With reference to the following web site https://msdn.microsoft.com/en-us/library/aa578470.aspx, I have learnt how to house keep the Biztalk tracking database by executing the following command.
declare @dtLastBackup datetime set @dtLastBackup = GetUTCDate()
exec dtasp_PurgeTrackingDatabase 0, 3, 4, @dtLastBackup
To further break it down to simplify this this is my understanding of what the arguments means. The meaning of each argument can be obtained from the link above. But the problems that I have run into when doing this purge is that the database log file will run out of space. I have to shrink the database log to clear the space and re-run it. I don't suppose you can do this in production, so it would be wise to do this together with a DBA.