Tables

Here’s some more code working with tables with different functions.

as_tibble(mtcars) # to glimpse

And now using DT.

mtcars %>% 
  DT::datatable()

No go. 🙁¹

How about htmlTable()?

library(htmlTable)
htmlTable(mtcars)

OK, so that works. How about knitr::kable()?

knitr::kable(mtcars, caption = "This is the `mtcars` dataset.")

Looks nice.

Alert notes and warnings

The theme I’m using, academic, has hooks for alerts. The syntax looks like this:

{{% alert note %}}
Here is a tip or note...
{{% /alert %}}

{{% alert warning %}}
Here is a warning note...
{{% /alert %}}

And here are the results.

Tweets

It is sometimes useful to include Twitter cards in posts. Here’s a tweet card using the blogdown::shortcode() command:

blogdown::shortcode('tweet', '842100683650273281')

Five Things You Didn’t Realize Were Funded by the National Endowment for the Humanities: https://t.co/ZsDhqDRJQD

— Rob Townsend (@rbthisted) March 15, 2017

Plotting

Let’s make a simple plot and see where the image file ends up.

mtcars %>% 
  ggplot(aes(x = mpg, y = hp)) +
  geom_point() +
  geom_smooth(method = "lm")

Figure 1: Basic plot using ggplot2.

Plots are generated and then copied to the /static/posts/<slug-name>/ directory and the plot is named by the code chunk’s handle.

Images

Adding images from other sources in Rmarkdown documents can be acheived through markdown directly with this basic syntax.

![](../path/image.png)

The path in Hugo for static images makes reference to the /post/ directory inside of the /static/ directory. So an image named app.png would be /post/app.png in the syntax but the image will live in the /static/post/ directory.

The problem with this is that you need to copy the image to the /static/img/ or /static/post/ directory. You can choose just make sure to include the correct path in your code. However, this process is a little tedious, I think.

I thought it would be more convenient to use the knitr::include_graphics() function to make reference to an image inside the content/post/ directory and a subdirectory images/ but that does do the copying of the image, like I thought it might. Instead, the image file is not copied to the static/post/ directory, so the path is invalid and the image is not displayed.

knitr::include_graphics("images/tortoise001.png")

However, using the EBImage package from the bioconductor repository, the same behavior as graphics generated by plots applies to the image. In this way the image is copied to the /static/post/ directory and lives in a subdirectory named by the slug of the post –just like plots. This seems to be a bit more complicated to have to load the EBImage library and import the image, but is more convenient in that it organizes images by post and the links are valid.

library(EBImage)
img <- EBImage::readImage(files = "images/tortoise001.png")
display(img)

Figure 2: This is a tortoise generated by EBImage.

Citations

You can even add citations through the citr package which will facilitate creating citations throug the use of the Tools > Addin dropdown menu. Just create a valid path to a .bib bibliography file in the YAML section of the .Rmd document.

---
bibliography: references.bib
---

Load the library and then use the dropdown tool to generate the citation syntax for markdown.

library(citr)

Here’s a citation (Gries 2013)