I need to expose a markdown syntax, for figures, i.e. "! [caption] (imagepath)".
If you write it as-is, it will be interpreted and rendered by markdown.
Same appears to be true, if you generate the syntax from an R chunk.
What is the best way to achieve this result in a R markdown file ?
r '' # works but displays nothing
r '! [caption] (imagepath)' # works, based on a visible hack as spaces are not so easy to capture for human eyes
Actual result with visual hack is "! [caption] (imagepath)". Perfect result should be the same without spaces and without markdown interpretation.
You can put it in backticks:
``
You can easily make a whole markdown chunk not to be interpreted by adding:
eval = FALSE to it.
so
{r ,eval=FALSE}
''
creates the output:
[1] ""
Related
I guess my question is a potential if not probable duplicate of How to use inline R code in a bookdown theorem or example environment. It's been nearly 3 years since this question was asked, so a refresh might be welcome in any case, all the more given #YiHui's comment: "That is not possible with bookdown (at least for now)"?
Background: I am trying to use #YiHui bookdown package to produce a book with lecture slides (see creating accompanying slides for bookdown project). A key feature for this purpose is to be able to use conditional formatting, such as eval = (out_type=="beamer"). The issue I am facing is therefore to be able to add code chunks or inline R code inside bookdown custom environments (see https://bookdown.org/yihui/bookdown/markdown-extensions-by-bookdown.html#theorems and https://bookdown.org/yihui/bookdown/custom-blocks.html). I would love to get the following to compile properly. Is there a solution? Would a hook work (see https://yihui.org/knitr/hooks/)? There is a hack that works for forcing pandoc to parse inside a latex environment, but i do no think it applies here. Would a lua filter work (I have no idea how to use this)?
En passant, I am also surprised to see $\digamma$ showing up properly in the html output, but not in the pdf output, though it is parsed correctly in the tex file. The amssymb package is loaded and it's supposedly defined in there - what am I missing?
Much appreciated any help on this. Here is a MWE - I just edited chapter 4 from the default bookdown project. You can simply replace the contents of the file 03-method.Rmd with the following:
# Methods
We describe our methods in this chapter.
So here is a theorem to prove 1+1 = `r 1+1`.
```{theorem, echo=TRUE}
we want to show that in R, 1+1 = 2.
We also wonder why `$\digamma$` ($\digamma$) not showing.
Shows in the html output only, not pdf.
But when I recompile the tex file produced by bookdown - shows up just fine!!
Indeed, is defined correctly from `\usepackage{amssymb}`.
```
```{proof, echo=TRUE}
- If I am not mistaken, I cannot get an Rmarkdown style list to work either in the proof environment.
- Well, this is where i would like to be able to use inline code.
- we use r to compute 1+1: `r 1+1`.
- Does not work.
- Just shows verbatim inline code.
```
With the current development version of bookdown:
remotes::install_github('rstudio/bookdown')
you can write theorems in Pandoc's fenced Divs, e.g.,
# Methods
We describe our methods in this chapter.
So here is a theorem to prove 1+1 = `r 1+1`.
::: {.theorem}
we want to show that in R, 1+1 = 2.
We also wonder why `$\digamma$` ($\digamma$) not showing.
Shows in the html output only, not pdf.
But when I recompile the tex file produced by bookdown - shows up just fine!!
Indeed, is defined correctly from `\usepackage{amssymb}`.
:::
::: {.proof}
- If I am not mistaken, I cannot get an Rmarkdown style list to work either in the proof environment.
- Well, this is where i would like to be able to use inline code.
- we use r to compute 1+1: `r 1+1`.
- Does not work.
- Just shows verbatim inline code.
:::
However, please note that this new syntax is not supported for beamer output yet.
I'm generating a knitr (focusing on .Rmd files) manual for a project and wanted to embed a code chunk that actually displays the " ``` " marks as well as the internal chunk syntax. E.g.
``` {r sample, eval= FALSE}
Code example
```
So basically the exact visual you see above. Any thoughts on how to do this?
You can do this by using four spaces before your code as follows:
So this:
Becomes this:
There also is this SO-meta discussion on how to escape this backtick in Markdown
If you mean how to display the three backticks, the answer is "indent by 4 spaces" (see Pandoc's four-space rule)". If you mean how to display a literal knitr code chunk, the answer has been given by knitr FAQ #8.
I am using knit()and markdownToHTML() to automatically generate reports.
The issue is that I am not outputting plots when using these commands. However, when I use RStudio's Knit HTML button, the plots get generated. When I then use my own knit/markdown function, it suddenly outputs the plot. When I switch to another document and knit that one, the old plot appears.
Example:
```{r figA, result='asis', echo=TRUE, dpi=300, out.width="600px",
fig=TRUE, fig.align='center', fig.path="figure/"}
plot(1:10)
```
Using commands:
knit(rmd, md, quiet=TRUE)
markdownToHTML(md, html, stylesheet=style)
So I guess there are 2 questions, depending on how you want to approach it:
What magic is going on in Rstudio's Knit HTML?
How can I produce/include without depending on RStudio's Knit HTML button?
The only issue I see here is that this doesn't work when you have the chunk options {...} spanning two lines. If it's all on one line, it works fine. Am I missing something?
See how this is not allowed under knitr in the documentation:
Chunk options must be written in one line; no line breaks are allowed inside chunk options;
RStudio must handle linebreaks in a non-standard way.
This is really embarrassing, I really thought I read the documentation carefully:
include: (TRUE; logical) whether to include the chunk output in the
final output document; if include=FALSE, nothing will be written into
the output document, but the code is still evaluated and plot files
are generated if there are any plots in the chunk, so you can manually
insert figures; note this is the only chunk option that is not cached,
i.e., changing it will not invalidate the cache
Simply adding {..., include=TRUE} did the trick. I would say it would be a pretty sensible default though.
In R, using knitr, is there a way to prevent line breaks in the HTML when results='hide' and echo=FALSE?
In this case:
First I do this,
```{r results='hide', echo=FALSE}
x=4;x
```
then I do that.
I get:
First I do this,
then I do that.
with both a break and an extra line between.
I'd like to get:
First I do this, then I do that.
instead.
Generally speaking, I'd like for code chunks to not insert new lines so that markdown is free to eat the one after the first line of text.
Thanks,
I assume you're creating an HTML document from an R Markdown document. In that case, you can use the inline R code capability offered by knitr by using the ` characters starting with the letter r.
Example:
In your R Markdown, write:
First I do this,`r x=4` then I do that. I can call x by doing `r x`.
And as output, you get:
First I do this, then I do that. I can call x by doing 4.
Note that in my example, I evaluated the variable x, but if you do not want to evaluate it, you do not have to. The variable x should still be assigned a value of 4 from the
`r x=4`
part of the R Markdown.
This is Inline R Code, and is documented here under the section "Inline R Code".
EDIT:
Note that Inline R Code has properties that are analogous to "echo=FALSE". And if you want to hide the results from inline R code, you can use base R functions to hide the output. See this question.
Try something like:
``` {r , results="asis", echo=F, eval=T}
if(showMe){
cat("printed")
} else {
cat("<!-- no break line -->")
}
```
I have written some custom R code that wraps a third-party binary. One of that binary's features is to produce a LaTeX document with a figure and some text. One of my code's features is to parse that document and return the LaTeX code for the figure.
The goal is to embed my R code in an Rnw document. When Sweave is run, I want my code to produce a document using the third-party binary, then extract the LaTeX code for the figure and drop it into Sweave's .tex output. Then when I run latex against that output the figure that was generated by the third-party binary should appear, automagically and nicely formatted, in my report.
Instead, the LaTeX code is printed out like this:
[1] " %\\begin{landscape}"
[1] " \\begin{center}"
[1] "\\psset{linecolor=black,tnsep=2pt,tnheight=0cm,treesep=.3cm,levelsep=40pt,radius[1] "% \\def\\psedge#1#2{\\ncangle{#2}{#1}}"
[1] "% \\pstree[treemode=R]"
[1] " \\pstree{\\Tcircle{ 1 }~[tnpos=l]{\\shortstack[r]{nwsprec\\\\$\\leq$ 1.93}}}{"
And so on...
Is there a way to make Sweave treat R's output as LaTeX code?
Thanks in advance.
-Wesley
I figured it out! The Sweave code needs to look like this:
<<echo=False, results=tex, include=True>>=
...R code goes here...
#
Where the option results=tex is the crucial change that tells Sweave to interpret the output from R as LaTeX code.
And to get rid of the quotes and line numbers, I needed to use cat command in R rather than print. Specifically, I changed print(line) to cat( paste(line, "\n", sep='') ).