The script run_analysis.R is set up to be started in the folder where it is residing. For running it from RStudio (using Windows 7) just double click the file. The data used is in a sub-folder in the folder where the script is residing. The dataset was downloaded from the link below.
https://d396qusza40orc.cloudfront.net/getdata%2Fprojectfiles%2FUCI%20HAR%20Dataset.zip
It was unzipped in the folder where the script is residing. The top folder unzipped are "UCI HAR Dataset". This has subfolders with train and test data. Higlighting the complete script (I do it in RStudio) and click run. It will do the complete task. The code is well documented, explaing the various steps. My main focus has been to make a simple well documented code. It is not optimized for speed.