerk mean - Z axis
    • Unit : 'g' gravity, acceleration
  • 'tBodyAccJerkStdX'
    • Body acceleration jerk standard deviation - X axis
    • Unit : 'g' gravity, acceleration
  • 'tBodyAccJerkStdY'
    • Body acceleration jerk standard deviation - Y axis
    • Unit : 'g' gravity, acceleration
  • 'tBodyAccJerkStdZ'
    • Body acceleration jerk standard deviation - Z axis
    • Unit : 'g' gravity, acceleration
  • 'tBodyGyroMeanX'
    • Body gyro (angular velocity vector) mean - X axis
    • Unit : radians/second
  • 'tBodyGyroMeanY'
    • Body gyro (angular velocity vector) mean - Y axis
    • Unit : radians/second
  • 'tBodyGyroMeanZ'
    • Body gyro (angular velocity vector) mean - Z axis
    • Unit : radians/second
  • 'tBodyGyroStdX'
    • Body gyro (angular velocity vector) standard deviation - X axis
    • Unit : radians/second
  • 'tBodyGyroStdY'
    • Body gyro (angular velocity vector) standard deviation - Y axis
    • Unit : radians/second
  • 'tBodyGyroStdZ'
    • Body gyro (angular velocity vector) standard deviation - Z axis
    • Unit : radians/second
  • 'tBodyGyroJerkMeanX'
    • Body gyro (angular velocity vector) jerk mean - X axis
    • Unit : radians/second
  • 'tBodyGyroJerkMeanY'
    • Body gyro (angular velocity vector) jerk mean - Y axis
    • Unit : radians/second
  • 'tBodyGyroJerkMeanZ'
    • Body gyro (angular velocity vector) jerk mean - Z axis
    • Unit : radians/second
  • 'tBodyGyroJerkStdX'
    • Body gyro (angular velocity vector) jerk standard deviation - X axis
    • Unit : radians/second
  • 'tBodyGyroJerkStdY'
    • Body gyro (angular velocity vector) jerk standard deviation - Y axis
    • Unit : radians/second
  • 'tBodyGyroJerkStdZ'
    • Body gyro (angular velocity vector) jerk standard deviation - Z axis
    • Unit : radians/second
  • 'tBodyAccMagMean'
    • Body acceleration magnitude mean
    • Unit : 'g' gravity, acceleration
  • 'tBodyAccMagStd'
    • Body acceleration magnitude standard deviation
    • Unit : 'g' gravity, acceleration
  • 'tGravityAccMagMean'
    • Gravity acceleration magnitude mean
    • Unit : 'g' gravity, acceleration
  • 'tGravityAccMagStd'
    • Gravity acceleration magnitude standard deviation
    • Unit : 'g' gravity, acceleration
  • 'tBodyAccJerkMagMean'
    • Body acceleration magnitude jerk mean
    • Unit : 'g' gravity, acceleration
  • 'tBodyAccJerkMagStd'
    • Body acceleration magnitude jerk standard deviation
    • Unit : 'g' gravity, acceleration
  • 'tBodyGyroMagMean'
    • Body gyro (angular velocity vector) magnitude mean
    • Unit : radians/second
  • 'tBodyGyroMagStd'
    • Body gyro (angular velocity vector) magnitude standard deviation
    • Unit : radians/second
  • 'tBodyGyroJerkMagMean'
    • Body gyro (angular velocity vector) jerk magnitude mean
    • Unit : radians/second
  • 'tBodyGyroJerkMagStd'
    • Body gyro (angular velocity vector) jerk magnitude standard deviation
    • Unit : radians/second
  • 'fBodyAccMeanX'
    • Body acceleration mean - X axis
    • Unit : 'g' gravity, acceleration
  • 'fBodyAccMeanY'
    • Body acceleration mean - Y axis
    • Unit : 'g' gravity, acceleration
  • 'fBodyAccMeanZ'
    • Body acceleration mean - Z axis
    • Unit : 'g' gravity, acceleration
  • 'fBodyAccStdX'
    • Body acceleration standard deviation - X axis
    • Unit : 'g' gravity, acceleration
  • 'fBodyAccStdY'
    • Body acceleration standard deviation - Y axis
    • Unit : 'g' gravity, acceleration
  • 'fBodyAccStdZ'
    • Body acceleration standard deviation - Z axis
    • Unit : 'g' gravity, acceleration
  • 'fBodyAccJerkMeanX'
    • Body acceleration jerk mean - X axis
    • Unit : 'g' gravity, acceleration
  • 'fBodyAccJerkMeanY'
    • Body acceleration jerk mean - Y axis
    • Unit : 'g' gravity, acceleration
  • 'fBodyAccJerkMeanZ'
    • Body acceleration jerk mean - Z axis
    • Unit : 'g' gravity, acceleration
  • 'fBodyAccJerkStdX'
    • Body acceleration jerk standard deviation - X axis
    • Unit : 'g' gravity, acceleration
  • 'fBodyAccJerkStdY'
    • Body acceleration jerk standard deviation - Y axis
    • Unit : 'g' gravity, acceleration
  • 'fBodyAccJerkStdZ'
    • Body acceleration jerk standard deviation - Z axis
    • Unit : 'g' gravity, acceleration
  • 'fBodyGyroMeanX'
    • Body gyro (angular velocity vector) mean - X axis
    • Unit : radians/second
  • 'fBodyGyroMeanY'
    • Body gyro (angular velocity vector) mean - Y axis
    • Unit : radians/second
  • 'fBodyGyroMeanZ'
    • Body gyro (angular velocity vector) mean - Z axis
    • Unit : radians/second
  • 'fBodyGyroStdX'
    • Body gyro (angular velocity vector) standard deviation - X axis
    • Unit : radians/second
  • 'fBodyGyroStdY'
    • Body gyro (angular velocity vector) standard deviation - Y axis
    • Unit : radians/second
  • 'fBodyGyroStdZ'
    • Body gyro (angular velocity vector) standard deviation - Z axis
    • Unit : radians/second
  • 'fBodyBodyAccMagMean'
    • Body body accelation magnitude mean
    • Unit : 'g' gravity, acceleration
  • 'fBodyBodyAccMagStd'
    • Body body accelation magnitude standard deviation
    • Unit : 'g' gravity, acceleration
  • 'fBodyBodyAccJerkMagMean'
    • Body body accelation jerk magnitude mean
    • Unit : 'g' gravity, acceleration
  • 'fBodyBodyAccJerkMagStd'
    • Body body accelation jerk magnitude standard deviation
    • Unit : 'g' gravity, acceleration
  • 'fBodyBodyGyroMagMean'
    • Body body gyro (angular velocity vector) magnitude mean
    • Unit : radians/second
  • 'fBodyBodyGyroMagStd'
    • Body body gyro (angular velocity vector) magnitude standard deviation
    • Unit : radians/second
  • 'fBodyBodyGyroJerkMagMean'
    • Body body gyro (angular velocity vector) jerk magnitude mean
    • Unit : radians/second
  • 'fBodyBodyGyroJerkMagStd'
    • Body body gyro (angular velocity vector) jerk magnitude standard deviation
    • Unit : radians/second