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I would like to know if there is any reference book about this topic.
I found the "They Say/ I say" book useful to write the Thesis discussion, but feel I need some guidelines on how to tackle this other part of the Thesis.
The best resource for how to write a thesis is to see other successful thesis that were written in the last 10 years, in your field, from your or other universities .
Search in Google Scholar; or check your university's library where they hold all the Ph.D. thesis done at your university.
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