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 deleting 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.
As technology and research methods advance, the data sets tend to be larger and the methods more exhaustive. Consequently, the analyses take longer to run. This poses a challenge when the results are to be presented using R Markdown. One has to balance reproducibility and efficiency. On the one hand, it is desirable to keep the R Markdown document as self-contained as possible, so that those who may later examine the document can easily test and edit the code.
When knitting an R Markdown document after the first time, errors may sometimes appear. Three tips are recommended below.
1. Close PDF reader window
When the document is knitted through the ‘Knit’ button, a PDF reader window opens to present the result. Closing this window can help resolve errors.
2. Delete service files
Every time the Rmd is knitted, some service files are created. Some of these files have the ‘.
In a highly recommendable presentation available on Youtube, Michael Frank walks us through R Markdown. Below, I loosely summarise and partly elaborate on Frank's advice regarding collaboration among colleagues, some of whom may not be used to R Markdown (see relevant time point in Frank's presentation).
The first way is using GitHub, which has a great version control system, and even allows the rendering of Markdown text, if the file is given the extension ‘.
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.