7 Tricks and tips
Learning resources
R Markdown
One of the authors of the bookdown package that we are using to make this manual wrote a book about R Markdown: https://bookdown.org/yihui/rmarkdown/.
It’s a great resource, and it gets updated regularly unlike the printed book.
knitr
knitr is one of the engines that turns RMarkdown into HTML, PDF, and other outputs.
By engine we mean it’s an R package.
The package also let’s us create ‘chunks’ of R code.
Make code chunk with {r} formatting
Here is how to make a code chunk appear with the formatting you need to type it into an R Markdown document.
To see what this looks like in the R Markdown document, you have to view the code.
```{r, out.width="100%", fig.align="center", fig.cap="Fig 1"}
knitr::include_graphics("path/to/img_file")
```Embed a video
```{r, echo=FALSE, out.width="100%", fig.align="center", fig.cap="Data Sharing and Management Snafu in 3 Short Acts: https://youtu.be/66oNv_DJuPc"}
knitr::include_url("https://www.youtube.com/embed/66oNv_DJuPc")
```And here is how that will look in the document.
I’ve added echo=FALSE to the knitr parameters so that the chunk itself doesn’t appear.
Figure 7.1: Data Sharing and Management Snafu in 3 Short Acts: https://youtu.be/66oNv_DJuPc
It’s good practice to put the URL to the video in the figure caption. That way if the embedding fails, you have a fallback. Also, it’s good academic practice to site all sources.
Notice that the URL for the embedded video is slightly different from the video’s landing page.
The landing page URL has https://youtu.be/66oNv_DJuPc while the embedded video has https://www.youtube.com/embed/66oNv_DJuPc.
The video’s identifier (66oNv_DJuPc) is the same in both.