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The function knit_deleting_service_files() helps avoid (R) Markdown knitting errors caused by files and folders remaining from previous knittings (e.g., manuscript.tex, ZHJhZnQtYXBhLlJtZA==.Rmd, manuscript.synctex.gz). The only obligatory argument for this function is the name of a .Rmd or .md file. The optional argument is a path to a directory containing this file. The function first offers szeleting potential service files and folders in the directory. A confirmation is required in the console (see screenshot below). Next, the document is knitted. Last, the function offers deleting potential service files and folders again.
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Three methods for balancing reproducibility and efficiency in R Markdown documents: embedding fast code directly, sourcing long but fast code from external scripts, and pre-running slow code while loading saved results.
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Three troubleshooting tips for resolving knitting errors in R Markdown: closing PDF reader windows, deleting service files with .tex and other extensions, and removing auto-generated appendix code chunks.
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Based on Michael Frank's presentation, three methods for collaborating on R Markdown documents: using GitHub for version control, copying text to trackable editors while preserving code, or knitting to Word/PDF formats.
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This document is part of teaching materials created for the workshop 'Open data and reproducibility v2.1: R Markdown, dashboards and Binder', delivered at the CarpentryCon 2020 conference. The purpose of this specific document is to practise R Markdown, including basic features such as Markdown markup and code chunks, along with more special features such as cross-references for figures, tables, code chunks, etc. Since this conference was originally going to take place in Madison, let's look at some open data from the City of Madison.