R chunk inside LaTeX in an rmarkdown document - r

I am trying to get an R chunk run inside LaTeX code in the following rmarkdown document:
---
title: "Untitled"
output: pdf_document
date: '2022-05-20'
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, results = "hide")
```
\begin{enumerate}
\item
{
```{r}
x <- 2+3
x
```
}
\end{enumerate}
The output is:
But I want:
Could you please help me?
EDIT: I want the R chunk to be both evaluated (but result hidden) and its code shown. I have meanwhile found this solution, but maybe there is a simpler one: https://tex.stackexchange.com/questions/210003/how-can-i-nest-a-code-chunk-within-an-enumerate-environment-when-using-r-markdow

You need this? See here https://bookdown.org/yihui/rmarkdown-cookbook/raw-latex.html
---
title: "Untitled"
output: pdf_document
date: '2022-05-20'
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, results = "hide")
```
```{=latex}
\begin{tabular}{ll}
x <- 2+3\\
x\\
\end{tabular}
```

In any of the following examples, you can substitute a double return instead of \\.
If you are wanting to just show those expressions then do not put it in a code chunk:
---
title: "Untitled"
output: pdf_document
date: '2022-05-20'
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, results = "hide")
```
\begin{enumerate}
\item
{
x <- 2 + 3\\x
}
\end{enumerate}
This will produce:
Otherwise, if you want to evaluate an inline expression use backticks and r:
---
title: "Untitled"
output: pdf_document
date: '2022-05-20'
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, results = "hide")
```
\begin{enumerate}
\item
{
`r x <- 2 + 3; x`
}
\end{enumerate}
Which produces:
Lastly, you can of course combine these two concepts to show the expression and evaluate the value by doing this:
x <- 2 + 3\\
`r x <- 2 + 3; x`
If your expression is more complex, I would recommend having the code chunk outside of your LaTeX for evaluation.
Update
For simpler expressions you could do something like:
```{r, include = F}
exprsn <- "x <- 2 + 3"
```
\begin{enumerate}
\item
{
`r exprsn`\\
`r eval(parse(text = exprsn)); x`
}
\end{enumerate}

Meanwhile, I found this: How can I nest a code chunk within an enumerate environment when using R Markdown?, which inspires the following solution:
---
title: "Untitled"
output:
pdf_document:
highlight: monochrome
date: '2022-05-20'
header-includes:
- \newcommand{\benum}{\begin{enumerate}}
- \newcommand{\eenum}{\end{enumerate}}
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE, results = "hide")
```
\benum
\item
```{r}
x <- 2+3
x
```
\eenum

Related

RMarkdown is not referencing tables

Somehow my RMarkdown document is not crossreferencing tables or figures. Here is a stripped down version of my document.
---
title: "Test"
author: "Me"
date: "01/04/2022"
output: bookdown::pdf_document2
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
var1<-sample(LETTERS)
tab1<-table(var1)
My table is in Table \#ref{tab:tab1}
library(knitr)
kable(tab1, caption="my table")
AS we see in Figure \#ref{fig:plot1}
plot(seq(1,10,1))
You should call your tab1 in the code chunk like this {r tab1}. And use () instead of {} for your #ref. In that case it reference to your figures and tables. You can use the following code:
---
title: "Test"
author: "Me"
date: "01/04/2022"
output: bookdown::pdf_document2
---
My table is in Table \#ref(tab:tab1)
```{r tab1, echo =FALSE}
var1<-sample(LETTERS)
tab1<-table(var1)
library(knitr)
kable(tab1, caption="my table")
```
\newpage
AS we see in Figure \#ref(fig:plot1)
```{r plot1, fig.cap ="plot", echo=FALSE}
par(mar = c(4, 4, .2, .1))
plot(seq(1,10,1))
```
Output:
As you can see on the image, when you click on 1 in will go to your table.

reactable in R markdown `asis` chunk with loop not displayed

I want to create dynamic sections in my R markdown document. For this, I use R chunks with the asis output type. The chunks contain tables created by the reactable package.
I cannot get the tables to print when I create them in a for-loop. I know that one usually must wrap plots or the like within print() in loops, but that had no effect in my case.
How can I get the tables to print?
---
title: "Test"
author: "Test"
date: "29 11 2021"
output: html_document
---
```{r include=FALSE}
library(reactable)
```
```{r results='asis', echo=FALSE}
cat("\n\n## My header 1 \n\n")
reactable(data.frame(test = rnorm(3))) ## This works
```
```{r results='asis', echo=FALSE}
for (i in 1:3) {
cat("\n\n## My header ", i+1, "\n\n")
print(reactable(data.frame(test = rnorm(3)))) ## shows nothing
}
```
I just found out, that reactable uses htmlwidgets under the hood. So one can wrap the result in shiny::tagList() to display it in a loop.
---
title: "Test"
author: "Test"
date: "29 11 2021"
output: html_document
---
```{r include=FALSE}
library(reactable)
```
```{r results='asis', echo=FALSE}
cat("\n\n## My header 1 \n\n")
reactable(data.frame(test = rnorm(3))) ## This works
```
```{r results='asis', echo=FALSE}
for (i in 1:3) {
cat("\n\n## My header ", i+1, "\n\n")
print(shiny::tagList(reactable(data.frame(test = rnorm(3))))) ## now it works
}
```
You could try to export your react-tables as temporary html-files that you then import as text and delete afterwards.
Here is a solution that worked for me:
---
title: "Test"
author: "Test"
date: "29 11 2021"
output: html_document
---
```{r include=FALSE}
library(reactable)
```
```{r results='asis', echo=FALSE}
cat("\n\n## My header 1 \n\n")
reactable(data.frame(test = rnorm(3))) ## This works
```
```{r results='asis', echo=FALSE}
for (i in 1:3) {
cat("\n\n## My header ", i+1, "\n\n")
htmlwidgets::saveWidget(reactable(data.frame(test = rnorm(3))),
file = 'temp.html')
cat(readr::read_lines('temp.html')[-1])
file.remove('temp.html')
}
```

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How do I go about including subscript in a figure caption when using {r fig.cap=""}?
Mock .Rmd file:
---
output:
pdf_document:
fig_caption: yes
---
```{r setup, include = FALSE}
library(knitr)
```{r fig.cap = "CO2 Concentration", echo = FALSE}
plot(rnorm(100))
I would like to get the 2 in CO2 in subscript. Is fig.cap the best way, or is something better?
You could use standard Markdown syntax
---
output:
pdf_document:
fig_caption: yes
---
This is ^superscript^
This is ~subscript~
```{r fig.cap = 'CO~2~ Concentration', echo = FALSE}
plot(rnorm(100))
```

How to Create Full Width Figures When Using the "twocolumn" "classoption" for Knitr to PDF?

How can one create a full width figure when using the twocolumn class option in knitr / R / RMarkdown / LaTex?
Based on the Knitr documentation, I've tried two approaches. Nothing short of editing the .tex file has worked for me so far.
This:
---
output: pdf_document
classoption: twocolumn
header-includes:
- \usepackage{lipsum}
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
\lipsum[1-2]
```{r fig.env = "figure*", fig.cap = "Test"}
plot(runif(10))
```
\lipsum[3-5]
```{r fig.fullwidth = T}
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Don't forget that you must include a caption for this to work.
---
output: pdf_document
classoption: twocolumn
header-includes:
- \usepackage{lipsum}
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
\lipsum[1-3]
```{r fig.env = "figure*"}
plot(runif(10))
```
\lipsum[2]
```{r fig.env = "figure*", fig.cap = ""}
plot(runif(10))
```
\lipsum[2]

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I have an R markdown file:
---
title: "Untitled"
author: "Me"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
## R Markdown
This is an R Markdown document.
As well as a DiagrammeR/mermaid chart:
graph LR
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Actually it is trivial:
---
title: "Untitled"
author: "Me"
output: html_document
---
```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```
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This is an R Markdown document.
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