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I think the question is self-explanatory but to add a bit of a background, I'll be starting my M.Sc. research quite soon and I want to create and maintain a workflow that allows me to devote my time to doing exploratory and inferential analysis, devoting my time to pondering on results, and assuring reproducibility.

With word processing tools like Microsoft Word, I fear I'd spend a great share of time focusing on editing and layout.

With that said, I'd like to know about your experience - bad or good - using rMarkdown to write your thesis? What were the advantages you felt by this choice, and what were the things that slowed you down?

In case you used an alternative "language" and are willing to share your reasons about your choice and how it went for you, please, go ahead.

closed as off-topic by scaaahu, Brian Tompsett - 汤莱恩, Jon Custer, Bob Brown, Enthusiastic Engineer Oct 6 at 13:12

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    I don't know rMarkdown. I've been using LaTeX forever, since it is customary in my field, all journals use it and not using it to write a thesis would raise an eyebrow at my faculty. See What are the advantages or disadvantages of using LaTeX for writing scientific publications. – user68958 Sep 30 at 13:57
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    @corey979 an an FYI, Journal and thesis templates with RMarkdown convert the Markdown code to LaTeX to a PDF. Basically, RMarkdown is an easier version of Sweave. – Richard Erickson Sep 30 at 14:47
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    @RichardErickson I think that's an important point. You can go to markdown to latex easily. Being able to edit the produced latex would be a plus, but that does not mean that your whole thesis should be written in latex, if markdown is easier and simpler for you. – Clément Sep 30 at 15:52
  • @Clément Correct and I agree with you. Also, I would also add you can use LaTeX templates with RMarkdown. Basically, unless somebody loves LaTeX, there is no reason to use it rather than Markdown for most situations. – Richard Erickson Sep 30 at 17:35
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RMarkdown allows you to put your code directly into you manuscript and is functionally an easier to use replacement for Sweave.

The same advantages and disadvantages listed in this previous answer hold for RMarkdown as well.

Last, Chester Ismay has created a thesisdown template, which would be a good starting place for you.

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