To change the leading characters for the output a knitr chunk in .Rmd has a comment option, like
```{r comment = ""}
1:100
```
Is there a way to set this globally, not separately for every chunk?
opts_knit$set(comment = "")
does not work and I cannot find it anywhere in the documentation.
Use opts_chunk$set() because that is a chunk option; opts_knit is for package options (sorry about the similar names which apparently confused you). See http://yihui.name/knitr/options
Related
Is there any nicer way to display console output without '##' symbol in pdf generated by Rmarkdown
I have tried searching around here and googling for a solution, but I haven't found anything that solves my problem.
In a code chunk at the top of your document, you can write e.g.
knitr::opts_chunk$set(comment = "")
The default is comment = "##".
Use knitr::opts_chunk$set(comment = NA) or {r chunk1, comment = NA} in the chunk options if you don't want to set it globally
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 have a .Rpres file in RStudio. I would like to include code, but not have it run (I am only showing the code to explain how it works). Is it possible to accomplish this (and ensure that it will not produce errors, because it is not running)?
Have you tried eval=FALSE in the knitr code chunk options? e.g.:
```{r eval=FALSE}
print("Don't run me")
```
{r, eval=F, echo=T} will include the R source code in the output file while it is not evaluated
Posting for anyone who may come across this like I have. I've found that for small examples (if you don't want to use chunks), you can also just use back ticks like you would with regular markdown inline, but just don't add the "r" at the beginning:
`plot(cars)`
Will print the code itself, but will not print the plot.
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.
Sounds like it should be a common problem, but I didn't find an obvious trick.
Consider the knitr Rnw file below,
\documentclass[twocolumn, 12pt]{article}
\usepackage{graphicx}
\begin{document}
%\SweaveOpts{dev=pdf, fig.align=center}
\begin{figure*}
<<aaa, fig.width=8, fig.height=5, fig.show=hold>>=
plot(1,1)
#
\end{figure*}
\end{document}
I would like this wide figure to span two columns, using a {figure*} LaTeX environment. Is there a hook for that?
EDIT: wrapping the chunk in figure* gives the following output.
Two facts:
knitr makes everything accessible for you, so LaTeX tricks are often unnecessary;
there is a chunk hook with which you can wrap your chunk results;
A simple-minded solutions is:
knit_hooks$set(chunk = function(x, options) {
sprintf('\\begin{figure*}\n%s\n\\end{figure*}', x)
})
I leave the rest of work to you to take care of more details in options (e.g. when options$fig.keep == 'none', you should not wrap the output in figure*). You may want to see how the default chunk hook for LaTeX is defined in knitr to know better how the chunk hook works.
However, in this case, I tend to write the LaTeX code by myself in the document instead of automatically creating it. After you have got figure*, you may start to think about \caption{} and \label{} (not hard, but I still want to see them in LaTeX).
Not sure about how knitr but for Sweave (and basic latex) there is in fact a trick: have the R code produce a pdf file, and then use standard \includegraphics to pull it in.
So with this:
\documentclass[twocolumn, 12pt]{article}
\usepackage{graphicx}
\begin{document}
%\SweaveOpts{dev=pdf}
<<aaa,fig=FALSE,print=FALSE,echo=FALSE>>=
pdf("mychart.pdf", width=6, height=3)
set.seed(42)
plot(cumsum(rnorm(100)), type='l', main="yet another random walk")
invisible(dev.off())
#
\begin{figure*}
\includegraphics{mychart.pdf}
\end{figure*}
\end{document}
I got the document below (which I then converted from pdf to png):
I also had a similar problem while preparing a figure that should span two columns in a IEEE two-column conference paper.
Setting the chunk hook caused some strange error in my setup.
Even this simple hook: knit_hooks$set(chunk = function(x, options) x)
But after looking into knitr::opts_chunk$get(), I realized that simply setting fig.env="figure*" solves the problem in an elegant way.
Here is how my chunk looks like in an Rnw file:
<<fig1, fig.width=18, fig.height=6, fig.env="figure*">>=
#