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@numericalguy It feels that rmarkdown has more in line with Jupyter notebooks, with a focus on creating documents powered by data and code. PreTeXt is more about semantic expression of static documents, particularly textbooks, with an emphasis on versatility and acessibility.
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@numericalguy It's much easier to author Markdown, and by extension rMarkdown. But the structure of PreTeXt XML means it's much easier to do more things with your document once written (e.g. take just the exercises from chapter 4 and create a solutions manual).