I would like to figure out how to apply the striped attribute to my pander tables in rmarkdown.
I can't really find it at the online help of the Pander library, and panderOptions doesn't list it either (or I can't find it), neither can I find it at pandoc.table
Hence the question, how can I use Bootstrap table classes on the following code?
```{r}
pander(mtcars)
```
Related
I have a series of .png images that I would like to add notes to in an Rmarkdown document that I am knitting to a .pdf. The basic code for each image looks like this:
```{r certs_coefplot, out.width="100%", fig.cap=fig.4_cap}
knitr::include_graphics("certs_coefplot.png")
```
With beamer slides, I have just inserted some basic latex like this:
\tiny \emph{Notes}: Put Notes here \normalsize
below each code chunk.
But if I try this in the context of a larger document, the notes do not appear below the figure.
A solution involving a custom hook was proposed to a similar question asked here about adding notes to figures in an .Rnw file. In particular, the version where you put the code for the hook at the beginning and then write:
notes = "Notes to explain the plot"
sources = "Explain the sources"
in each chunk seems really convenient.
Is it possible to apply a similar solution an RMarkdown file?
Is there a way to set R markdown so that the chunk name does not get included with the figure caption.
Below is an example. I would like to use "Figure Caption" as the caption instead of "chunkname Figure Caption". I just want to use chunkname as a reference for navigating through the markdown file when editing.
```{r chunkname, fig.cap="Figure Caption"}
knitr::include_graphics("image.png")
```
I was using blogdown. The error was caused by using an underscore in the chunk name.
https://github.com/rstudio/bookdown/issues/336
I'm not sure what the proper etiquette on this site is. Should I remove this post?
Not exactly sure what your other code looks like in the Rmarkdown file, but that is not how Rmarkdown normally works, when I use your Code, I get the outcome you are wanting
Based on the answer to this question, I was able to get 2-column papaja with listings wrapping (rather than overflowing column width). But the listings package turns off various features that help code listings and R output stand out relative to the main text.
A simple solution would be if I could globally change the font faces and/or sizes selectively for code and R output. Is there a way to do that in papaja? I haven't been able to figure this out from papaja or Rmarkdown documentation. Thank you!
When you use the listings package in a papaja (or bookdown) document, what is technically happening is that all code is wrapped into an lstlisting LaTeX environment that comes with its own capabilities of customizing code appearance. Hence, you don't see the syntax highlighting that you would otherwise see if you would not use the listings package. The documentation of the listings package with instructions how to style your code can be found here.
To make use of this, you can extend the YAML header of your papaja document like this:
documentclass : "apa6"
classoption : "jou"
output :
papaja::apa6_pdf:
pandoc_args: --listings
header-includes:
- \lstset{breaklines=true,language=R,basicstyle=\tiny\ttfamily,frame=trB,commentstyle=\color{darkgray}\textit}
Here, I first specify the code's language, and use a tiny monospace font. With frame, I add a frame around the code block, and with commentstyle I set comments in italic and gray.
I am using the MDPI template (from the rticles package), and keen to also use the glossaries packages so I don't have to manually feed all the abbreviation on the appropriate YAML field.
For such, I have loaded the LaTex package glossaries using the header-includes:
header-includes:
\usepackage{inputenc}
\usepackage[acronym, section=section]{glossaries}
\setacronymstyle{long-short}
\makeglossaries
\makeindex
\input{glossary}
after creating several acronyms within the Rmarkdown body, I would be willing to either input the latex commands and have it printed in within the "Abbreviations" section of the template.
Currently, I am able to hack it through the following steps (I am sure there is a better way):
1- keep all the aux files chunk with :
options(tinytex.clean = FALSE)
2- cmd makeglossaries "filename"
3- Raw Latex on Rmarkdown file:
\begin{abbreviations}
\setabbreviationstyle[acronym]{long-short}
\printglossary[type=\acronymtype,title={}]
\end{abbreviations}
However, I would be keen to know if I could insert something on the YAML and use the MDPI formatting.
Alternatively, I could edit the rticles MDPI template (but I am not sure how).
Any ideas?
Cheers,
Include in YAML:
include-after: glossary.tex
I tried without success, but it seems reasonable that this approach might work with a few modifications
I teach an introductory statistics course using R Markdown in RStudio (Server). We have students knit to html_notebooks, and we often have them use inline code to report various elements of their statistical analyses. It'd be really helpful for grading purposes if we could have the result of inline code output in a different color -- that way we could easily see if they were indeed using inline code or if they copy-pasted a number from their output into raw text.
There's a couple of ideas for solutions posted here, but these won't super work in my case. These are introductory students who are generally kinda afraid of RStudio to begin with, so asking them to do anything complicated with text_spec or sprintf will likely cause mild riots. I really need something that won't change students' workflow at all.
I wonder if there's any way to configure things either on the backend in RStudio Server (maybe by messing with knitr?), or through some kind of <style> tag wizardry in the preamble, so that inline code will print its results in a different color.
Thanks!
EDIT: Arthur Berg below has provided something that's almost exactly what I need. Here's a MWE:
---
title: "test knit_hook"
output: html_document
---
```{r, setup, include="FALSE"}
knitr::knit_hooks$set(inline=function(x){paste0("<span style=\"color: #0000FF;\">",
x,"</span>")})
```
`r pi`
The only issue with this is that it doesn't work if I change to html_notebook in the YAML header and thus use the "Preview" button in the RStudio IDE. For external reasons, it's important for us to have the output type as html_notebook. Anyone know how we might modify this to get it to work with html_notebook?
A way to achieve this without changing the workflow too much is to create your own format (e.g. html_notebook2) that is derived from the original but modifies the inline hook of knitr.
To get started you can check out this document.
Basic steps include
Create a new R package
Within this project run usethis::use_rmarkdown_template(). This creates the folder structure for your new format.
Edit skeleton.rmd and template.yaml
Define your format in a R file which has the same name html_notebook2.R(kind of a convention).
The content of the html_notebook2.R file could be
#'#import knitr
set_hooks <- function() {
default_hooks <- knit_hooks$get()
list(
inline = function(x) {
paste0("<span style=\"color: #FF0000;\">", x,"</span>")
})
}
#' #importFrom rmarkdown output_format knitr_options pandoc_options html_notebook
#' #export
html_notebook2 = function() {
output_format(
knitr = knitr_options(knit_hooks = set_hooks()),
pandoc = pandoc_options(to = "html"),
clean_supporting = FALSE,
base_format = html_notebook()
)
}
In the first part we define a new inline hook which only changes the font color.
The second part is the definition of the new format.
After building and installing the package you can create a new rmarkdown document and use output: packagename::html_notebook2 as the output format. All inline code output will be colored red using my code. Here is an example:
---
title: "Inline"
output: cformat::html_notebook2
---
## R Markdown
`r pi`
I created such a package and you can find it on GitHub. Feel free to copy it and rename it (cformat is a pretty lame working title ;) ).
Notice though that your students could change the color manually using HTML/CSS anyways. A way around could be some kind of key generation using a certain rule (unknown to the students obviously). For each inline chunk a key is generated and embedded using
paste0("<span code=", key," style=\"color: #FF0000;\">", x,"</span>")
If a valid key is embedded, the output was generated using R and not simply copied.
For those looking for a fix to a simple R markdown document, adding this line changes the inline output to blue.
knitr::knit_hooks$set(inline=function(x){paste0("<span style=\"color: #0000FF;\">", x,"</span>")})