I wish to use in line R code as part of a header in a r markdown file. However when i knit the file the fonts used on the header are different. How can I ensure the fonts are the same. A simple example is below.
`r 1+1` Header
-------------------------
You can wrap content in backticks to denote r code inline, as follows:
## Title `r 1+1` Header
Without a reproducible example it is hard to be precise, but one thing you might want to consider is to use the results="asis" chunk option in your R code so that the results are not wrapped in a code markup block. I am not sure how this works with inline commands, but you could use a regular R block and have it create the entire header from the R code, something like:
```r results="asis"
cat('# ', 1+1, " Header")
```
Related
In bookdown how can I include R code within a custom block, whereby the R code will be parsed. Like in the example below the r code (plot function) will not be parsed. Is there a way to make this work?
```{block2 type='test'}
some text here
plot(1:10)
```
You can use text references as a hack. This seems to work as long as valid_markdown contains a single paragraph/line of markdown.
```{r}
valid_markdown <- your_function()
```
(ref:my_hack) `r valid_markdown`
```{block2, type="block"}
(ref:my_hack)
```
This hack works fine with text. Getting it work with plots will require a bit more work.
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 trying to insert a pdf image into an r markdown file. I know it is possible to insert jpg or png images. I was just wondering if it is also possible to insert a pdf image. Thanks very much!
If you are just trying to insert an image that has been exported from, for example, some R analysis into a pdf image, you can also use the standard image options from the knitr engine.
With something like:
```{r, out.width="0.3\\linewidth", include=TRUE, fig.align="center", fig.cap=c("your caption"), echo=FALSE}
knitr::include_graphics("./images/imagename.pdf")
```
Unfortunately you can't specify the initial dimensions of your image output (fig.width and fig.height), which you would need to pre-define in your initial output, but you can specify the ultimate size of the image in your document (out.width). As noted below, however, this is limited to scaling down.
You could also of course leave out the initial directory specification if your files are in the same working directory. Just be aware of operating system differences in specifying the path to the image.
An alternative method is to use Markdown syntax noted by #hermestrismegistus on this post:
{width=65%}
This can also be collected for multiple images side-by side:
{width=33%}{width=33%}{width=33%}
Edit:
After working more extensively with in-text referencing, I have found that using r chunks and the include_graphics option to be most useful. Also because of the flexibility in terms of image alignment (justification).
As an example:
```{r image-ref-for-in-text, echo = FALSE, message=FALSE, fig.align='center', fig.cap='Some cool caption', out.width='0.75\\linewidth', fig.pos='H'}
knitr::include_graphics("./folder/folder/plot_file_name.pdf")
```
The reference can later be used in-text, for example, Figure \#ref(fig:image-ref-for-in-text) illustrates blah blah.
Some important things to note using this format:
You can only expand PDF images via a code chunk up to the out.width and out.height conditions set in the original .pdf file. So I would recommend setting them slightly on the larger side in your original image (just note that any chart text will scale accordingly).
The in-text reference code (in this case image-ref-for-in-text) CANNOT contain any underscores (_) but can contain dashes (-). You will know if you get this wrong by an error message stating ! Package caption Error: \caption outside float.
To stop your plots drifting to the wrong sections of your document, but in a way that unfortunately will generate some white space, the above example includes fig.pos='H'. Where H refers to "hold" position. The same can be achieved for the former Markdown option by placing a full-stop (period .) immediately after the last curly bracket.
Example:
{width=75%}.
Unfortunately, this latter option results in some unsightly full-stops. Another reason I prefer the include_graphics option.
Sorry, I found that there is a similar post before:
Add pdf file in Rmarkdown file
Basically, I can use something like below works well for the html output:
<img src="myFirstAlignment2.pdf" alt="some text" width="4200" height="4200">
And something like below works well for the pdf output:
(1)possible solution
\begin{center} <br>
\includegraphics[width=8in]{myFirstAlignment2.pdf} <br>
\end{center}
(2)possible solution
The myFirstAlignment2.pdf should be replaced with path\myFirstAlignment2.pdf if the pdf file is not in your working directory.
In relation to the comment of the best answer, there is a way to use the second option, and the output not come out tiny.
Use the following syntax below with the height being a large number. Having text in the brackets is necessary for it to work.
{width=100% height=400}
None of the answers outlined worked well for me in terms of sizing the pdf, so adding another answer using the code chunk options for out.height and out.width to control the size:
```{r out.height = "460px", out.width='800px', echo=F}
knitr::include_graphics("./images/imagename.pdf")
```
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 am looking to render a 2 column report as a stand-alone HTML file using R and Markdown only. I am very new to markdown within R, so I need some help with the layout.
The image below displays the layout of what I would like to render using RMarkdown.
The HTML is on the left hand side and some data along the right hand side.
The raw HTML and the example dataframe can be found here:
Note: I used the pander package to create the table using the following command:
pandoc.table(df, style="rmarkdown")
Although this is not a perfect solution, it is a place to get started: Yihui recently added HTML templates to knitr, and docco is a example two-column page: http://cran.r-project.org/web/packages/knitr/vignettes/docco-classic.html .
You can see the template file used for that output here: https://github.com/yihui/knitr/blob/master/inst/misc/docco-template.html.
Alternatively, you can try placing inline HTML right in your R Markdown chunks, but this is terribly hacky and you might feel like a bad person for doing it. We use results='asis' so that the cated HTML is rendered properly, and out.extra='' to ensure that the HTML used to generate the figures is generated right away, rather than the Markdown language for image inclusion.
```{r two-column, results='asis', echo=FALSE, out.extra=''}
library(knitr)
cat("<table class='container'><tr>")
cat("<td>")
plot( rnorm(10) )
cat("</td>")
cat("<td>")
kable( rnorm(10), format="html" )
cat("</td>")
cat("</tr></table>")
```
Calling knit on that should produce a 2 column layout for that particular chunk (although without any nice styling for the table; you might add that in yourself with some CSS)