Requests by PhD assistant to Master's Student - Avoiding an unreasonable request
There are three people involved at least, including the professor. I think the request is not reasonable for the reasons you state. Clearly the junior advisor has expectations, but they seem to be un-doable. 

You have to judge personalities, but I'd suggest trying to see if you can have a meeting very soon with all three of you present. Try to come to an understanding about what can be reasonably done in the time remaining. 

Try to find a backup plan if not all expectations can be met. Don't be shy about saying why such things are unreasonable and that melding your work to the advisors preferred work-flow at such a late date isn't feasible - or even desirable. Your use of R and LaTex seem to be good choices. I don't know why the PhD advisor wants to check your work independently of you and the professor. Maybe you can get an answer to that in a three person meeting. 

My personal opinion is that you have been put in an untenable position. Unfortunately, I have no say or authority in the outcome.