Multiple bibliographies using apacite - R Markdown to pdf) - pdf

Novice here so apologise for my gross incompetence. Thanks in advance for any help or support you can offer.
I am using R bookdown to write my thesis, supplemented by some embedded latex to help prepare and format my pdf. It has gone quite well so far however I have now come across an issue that I just can't solve...
My thesis is split into two large sections and each section requires its own bibliography. I have seperate bib files for each bibliography. My problem is that I cannot manage to work out how to get the two bibliographies into my document (using apacite). I have had a look at the latex package documentation for apacite and bibunits but my attempts to follow there examples repeatedly do not work.
If anyone could post a working example of how to achieve this I would be eternally grateful!
Many thanks!

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!Dimension too large when knitting file to PDF using rmarkdown in RStudio

I receiving the following error when I try to knit into a pdf:
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\fb#put#frame ...p \ifdim \dimen# >\ht \#tempboxa
\fb#putboxa #1\fb#afterfra...
It's an extremely long line of code that I need to knit into a pdf (about 5000 lines). A lot of preprocessing data. The output itself is quite small maybe a line or more. Has anyone had this issue with huge blocks of code? If so, could you tell me how you solved it? I'm up for suggestions.
That's a LaTeX framed package error. RMarkdown tries to put all of that code into a single environment (I believe it's a snugshade environment, but I might be wrong), and that environment isn't ready for something that's going to stretch over many pages. The most I managed to get was about 1300 lines which were broken up into 48 pages of code.
The simplest solution would be to break that up into 4 or 5 pieces, but that might not be easy for you to do.
Next simplest might be not to show it as code at all: use echo = FALSE in the code chunk that runs it, and include it some other way (e.g. in a verbatim environment, or using the listings package). With that much code, showing it as a couple of hundred pages of text doesn't really make much sense anyway.

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This seems to be hell lot of work and this goes on multiple times sometimes. Is there any software in current world that makes the task easier? For example, if a text stuck out for grammar errors and suggested alternatives, can I accept the changes to replace old one with new phrase or sentence and also able to blank out the striked text. Please suggest me a tool which really makes my life easier.
You may want to take a look at the following link. It has some good information about version controlling.
http://en.wikibooks.org/wiki/LaTeX/Collaborative_Writing_of_LaTeX_Documents
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If anyone is still interested in this question, there are a bunch of options for formatting comments and for text editor helpers.
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I am trying to simplify a process where I currently use my hand calculations of X & Y Co-Ordinates of each value. Which works fine, but is causing me a lot of pain as I have to do quite a number of PDF's.
I know that I can open a PDF and insert "input fields" within Adobe Acrobat Pro, which it would be great if I could use PHP to connect to those input fields and insert a value from a PHP Form.
WORKFLOW::
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I know this is not a direct answer to your question, but maybe it will save you some time.
We tried doing something similar and ended up abandoning the idea of doing this programatically ourselves. It was much more cost-efficient to just buy this product: http://www.evermap.com/automailmerge.asp?gclid=CPfW44DNsKYCFULNKgodyV6Rnw
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However, a similar (but not exact duplicate) qhestion has been asked here, and you may be able to get ideas from it.
How to do mail merge on top of a PDF?
Your PHP script could generate an FDF that your PDF could import and obtain values from.