To install the scripts on your computer, navigate to the MSDTracking folder and run
cp *.R *.py *.sh /usr/local/bin/
To use, simply run
MSD.sh Tracking_file.txt Output_prefix Frame_duration
All the files/plots will be created in your current directory.
To combine several tracking files into one, run the following command with all the files you need to merge
combineFiles.sh Tracking_file.txt name_of_output_file.txt
Running the command in sequence with different tracking files will append trajectories and update the output file.