**update: Brandon Bertelsen&#39;s answer**:


Brandon&#39;s answer produces the following output. 
It doesn&#39;t produce nice tables or highlight code like Rstudio does, and it crashes on some html files with unicode, so I&#39;m not using it to automate my email reports. 

My current approach is to compile with Rstudio to html, open the html document in chrome, and then copy and paste the html document into gmail. This works pretty well, see this gist: https://gist.github.com/nelsonauner/a68b5a808c232ce7817e


 [![enter image description here][1]][1]


Original question:
========


Is there an easy way to send an R markdown document as the body of an email, so that the body of the email looks similar to the results of using Rstudio&#39;s &quot;Knit HTML&quot; ?  

Here&#39;s a basic reproducible example using `knitr`, `rmarkdown`, and `mailR`
## example.Rmd

    ---
    title: &quot;Report for email&quot;
    output: 
      html_document: 
        self_contained: no
    ---
    
    ```{r}
    summary(cars)  
    ```
    
    You can also embed plots, for example:
    
    ```{r, echo=FALSE}
    plot(cars)
    ```

I&#39;m using `self_contained: no` since the default base64 encoding does not work with `mailR` (recommended by Yihui in [this SO post](https://stackoverflow.com/questions/32520928/in-r-is-there-any-way-to-send-an-rmarkdown-v2-html-file-as-the-body-of-an-email))


## knit_and_send.R
    # compile using rmarkdown
    library(rmarkdown)
    rmarkdown::render(&quot;example.Rmd&quot;)
    
    library(mailR)
    
    send.mail(from = &quot;me@gmail.com&quot;,
              to = &quot;me@gmail.com&quot;,
              subject = &quot;R Markdown Report - rmarkdown&quot;,
              html = T,
              inline = T,
              body = &quot;example.html&quot;,
              smtp = list(host.name = &quot;smtp.gmail.com&quot;, port = 465, user.name = &quot;me&quot;, passwd = &quot;password&quot;, ssl = T),
              authenticate = T,
              send = T)

    #compile using knitr
    library(knitr)
    knit2html(&quot;example.Rmd&quot;,options=&quot;&quot;)
    
    send.mail(from = &quot;me@gmail.com&quot;,
              to = &quot;me@gmail.com&quot;,
              subject = &quot;R Markdown Report - knitr&quot;,
              html = T,
              inline = T,
              body = &quot;example.html&quot;,
              smtp = list(host.name = &quot;smtp.gmail.com&quot;, port = 465, user.name = &quot;me&quot;, passwd = &quot;password&quot;, ssl = T),
              authenticate = T,
              send = T)


Both emails send successfully. 

The knitted email looks like this: 


-----

[![knitted and emailed report][2]][2]

-----

and the rmarkdown email looks like this. (Notice that it also includes a bunch of javascript files--I think I&#39;d have to write some scripts to remove them)

-------

[![enter image description here][3]][3]

----------

But neither of them look as nice as the report that is produced from Rstudio&#39;s &quot;Knit as HTML&quot;, which looks like this: 

[![enter image description here][4]][4]



Any suggestions? 


I think a true fix might involve some postprocessing of the html file that incorporate the css styling in an email-friendly way while removing the javascript files. 

For now, I&#39;ll use the `knitr` package. 

Please let me know if something isn&#39;t clear and I&#39;ll improve the question. 


Relevant SO posts: 

https://stackoverflow.com/questions/32520928/in-r-is-there-any-way-to-send-an-rmarkdown-v2-html-file-as-the-body-of-an-email

https://stackoverflow.com/questions/24346856/mailr-how-to-send-rmarkdown-documents-as-body-in-email


  [1]: http://i.stack.imgur.com/YNuCw.png
  [2]: http://i.stack.imgur.com/83khP.png
  [3]: http://i.stack.imgur.com/avVaD.png
  [4]: http://i.stack.imgur.com/3eGNm.png

How to send R markdown report in body of email?

In knitr, the size option works fine in a `.Rnw` file, the following code generates:

    \documentclass{article}
    
    \begin{document}
    
    &lt;&lt;chunk1, size=&quot;huge&quot;&gt;&gt;=
    summary(mtcars)
    @
    
    
    \end{document}
![rnw][1]

However, I can&#39;t get it to work in Rmarkdown. The following code does not change the font size, as it did in `.rnw` file. The same thing happens when trying to set options with `opts_chunk$set(size=&quot;huge&quot;)`.

Is this the expected behavior? How does one change the chunk code font size? (I mean using knitr options, not by adding `\huge` before the code)


    ---
    title: &quot;Untitled&quot;
    output: pdf_document
    ---
    
    ```{r, size=&quot;huge&quot;}
    summary(mtcars)
    ```

![enter image description here][2]

I am using RStudio Version 0.98.987, knitr 1.6 and rmarkdown 0.2.68.


  [1]: http://i.stack.imgur.com/2iZ4I.png
  [2]: http://i.stack.imgur.com/bHgr0.png

Code chunk font size in Rmarkdown with knitr and latex

I&#39;m aware that R markdown can produce superscripts:

    text^superscript

But is it possible to produce proper subscripts? Or is the only way to do so to cheat and use `LaTeX` math mode:

    $\sf{text_{subscript}}$

The intended final output is HTML.

Producing subscripts in R markdown

I&#39;m wondering if there&#39;s a trick to put the current date in the YAML front-matter of a `.rmd` document to be processed by `knitr` and the `rmarkdown` package. I used to have the following line at the top of my wiki pages,

       _baptiste, `r format(Sys.time(), &quot;%d %B, %Y&quot;)`_

and it would get converted to _baptiste, 03 May, 2014_ in the html output. Now, I would like to take advantage of the advanced pandoc wrapper provided by `rmarkdown`, but having r code in the YAML header doesn&#39;t seem to work:

    ---
    title: &quot;Sample Document&quot;
    output:
      html_document:
        toc: true
        theme: united
    date: `r format(Sys.time(), &quot;%d %B, %Y&quot;)`
    author: baptiste
    ---

    Error in yaml::yaml.load(front_matter) : 
      Scanner error: while scanning for the next token at line 6, column 7
     found character that cannot start any token at line 6, column 7
    Calls: &lt;Anonymous&gt; ... output_format_from_yaml_front_matter -&gt; 
           parse_yaml_front_matter -&gt; &lt;Anonymous&gt; -&gt; .Call

Any workaround?


YAML current date in rmarkdown

I am using knitr (1.9.5 and 1.9.17) and rmarkdown (0.5.3.1), and would like to hold figure position in the pdf output. The generated pdf file is working fine when chunk option `fig.pos=&quot;H&quot;` is used. 

However, the figure position is not hold when `fig_caption: yes` is set in the 
yaml header.

How should I fix this problem? Thanks for any suggestions.

EDIT:

After learning the float environment of Latex. I add `float` package into header.

    \usepackage{float}

But the generated tex file always use `htbp` in the `figure` environment regard to any `fig.pos` options are used. After manually changing `htbp` to `H`, positions of all figures are hold.

This is my example of rmd file:

    ---
    title: &quot;Untitled&quot;
    output:
      pdf_document:
        fig_caption: yes
        includes:
            in_header: mystyles.sty
    ---
    
    # Section 1
    
    
    Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
    
    Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
    
    Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
    
    Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.
    
    
    ```{r fig1, echo=FALSE, fig.height=8.5, fig.pos=&quot;H&quot;}
    plot(cars)
    ```
    
    # Section 2
    
    More test
    
    ```{r fig2, echo=FALSE, fig.height=8.5, fig.pos=&quot;H&quot;}
    plot(cars)
    ```
    
    # Section 3
    
    ```{r fig3, echo=FALSE, fig.height=8.5, fig.pos=&quot;H&quot;}
    plot(cars)
    ```
    
    More test

How to hold figure position with figure caption in pdf output of knitr?

I&#39;m trying to control the position of a plot when converting to PDF using knitr and pandoc. My .Rmd file looks this:

    # My report
    
    Some text some text some text some text some text some text some text some text some text
    
    
    ```{r myplot, echo=FALSE, fig.pos=&quot;placeHere&quot;, results=&#39;hide&#39;}
    
    library(ggplot2)
    
    ggplot(mtcars, aes(mpg, drat)) + geom_point()
    
    ```
    
    Some text some text some text some text some text some text some text some text some text
    
    \usepackage{graphicx}
    \begin{figure}[placeHere]
      \centering
        \includegraphics[width=0.5\textwidth]{placeHere}
    \end{figure}
    
    Some text some text some text some text some text some text some text some text some text


I&#39;m converting to PDF using the functions provided here: http://quantifyingmemory.blogspot.co.uk/2013/02/reproducible-research-with-r-knitr.html

How can I place the plot between the second and third blocks of text? The latex code is not working as it currently stands.

**EDIT:** This is what I&#39;m trying now.

    # My report
    
       ```{r setup, include=FALSE}
    # set global chunk options
    opts_chunk$set(cache=FALSE)
    library(ggplot2)
    ```
    
    ```{r, echo=FALSE, fig.height=3}
    
    ggplot(mtcars, aes(disp, hp)) + geom_point()
    
    
    ```
    
    
    
    Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 
    
    Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 
    
    
    Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 
    
    
    Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 
    
    
    ```{r, echo=FALSE, fig.height=3}
    
    
    
    ggplot(mtcars, aes(vs, am)) + geom_point()
    
    
    ```
    
    
    
    Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 
    
    Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 
    
    
    Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 
    
    
    ```{r, echo=FALSE, fig.height=6}
    
    
    
    ggplot(mtcars, aes(disp, cyl)) + geom_point()
    
    ```
    
    
    ```{r, echo=FALSE, fig.height=6}
    
    ggplot(mtcars, aes(hp, qsec)) + geom_point()
    
    
    ```
    
    
    Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 
    
    
    
    
    ```{r, echo=FALSE, fig.height=3}
    
    ggplot(mtcars, aes(hp, wt)) + geom_point()
    
    ```
    
    
    
    Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 
    
    
    
    ```{r, echo=FALSE, fig.height=5}
    
    ggplot(mtcars, aes(mpg, drat)) + geom_point()
    
    ```
    
    
    
    
    Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some text Some textSome text Some text Some text 

Figure position in markdown when converting to PDF with knitr and pandoc

I&#39;m trying to use knitr to generate a report that performs the same set of analyses on different subsets of a data set. The project contains two Rmd files: the first file is a master document that sets up the workspace and the document, the second file only contains chunks that perform the analyses and generates associated figures.

What I would like to do is knit the master file, which would then call the second file for each data subset and include the results in a single document. Below is a simple example.


Master document:

    # My report

    ```{r}
    library(iterators)
    data(mtcars)
    ```

    ```{r create-iterator}
    cyl.i &lt;- iter(unique(mtcars$cyl))
    ```

    ## Generate report for each level of cylinder variable
    ```{r cyl4-report, child=&#39;analysis-template.Rmd&#39;}
    ```

    ```{r cyl6-report, child=&#39;analysis-template.Rmd&#39;}
    ```

    ```{r cyl8-report, child=&#39;analysis-template.Rmd&#39;}
    ```

analysis-template.Rmd:

    ```{r, results=&#39;asis&#39;}
    cur.cyl &lt;- nextElem(cyl.i)
    cat(&quot;###&quot;, cur.cyl)
    ```

    ```{r mpg-histogram}
    hist(mtcars$mpg[mtcars$cyl == cur.cyl], main = paste(cur.cyl, &quot;cylinders&quot;))
    ```

    ```{r weight-histogam}
    hist(mtcars$wt[mtcars$cyl == cur.cyl], main = paste(cur.cyl, &quot;cylinders&quot;))
    ```

The problem is knitr does not allow for non-unique chunk labels, so knitting fails when `analysis-template.Rmd` is called the second time. This problem could be avoided by leaving the chunks unnamed since unique labels would then be automatically generated. This isn&#39;t ideal, however, because I&#39;d like to use the chunk labels to create informative filenames for the exported plots.

----------

A potential solution would be using a simple function that appends the current cylinder to the chunk label:

    ```r{paste(&#39;cur-label&#39;, cyl, sep = &quot;-&quot;)}
    ```
But it doesn&#39;t appear that knitr will evaluate an expression in the chunk label position.

----------

I also tried using a custom [chunk hook](http://yihui.name/knitr/hooks#chunk_hooks) that modified the current chunk&#39;s label: 

    knit_hooks$set(cyl.suffix = function(before, options, envir) {
        if (before) options$label &lt;- &quot;new-label&quot;
    })

But changing the chunk label didn&#39;t affect the filenames for generated plots, so I didn&#39;t think knitr was utilizing the new label.


----------

Any ideas on how to change chunk labels so the same child document can be called multiple times? Or perhaps an alternative strategy to accomplish this? 

R knitr: Possible to programmatically modify chunk labels?

I am using `Rmarkdown` and  `Knitr` using Rstudio. 

The following both print script and output to html. 

    ```{r}
    summary(cars)
    ```

However the following will only print the output, that is embedded plot. 

    ```{r, echo=FALSE}
    plot(cars)
    ```

I have situation different than above, I want to present the script but should not run in html as this will take very long time (hours if not days) to run. So I just did was put comment sign.

    ```{r}
    #summary(cars)
    ```
But I need a better way to do this - Is there any better way presenting script without running it. 




preventing a chunk run in rmarkdown

I have created an RMarkdown file in RStudio and managed to knit it with knitr into an HTML and .md file.  Next, I used pandoc to convert the .md file into a PDF file (I get an error if I try and convert from the .html file).  However, the PDF that is produced have massive margins (like this [http://johnmacfarlane.net/pandoc/demo/example13.pdf][1]).  How can I get pandoc to produce something with smaller margins?  I have looked through the pandoc user guide, but haven&#39;t found anything useful.


  [1]: http://johnmacfarlane.net/pandoc/demo/example13.pdf

Set margin size when converting from Markdown to PDF with pandoc

I have been using Knitr via R-Studio, and think it is pretty neat. I have a minor issue though. When I source a file in an R-Chunk, the knitr output includes external comments as follows: 


    + FALSE Loading required package: ggplot2
    + FALSE Loading required package: gridExtra
    + FALSE Loading required package: grid
    + FALSE Loading required package: VGAM
    + FALSE Loading required package: splines
    + FALSE Loading required package: stats4
    + FALSE Attaching package: &#39;VGAM&#39;
    + FALSE The following object(s) are masked from &#39;package:stats4&#39;:

I have tried to set R-chunk options in various ways but still didn&#39;t seem to avoid the problem: 

    ```{r echo=FALSE, cache=FALSE, results=FALSE, warning=FALSE, comment=FALSE, warning=FALSE} 
    source(&quot;C:/Rscripts/source.R&quot;);
    
    ```

Is there any way to comment out these messages?



R - Markdown avoiding package loading messages

I am trying to understand at a high level what the differences between `R Markdown` and `R NoteBook`. I know they are interrelated but I would like to figure out how they are related. My understanding is this:

I know R Notebooks are really R Markdown documents but I am confused about the terminologies.

RStudio new file option has both `R Markdown` and `R NoteBook` and selecting either of them opens an `R Markdown` file but with minor differences. **So just trying to figure out why are there two options and what is the difference between the two?** 

[![enter image description here][1]][1]


  [1]: https://i.stack.imgur.com/oyKmv.png

I understand R Notebooks are newly introduced and R Markdown has been there for a while. Part of the confusion could be because I never used `R Markdown` before R Notebook was introduced so my related or more specific question is

**What is R NoteBook doing differently than just using R MarkDown or what new capabilities is R NoteBook bringing?**
 
All my hits on web search are pointing that R Notebook uses R Markdown but I did not find any help on what is specifically different between the two. 


Difference between R MarkDown and R NoteBook

I have a local image that I would like to include in an `.Rmd` file which I will then `knit` and convert to HTML slides with `Pandoc`. Per [this post](https://stackoverflow.com/questions/10517020/how-to-import-local-image-using-knitr-for-markdown/10522029#10522029), this will insert the local image :  
`![Image Title](path/to/your/image)`

Is there a way to modify this code to also set the image size?

How to set size for local image using knitr for markdown?

In an R Markdown (`.Rmd`) file, how do you comment out unused text?  I&#39;m not referring to the text in the R code chunk, but the general texts, like **%** in **LaTex** for example.

Comment out text in R Markdown (Rmd file)

I&#39;ve previously asked about the [commands for converting R Markdown to HTML](https://stackoverflow.com/q/10646665/180892). 

**What is a good way to convert R Markdown files to PDF documents?**

A good solution would preserve as much as possible of the content (e.g., images, equations, html tables, etc.). The solution needs to be able to be run from the command-line. A good solution would also be cross-platform, and ideally minimise dependencies to make it easier to share makefiles and so forth.


Specifically, there are a lot of options:

* Whether to convert RMD to MD to HTML to PDF; or RMD to MD to PDF; or RMD to PDF
* If using the `markdown` package in R, which options to specify
* Whether to use `pandoc`, a package built into R, or something else

Here&#39;s an example [rmd file](https://gist.github.com/jeromyanglim/2716336) that presumably provides a reasonable test of any proposed solution. It was used as the basis for [this blog post](http://jeromyanglim.blogspot.com.au/2012/05/getting-started-with-r-markdown-knitr.html).


How to convert R Markdown to PDF?

I have two files in the same folder: chapter1.Rmd and chapter2.Rmd, with the following content:

**chapter1.Rmd**

    ---
    title: &quot;Chapter 1&quot;
    output: pdf_document
    ---
    
    ## This is chapter 1. {#Chapter1}
    
    Next up: [chapter 2](#Chapter2)

**chapter2.Rmd**

    ---
    title: &quot;Chapter 2&quot;
    output: pdf_document
    ---
    
    ## This is chapter 2. {#Chapter2}
    
    Previously: [chapter 1](#Chapter1)

How can I knit these so that they combine into a single pdf output?

Of course, `render(input = &quot;chapter1.Rmd&quot;, output_format = &quot;pdf_document&quot;)` works perfectly but `render(input = &quot;chapter1.Rmd&quot;, input = &quot;chapter2.Rmd&quot;, output_format = &quot;pdf_document&quot;)` does not. 

Why do I want to do this? To break up a [giant document][1] into logical files.

I&#39;ve used @hadley &#39;s [bookdown](https://github.com/hadley/bookdown) package to build latex from .Rmd but this seems like overkill for this particular task. Is there a simple solution using knitr/pandoc/linux command line I&#39;m missing? Thanks.


  [1]: https://github.com/Robinlovelace/spatial-microsim-book/blob/master/book-cambridge.Rmd

How to combine two RMarkdown (.Rmd) files into a single output?

What is the relationship between the functionality of R Markdown, Knitr, Pandoc, and Bookdown?

Specifically what is the &#39;division of labour&#39; between these packages in converting markup documents with embedded R code (e.g. `.Rnw` or `.Rmd`) into final outputs (e.g. `.pdf` or `.html`)?  And if Knitr is used to process RMarkdown, what does the `rmarkdown` package do and how is it different to the `markdown package`?


Relationship between R Markdown, Knitr, Pandoc, and Bookdown

Is there any modification of an existing tool or new tool that will syntax-highlight (colour) blocks of R code in a knitr markdown document when opened in Emacs?

The knitr chunks I am looking at are triple-backtick blocks `[```]` that contain R code inside.

**EDIT:** things that I tried so far:

 ***- [Ubuntu][1] 12.04 with Emacs 23***

&lt;!-- language: lang-sh --&gt;

    emacs --version
    GNU Emacs 23.3.1

 **1. Polymode**

https://github.com/vitoshka/polymode/issues/3

I am trying to get polymode to syntax-highlight my Rmd files, but it&#39;s complaining about a &#39;color&#39; load file:

&lt;!-- language: lang-sh --&gt;

    cd ~/.emacs.d
    git clone https://github.com/vitoshka/polymode.git

In my .emacs file:

&lt;!-- language: lang-lisp --&gt;

    (add-to-list &#39;load-path &quot;/home/avilella/.emacs.d/polymode/&quot;)
    (add-to-list &#39;load-path &quot;/home/avilella/.emacs.d/polymode/modes/&quot;)

    ;; Require any polymode bundles that you are interested in:

    (require &#39;poly-R)
    (require &#39;poly-markdown)

eval-buffer:

&lt;!-- language: lang-lisp --&gt;

    Cannot open load file: color

-------------------------------------------------------------------------

 ***- [CentOS][2] with Emacs 24:***

&lt;!-- language: lang-sh --&gt;

    emacs --version
    GNU Emacs 24.2.1

 **1. Polymode installed correctly**

Open a Rmd file, `M-x polymode-minor-mode`, no change to the syntax highlighting.

-------------------------------------------------------------------------

&lt;!-- language: lang-sh --&gt;

    emacs --version
    GNU Emacs 24.3.1

 **1. Polymode installed correctly**

Open a Rmd file, `M-x poly-markdown+r-mode`, some of the syntax highlighting starts to appear, but I need to manually modify the test in each triple-tick block of code for it to fully show the syntax.

![Enter image description here][3]

![Enter image description here][4]

The second image is just after typing a Return before the knitr block.

  [1]: http://en.wikipedia.org/wiki/Ubuntu_%28operating_system%29
  [2]: http://en.wikipedia.org/wiki/CentOS
  [3]: http://i.stack.imgur.com/bHbBY.png
  [4]: http://i.stack.imgur.com/a6pVA.png


knitr Markdown highlighting in Emacs?

I am just starting to learn about KnitR and the use of Markdown in generating R documents and reports. This looks to be perfect for a lot of the day to day reporting that I have to do with my job. However, one thing that I&#39;m not seeing is an easy way to print data frames and tables using Markdown formatting (sort of like `xtable`, but with Markdown instead of LaTeX or HTML). I know that I can just embed the HTML output from xtable, but I was wondering if there were any Markdown-based solutions?

Programmatically creating Markdown tables in R with KnitR

I wonder how to use `rmarkdown` to generate a pdf which has both portrait and landscape layout in the same document. If there is a pure `rmarkdown` option that would be even better than using latex.

Here&#39;s a small, reproducible example. First, rendering this `.Rmd` in RStudio (press **Knit PDF** button) results in a pdf with all pages in landscape layout:

    ---
    title: &quot;All pages landscape&quot;
    output: pdf_document
    classoption: landscape
    ---
      
    ```{r}
    summary(cars)
    ```
    
    \newpage
    ```{r}
    summary(cars)
    ```

Then an attempt to create a document which mixes portrait and landscape layout. The basic setup in the `YAML` is done according to the &#39;Includes&#39; section [**here**](http://rmarkdown.rstudio.com/pdf_document_format.html). The `in_header` file &#39;header.tex&#39; only contains `\usepackage{lscape}`, a package suggested for `knitr` landscape layout [**here**](https://github.com/yihui/knitr-examples/blob/master/030-landscape.Rnw). The `.tex` file is in the same directory as the `.Rmd` file.  

    ---
    title: &quot;Mixing portrait and landscape&quot;
    output:
        pdf_document:
            includes:
                in_header: header.tex
    ---
    
    Portrait:
    ```{r}
    summary(cars)
    ```
    
    \newpage
    \begin{landscape}
    Landscape:
    ```{r}
    summary(cars)
    ```
    \end{landscape}
    
    \newpage
    More portrait:
    ```{r}
    summary(cars)
    ```

However, this code results in an error:

    # ! You can&#39;t use `macro parameter character #&#39; in horizontal mode.
    # l.116 #
    
    # pandoc.exe: Error producing PDF from TeX source
    # Error: pandoc document conversion failed with error 43

Any help is much appreciated.

Rstudio rmarkdown: both portrait and landscape layout in a single PDF

I often have a main R Markdown file or knitr LaTeX file where I `source` some other R file (e.g., for data processing). However, I was thinking that in some instances it would be beneficial to have these sourced files be their own reproducible documents (e.g., an R Markdown file that not only includes commands for data processing but also produces a reproducible document that explains the data processing decisions).

Thus, I would like to have a command like `source(&#39;myfile.rmd&#39;)` in my main R Markdown file. that would extract and source all the R code inside the R code chunks of `myfile.rmd`. Of course, this gives rise to an error. 

The following command works:

    ```{r message=FALSE, results=&#39;hide&#39;}
    knit(&#39;myfile.rmd&#39;, tangle=TRUE)
    source(&#39;myfile.R&#39;)
    ```


where `results=&#39;hide&#39;` could be omitted if the output was desired. I.e., knitr outputs the R code from `myfile.rmd` into `myfile.R`.

However, it doesn&#39;t seem perfect:

* it results in the creation of an extra file
* it needs to appear in its own code chunk if control over the display is required.
* It&#39;s not as elegant as simple `source(...)`.

Thus my question:
**Is there a more elegant way of sourcing the R code of an R Markdown file?**

How to source R Markdown file like `source(&#39;myfile.r&#39;)`?

I want my html file to show the code, but not the output of this chunk:

    ```{r echo=True, include=FALSE}
    fun &lt;- function(b)
        {
        for(a in b)
            {print(a)
            return(a * a)}
        }
    y &lt;- fun(b)
    ```

When I run the code, i need the print to see the progress (it is quite a long function in reality).

But in the knitr file, I use the output in a further chunk, so I do not want to see it in this one (and there&#39;s no notion of progress, since the code has already been run).

This `echo=True, include=FALSE` here does not work: the whole thing is hidden (which is the normal behavior of `include=FALSE`).

&lt;b&gt;What are the parameters I could use to hide the prints, but show my code?&lt;/b&gt;

How to show code but hide output in RMarkdown?

In my R Markdown documents, I sometimes want to just generate a report without showing the actual code (specially when I send it to my boss). How can I hide the R code and just show the graph and results?

For example:

    ---
    output: html_document
    ---
    
    ```{r fig.width=16, fig.height=6}
    plot(cars)
    ```

This shows both the commands and the plot. How can I remove the commands from my HTML report?

Hiding the R code in Rmarkdown/knit and just showing the results

I am using R Markdown in RStudio and the knit HTML option to create HTML output. However, the font used in the ouput for plain text blocks is rather small and I would like to change it to a differnt font and increase the font size. Can someone show an example how to set the output font - workable without a lot of knowledge in html?

So far I tried at the top of my markdown document, but this doesn&#39;t work. 

    ---
    fontsize: 24pt
    ---

R Markdown - changing font size and font type in html output

I am producing an HTML output but I am having issues with the output width of R code output.

I&#39;m able to adjust the figure width with no difficulty but when I try to write a data table or the factor loadings, R is outputting at a fixed width which is only about a third of my screen width.  This results in the columns of the table being split up rather than all of the columns displayed in a single table.

Here is a reproducible example:

    ---
    output: html_document
    ---
    
    # Title
    
    ```{r echo = FALSE, fig.width=16, fig.height=6}
    x = matrix(rnorm(100),ncol=10)
    x
    plot(x)
    ```
[![enter image description here][1]][1]


  [1]: https://i.stack.imgur.com/gPLR4.png

Adjust the output width of R Markdown HTML output

I would like to create an automated knitr report that will produce histograms for each numeric field within my dataframe. My goal is to do this without having to specify the actual fields (this dataset contains over 70 and I would also like to reuse the script). 

I&#39;ve tried a few different approaches:

- saving the plot to an object, `p`, and then calling `p` after the loop
  - This only plots the final plot
- Creating an array of plots, `PLOTS &lt;- NULL`,  and appending the plots within the loop `PLOTS &lt;- append(PLOTS, p)`
  - Accessing these plots out of the loop did not work at all
- Even tried saving each to a `.png` file but would rather not have to deal with the overhead of saving and then re-accessing each file
 
I&#39;m afraid the intricacies of the plot devices are escaping me. 

## Question
How can I make the following chunk output each plot within the loop to the report? Currently, the best I can achieve is output of the final plot produced by saving it to an object and calling that object outside of the loop.

R markdown chunk using `knitr` in RStudio:

    ```{r plotNumeric, echo=TRUE, fig.height=3}
    suppressPackageStartupMessages(library(ggplot2))
    FIELDS &lt;- names(df)[sapply(df, class)==&quot;numeric&quot;]
    for (field in  FIELDS){
      qplot(df[,field], main=field)  
    }
    ```

From this point, I hope to customize the plots further. 

R knitr Markdown: Output Plots within For Loop

**What commands are run when pressing &quot;Knit HTML&quot; on an R Markdown file in Rstudio 0.96?**

My motivation is that I might want to run the same command when I&#39;m in another text editing environment or I might want to combine the command in a larger `makefile`.

How to convert R Markdown to HTML? I.e., What does &quot;Knit HTML&quot; do in Rstudio 0.96?

I am using RStudio to write my R Markdown files.  How can I remove the hashes (`##`) in the final HTML output file that are displayed before the code output?

As an example:

    ---
    output: html_document
    ---
    
    ```{r}
    head(cars)
    ```

[![enter image description here][1]][1]


  [1]: https://i.stack.imgur.com/CVtZn.png

Remove Hashes in R Output from R Markdown and Knitr

Doesn&#39;t fit on the slide by default, doesn&#39;t even print by any other means.

Here&#39;s the .Rmd: **Edit: it seems you have to use plot() in every chunk.  Second plot now prints.**

    # Plot should show at high resolution
    
    ```{r echo=FALSE, comment = &quot;&quot;}
    # load some data
    require(plyr)
    rbi &lt;- ddply(baseball, .(year), summarise,  
      mean_rbi = mean(rbi, na.rm = TRUE))
    ```
    
    ```{r}
    # plot
    plot(mean_rbi ~ year, type = &quot;l&quot;, data = rbi)
    ```
    
    # Second attempt
    ```{r, fig.width = 2, fig.height = 2}
    plot(mean_rbi ~ year, type = &quot;l&quot;, data = rbi)
    ```
    
    # Third attempt
    ```{r, out.width = 2, out.height = 2}
    plot(mean_rbi ~ year, type = &quot;l&quot;, data = rbi)
    ```
    
    # Fourth attempt
    ```{r, out.width = &#39;200px&#39;, out.height = &#39;200px&#39;}
    plot(mean_rbi ~ year, type = &quot;l&quot;, data = rbi)
    ```
    
    # Fifth attempt
    ```{r, out.width = &#39;\\maxwidth&#39;}
    plot(mean_rbi ~ year, type = &quot;l&quot;, data = rbi)
    ```

Save that as `test.Rmd`
Then compile to tex using beamer:

    knit(&quot;test.Rmd&quot;)
    system(&quot;pandoc -s -t beamer --slide-level 1 test.md -o test.tex&quot;)

Open `test.tex` in RStudio and click &quot;Compile PDF&quot;.

I&#39;ve read Yihui&#39;s [documentation][1] and hope I haven&#39;t missed something really obvious.


**Edit** new code incorporating Yihui&#39;s suggestions.

    ```{r setup, include=FALSE}
    opts_chunk$set(dev = &#39;pdf&#39;)
    ```
    
    # Plot should show at high resolution
    
    ```{r echo=FALSE, comment = &quot;&quot;}
    # load some data
    require(plyr)
    rbi &lt;- ddply(baseball, .(year), summarise,  
      mean_rbi = mean(rbi, na.rm = TRUE))
    ```
    
    ```{r}
    # plot
    plot(mean_rbi ~ year, type = &quot;l&quot;, data = rbi)
    ```
    
    # Second attempt
    ```{r, fig.width = 4, fig.height = 4}
    plot(mean_rbi ~ year, type = &quot;l&quot;, data = rbi)
    ```

`sessionInfo()`

     R version 3.0.1 (16/05/2013)
    Platform: x86_64-pc-linux-gnu (64-bit)
    
    Local:
     [1] LC_CTYPE = en_US.UTF-8 LC_NUMERIC = C LC_TIME = C LC_COLLATE = C        
     [5] LC_MONETARY=C        LC_MESSAGES=C        LC_PAPER=C           LC_NAME=C           
     [9] LC_ADDRESS=C         LC_TELEPHONE=C       LC_MEASUREMENT=C     LC_IDENTIFICATION=C 
    
    attached base packages:
    [1] stats     graphics  grDevices utils     datasets  methods   base     
    
    other attached packages:
    [1] plyr_1.8       markdown_0.6   knitr_1.2      rCharts_0.3.51 slidify_0.3.52
    
    loaded via a namespace (and not attached):
     [1] RJSONIO_1.0-3   codetools_0.2-8 digest_0.6.3    evaluate_0.4.3  formatR_0.8    
     [6] grid_3.0.1      lattice_0.20-15 stringr_0.6.2   tools_3.0.1     whisker_0.3-2  
    [11] yaml_2.1.7  

  [1]: http://yihui.name/knitr/options#chunk_options

Plot size and resolution with R markdown, knitr, pandoc, beamer

***Let me caveat by saying that this may be better suited as an html/css question but (a) I&#39;m not too familiar with those techniques and (b) I wanted to keep it all in the family (R family) if possible.***

I would like to use `knitr` to write academic style reports (**APA 6 type guidelines**) using Rmarkdown.  I&#39;ve got most aspects worked out but not page breaking.  I can manually set page breaks with something like:

    # report
    
    ```{r setup, include=FALSE}
    # set global chunk options
    opts_chunk$set(cache=TRUE)
    ```
    ------
    ## Page 1
    
    ```{r plot1}
    plot(1:10, 1:10)
    ```
    ------
    ## Page 2

In the following .Rmd I&#39;d like to programatically set those breaks after n lines/n distance.  So let&#39;s say after 8 inches or 140 lines. 

    # report
    
    ```{r setup, include=FALSE}
    # set global chunk options
    opts_chunk$set(cache=TRUE)
    ```
    Initial Text. Yay!

    ```{r plot1}
    plot(1:10, 1:10)
    ```
   
    More Text.  Outstanding.  What Hadley&#39;s not calling it plyr2?

    ```{r plot2, fig.width=4, fig.height=4}
    plot(1:10, 1:10)
    ```

    `r paste(rep(&quot;So much text so little time!&quot;, 10000))`

How can I programatically set page breaks after n distance.  This is similar to how `LaTeX` would break a file into pages so if a figure takes too much space it would be forced to the next page.

**EDIT** Found this from a friend: http://www.w3.org/TR/css3-page/  may be helpful.


knitr/Rmd: page break after n lines/n distance

I am operating matrices with R 3.1 and RStudio 0.99.

I have my R Script and with cmd+enter it works without problem. 

I created an Rmd for reporting but I have this error

    Error in lazyLoadDBinsertVariable(vars[i], from, datafile, ascii, compress,  : 
      long vectors not supported yet: ../../../../R-3.3.1/src/main/connections.c:5600
    Calls: &lt;Anonymous&gt; ... &lt;Anonymous&gt; -&gt; &lt;Anonymous&gt; -&gt; lazyLoadDBinsertVariable
    Execution halted

Is there a way to bypass that error?

This seems to be a dupicate of https://stackoverflow.com/questions/24335692/large-matrices-in-r-long-vectors-not-supported-yet

but the difference is that this only happens when trying to create an Rmd, not in any other case


&quot;long vectors not supported yet&quot; error in Rmd but not in R Script

I&#39;m trying to cross-reference figures and tables in a PDF produced with knitr/rmarkdown. There are some questions on SO and tex.stackexchange ([here](https://tex.stackexchange.com/a/296010/4762) and [here](https://stackoverflow.com/questions/31064353/how-to-make-a-figure-caption-in-rmarkdown/31071430#31071430), for example), that suggest the way to do this inline is to add `\ref{fig:my_fig}`, where `my_fig` is the chunk label. However, when I try that in my `rmarkdown` document, I get `??` where the figure number should be. I&#39;d like to find out how to get cross-referencing to work properly.  

A reproducible example is below. There are two files: the `rmarkdown` file plus a `header.tex` file that I&#39;ve included just in case it affects the answer (though I have the same problem whether I include the `header.tex` file or not).

In the `rmarkdown` file there are three cross-reference examples. Example 1 is a figure for which cross-referencing fails (`??` is displayed instead of the figure number). There&#39;s also a second, commented-out attempt (based on [this SO answer](https://tex.stackexchange.com/a/296010/4762)), where I try setting the figure environment, label, and caption with `latex` markup before and after the chunk, but this results in a `pandoc` error when I try to knit the document. The error is:

&gt;     ! Missing $ inserted.
&gt;     &lt;inserted text&gt; 
&gt;                     $
&gt;     l.108 ![](testCrossRef_

Example 2 uses `xtable` and cross-referencing works. Example 3 uses `kable` and cross-referencing fails.

A screenshot of the PDF output is included at the bottom of this post. 

### `rmarkdown` file

    ---
    title: | 
      | My Title  
    author: | 
      | eipi10  
      | Department of Redundancy Department  
    date: &quot;`r format(Sys.time(), &#39;%B %e, %Y&#39;)`&quot;
    output: 
      pdf_document:
        fig_caption: yes
        includes:
          in_header: header.tex
        keep_tex: yes
    fontsize: 11pt
    geometry: margin=1in
    graphics: yes
    ---
    
    ```{r setup, include=FALSE}
    knitr::opts_chunk$set(echo = FALSE, message=FALSE, warning=FALSE, fig.height=2, fig.width=4)
    ```
    
    # Example 1. Figure
    
    This is a report. Take a look at Figure \ref{fig:fig1}.  
    
    ```{r fig1, echo=FALSE, fig.cap=&quot;This is a caption&quot;}
    plot(mtcars$wt, mtcars$mpg)
    ```
    
    &lt;!-- Now, let&#39;s take a look at this other plot in Figure \ref{fig:fig2}. --&gt;
    
    &lt;!-- \begin{figure} --&gt;
    &lt;!-- ```{r fig2, echo=FALSE} --&gt;
    &lt;!-- plot(mtcars$cyl, mtcars$mpg) --&gt;
    &lt;!-- ``` --&gt;
    &lt;!-- \caption{This is another caption} --&gt;
    &lt;!-- \label{fig:fig2} --&gt;
    &lt;!-- \end{figure} --&gt;
    
    # Example 2: `xtable`
    
    Some more text. See Table \ref{tab:tab1} below. 
    
    ```{r echo=FALSE, results=&quot;asis&quot;}
    library(xtable)
    print.xtable(
      xtable(mtcars[1:3,1:4], label=&quot;tab:tab1&quot;, caption=&quot;An xtable table&quot;), 
      comment=FALSE)
    ```
    
    # Example 3: `kable`
    
    Some more text. See Table \ref{tab:tab2} below. 
    
    ```{r tab2, echo=FALSE}
    library(knitr)
    kable(mtcars[1:3,1:4], caption=&quot;A `kable` table&quot;)
    ```

### `header.tex` file

    % Caption on top
    % https://tex.stackexchange.com/a/14862/4762
    \usepackage{floatrow}
    \floatsetup[figure]{capposition=top}
    \floatsetup[table]{capposition=top}

### PDF output

[![enter image description here][1]][1]


  [1]: http://i.stack.imgur.com/bIhhT.png

knitr/rmarkdown/Latex: How to cross-reference figures and tables?

Using the following code I got the data I wanted, but for some reason I can&#39;t figure out `knitr` doesn&#39;t let me compile a PDF document, as shown further below:

My code:

    install.packages(&quot;weatherData&quot;)
    library(weatherData)
    istanbul &lt;- getWeatherForDate(&quot;Istanbul&quot;,
                                  start_date = Sys.Date() - 41, 
                                  end_date = Sys.Date())

Works out with no problem but I get the following message trying compile the PDF:

    Quitting from lines 3-31 (ist_weather.spin.Rmd) 
    Error in contrib.url(repos, type) : 
      trying to use CRAN without setting a mirror
    Calls: &lt;Anonymous&gt; ... eval -&gt; eval -&gt; install.packages -&gt; grep -&gt; contrib.url
    Execution halted

install.packages fails in knitr document: &quot;trying to use CRAN without setting a mirror&quot;

I&#39;m trying to come up with a good system for generating slides and accompanying handouts. The ideal system would have the following properties:

* beautiful in both presentation (PDF/HTML) and handout (PDF) layouts (handouts should have room for taking notes)
* embedded R chunks, figures, other JPG/PNG pictures, etc.
* easy to compose
* build using command-line tools
* bibliography support
* `pandoc` slide separator format (automatically generate a new slide after headers of a specified level) is preferred
* I can live with a little bit of additional processing (e.g. via `sed`), but would prefer not to write a huge infrastructure
* **two-column layouts**: there is a [SO post on how to get multi-column slides from pandoc](https://stackoverflow.com/questions/15142134/slides-with-columns-in-pandoc), but it is LaTeX- rather than HTML-oriented.
* ability to adjust sizes of embedded images (other than R-generated figures) and column widths on the fly

Here&#39;s what I&#39;ve discovered so far about the various options:
 
* *Slidify*: 
    * doesn&#39;t do `pandoc` slide separator format, although [there is a workaround](https://github.com/ramnathv/slidify/issues/15‎)
	* the suggestion for creating handouts is to print to PDF; I&#39;d like to leave room for notes etc. (I could probably figure out a way to do that using something like [PDFtk](http://www.pdflabs.com/tools/pdftk-the-pdf-toolkit/) or `psnup` ...)
* `RStudio` presentations (`.Rpres` files): 
    * does lots of things nicely, including multi-columns with specified widths
    * doesn&#39;t support `pandoc` slide separator format 
    * I can&#39;t figure out what&#39;s going on under the hood. There is [RStudio documentation](http://www.rstudio.com/ide/docs/r_markdown) that describes the translation process for regular HTML, but it doesn&#39;t seem to cover the R presentation format (which isn&#39;t quite the same). (I have previously invested some effort in [figuring out how to get RStudio-like output via pandoc](http://ms.mcmaster.ca/~bolker/misc/pandoc_diffs.html) ...), which means I can&#39;t generate slides etc. from the command line.
* [RStudio&#39;s Development Version](http://www.rstudio.com/ide/download/preview) (as of March 2014) comes bundled with Pandoc and version 2 of `rmarkdown`. It addresses many of the above issues with the `.Rpres` format.
* `pandoc`: may be the only markdown-translator that has features such as footnotes, bibliography support, etc..  I can also use `pandoc` to generate LaTeX using the [tufte-handout class](http://code.google.com/p/tufte-latex/), which meets my criteria of beauty. 
    * Unfortunately, it seems not to have built-in two-column format support. [Yihui Xie&#39;s HTML5 example](http://yihui.name/knitr/demo/slides/) doesn&#39;t show any two-column examples, and it claims (on slide 5) that clicking the &quot;Knit HTML&quot; button in RStudio is equivalent to `pandoc -s -S -i -t dzslides --mathjax knitr-slides.md -o knitr-slides.html`, but it doesn&#39;t seem to be ...
* LaTeX/beamer: I could simply compose in `Rnw` (knitr-dialect Sweave) rather than R markdown to begin with.  This would give me ultimate flexibility ...
    * despite many years of LaTeX use I do find LaTeX composition more of a pain than markdown composition.  

After all that, my specific question is: *what&#39;s the best (easiest) way to generate a two-column layout for HTML output*?

Any other advice will also be appreciated.



two-column layouts in RStudio presentations/slidify/pandoc

In R markdown (knitr package), can I access a variable within the body of the document that was calculated in a code chunk?

R markdown: Accessing variable from code chunk (variable scope)

How can I manually and simply format a table in RMarkdown that will look good when converted to HTML (using the knitr and markdown packages), PDF (using pandoc and miktex) and docx (using pandoc)? 

I want to be able to write small tables in RMarkdown that are not a result of R functions that look good in the three formats I use most often. So far I&#39;ve found a format that looks good in 2 of the 3 formats, is 3/3 possible?

One. This looks good after Knit HTML but not good in the PDF or docx

    &lt;table&gt;
    &lt;tr&gt;
    &lt;td&gt;Eggs&lt;/td&gt;
    &lt;td&gt;Ham&lt;/td&gt;
    &lt;/tr&gt;
    &lt;tr&gt;
    &lt;td&gt;Basil&lt;/td&gt;
    &lt;td&gt;Tomato&lt;/td&gt;
    &lt;/tr&gt;
    &lt;/table&gt;


Two. This one looks good after Knit HTML but not good in the PDF or docx
 

    | Tables        | Are           | Cool  |
    | ------------- |:-------------:| -----:|
    | col 3 is      | right-aligned | $1600 |
    | col 2 is      | centered      |   $12 |
    | zebra stripes | are neat      |    $1 |


Three. This one does not look good after Knit HTML but is good in the PDF and docx (best option so far)

    V1         Tweedledee       Tweedledum
    --------   --------------   ----------------
    Age        14               14
    Height     3&#39;2&quot;             3&#39;2&quot;
    Politics   Conservative     Conservative
    Religion   &quot;New Age&quot;        Syrian Orthodox
    ---------  --------------   ----------------


Four. This looks good after Knit HTML and make PDF and docx (winner!) but is not the manual formatting I&#39;m after. 
 

    ```{r table1, echo=FALSE, message=FALSE, warnings=FALSE, results=&#39;asis&#39;}
    require(pander)
    panderOptions(&#39;table.split.table&#39;, Inf)
    set.caption(&quot;Data on cars&quot;)
    pander(mtcars, style = &#39;rmarkdown&#39;)
    ```


This is how I&#39;m making the PDF and docx files:

    filen &lt;- &quot;table&quot; # name of my RMarkdown file without suffix
    knit(paste0(filen,&quot;.Rmd&quot;))
    
    # make PDF
    system(paste0(&quot;pandoc -s &quot;, paste0(filen,&quot;.md&quot;), &quot; -t latex -o &quot;, paste0(filen,&quot;.pdf&quot;), &quot; --highlight-style=tango  -S&quot;))
    
    # make docx
    system(paste0(&quot;pandoc -s &quot;, paste0(filen,&quot;.md&quot;), &quot; -o &quot;, paste0(filen,&quot;.docx&quot;), &quot; --highlight-style=tango  -S&quot;))



Simple manual RMarkdown tables that look good in HTML, PDF and DOCX

I&#39;ve seen similar questions on Stack Overflow but virtually no conclusive answers, and certainly no answer that worked for me.

What is the easiest way to access and use objects (regression fits, data frames, other objects) that are located in the global R environment in the Markdown (Rstudio) script.

I find it surprising that there is no easy solution to this, given the tendency of the RStudio team to make things comfortable and effective.

Thanks in advance.

How to use objects from global environment in Rstudio Markdown

### TL;DR ###
What are the (possibly unwanted) side-effects of using `knit()`/`knit2pdf()` instead of the &quot;Compile PDF&quot;&lt;sup&gt;1&lt;/sup&gt; button in RStudio?

## Motivation ##

Most users of `knitr` seem to write their documents in RStudio and compile the documents using the &quot;Compile PDF&quot; / &quot;Knit HTML&quot; button. This works smoothly most of the time, but every once a while there are special requirements that cannot be achieved using the compile button. In these cases, the solution is usually to call `knit()`/`knit2pdf()`/`rmarkdown::render()` (or similar functions) directly.

 Some examples:

 - [How to knit/Sweave to a different file name?](https://stackoverflow.com/questions/21883761/how-to-knit-sweave-to-a-different-file-name)
 - [Is there a way to knitr markdown straight out of your workspace using RStudio?](https://stackoverflow.com/questions/11155182/is-there-a-way-to-knitr-markdown-straight-out-of-your-workspace-using-rstudio?lq=1)
 - [Insert date in filename while knitting document using RStudio Knit button](https://stackoverflow.com/questions/32377291/insert-date-in-filename-while-knitting-document-using-rstudio-knit-button)
 
Using `knit2pdf()` instead of the &quot;Compile PDF&quot; button usually offers a simple solution to such questions. However, this comes at a price: There is the fundamental difference that &quot;Compile PDF&quot; processes the document [in a separate process and environment](https://support.rstudio.com/hc/en-us/articles/200552056-Using-Sweave-and-knitr) whereas `knit2pdf()` and friends don&#39;t. 
 
*This has implications and the problem is that not all of these implications are obvious.* Take the fact that `knit()` uses objects from the global environment (whereas &quot;Compile PDF&quot; does not) as an example. This might be obvious and the desired behavior in cases like the second example above, but it is an *unexpected consequence* when `knit()` is used to overcome problems like in example 1 and 3. 
 
 Moreover, there are more subtle differences:

  - The [working directory](https://stackoverflow.com/questions/33555002/difference-between-compile-pdf-and-knit2pdf) might not be set as expected. 
  - [Packages need to be loaded](https://stackoverflow.com/questions/31856298/function-is-not-found-in-knitr).
  - Some options that are usually set by RStudio may have [unexpected values](https://stackoverflow.com/questions/33969024/knitr-gives-error-message).

## The Question and it&#39;s goal ##
Whenever I read/write the advice to use `knit2pdf()` instead of &quot;Compile PDF&quot;, I think *&quot;correct, but the user should understand the consequences …&quot;*. 

Therefore, the question here is:

&gt; What are the (possibly unwanted) side-effects of using `knit()`/`knit2pdf()` instead of the &quot;Compile PDF&quot; button in RStudio?

If there was a comprehensive (community wiki?) answer to this question, it could be linked in future answers that suggest using `knit2pdf()`.

## Related Questions ##

There are dozens of related questions to this one. However, they either propose only code to (more or less) reproduce the behavior of the RStudio button or they explain what &quot;basically&quot; happens without mentioning the possible pitfalls. Others look like being very similar questions but turn out to be a (very) special case of it. Some examples:

  - [Knit2html not replicating functionality of Knit HTML button in R Studio](https://stackoverflow.com/questions/11275255/knit2html-not-replicating-functionality-of-knit-html-button-in-r-studio?lq=1): Caching issue.
  - [HTML outputs are different between using knitr in Rstudio &amp; knit2html in command line](https://stackoverflow.com/questions/25576095/html-outputs-are-different-between-using-knitr-in-rstudio-knit2html-in-command): Markdown versions.
  - [How to convert R Markdown to HTML? I.e., What does “Knit HTML” do in Rstudio 0.96?](https://stackoverflow.com/questions/10646665/how-to-convert-r-markdown-to-html-i-e-what-does-knit-html-do-in-rstudio-0-9): Rather superficial answer by Yihui (explains what &quot;basically&quot; happens) and some options how to reproduce the behavior of the RStudio button. Neither the [suggested](https://stackoverflow.com/a/10654295/2706569) `Sys.sleep(30)` nor [the &quot;Compile PDF&quot; log](https://stackoverflow.com/a/17515963/2706569) are insightful (both hints point to the same thing).
  - [What does “Knit HTML” do in Rstudio 0.98?](https://stackoverflow.com/questions/27881289/what-does-knit-html-do-in-rstudio-0-98): Reproduce behavior of button.
  
## About the answer ##

I think this question raised many of the issues that should be part of an answer. However, there might be many more aspects I don&#39;t know about which is the reason why I am reluctant to self-answer this question (though I might try if nobody answers).

 Probably, an answer should cover three main points:

  - The new session vs. current session issue (global options, working directory, loaded packages, …).
  - A consequence of the first point: The fact that `knit()` uses objects from the calling environment (default: `envir = parent.frame()`) and implications for reproducibility. I tried to tackle the issue of preventing `knit()` from using objects from outside the document in [this answer](https://stackoverflow.com/a/34017805/2706569) (second bullet point).
  - Things RStudio secretly does …
     - … when starting an interactive session ([example](https://stackoverflow.com/a/33970452/2706569)) --&gt; Not available when hitting &quot;Compile PDF&quot;
     - … when hitting &quot;Compile PDF&quot; (anything special besides the new session with the working directory set to the file processed?)


I am not sure about the right perspective on the issue. I think both, &quot;What happens when I hit &#39;Compile PDF&#39; + implications&quot; as well as &quot;What happens when I use `knit()` + implications&quot; is a good approach to tackle the question. 


----------
&lt;sup&gt;&lt;sup&gt;1&lt;/sup&gt; The same applies to the &quot;Knit HTML&quot; button when writing RMD documents.&lt;/sup&gt;

Difference: &quot;Compile PDF&quot; button in RStudio vs. knit() and knit2pdf()

What is the command-line [knitr](http://yihui.name/knitr/demo/minimal/) equivalent of `R CMD Sweave myfile.rnw`?


What is the knitr equivalent of `R CMD Sweave myfile.rnw`?

I want to include animated `rgl` graphs in my `.Rnw` document through `knitr`. Here is my MWE:

    \documentclass{article}
    
    &lt;&lt; label = setup, include = FALSE&gt;&gt;=
    opts_chunk$set(fig.path = &#39;figure/&#39;,  cache = FALSE, dev = &quot;pdf&quot;,  fig.align = &#39;center&#39;, fig.show = &#39;hold&#39;, fig.width = 3, fig.height = 3,  echo = TRUE, warning = FALSE, message = FALSE, size = &#39;footnotesize&#39;, comment=NA, results=&#39;hold&#39;)
    
    knit_hooks$set(par = function(before, options, envir){
    if (before &amp;&amp; options$fig.show!=&#39;none&#39;)
     par(mar = c(4, 4, 0.1, 0.1), cex.lab = 0.95, cex.axis = 0.9, mgp = c(2, 0.7, 0), tcl = -0.3)
    }
    )
    knit_hooks$set(rgl = function(before, options, envir) {
      if (!before) {
        ## after a chunk has been evaluated
        if (rgl.cur() == 0) return()  # no active device
        name = paste(options$fig.path, options$label, sep = &#39;&#39;)
        rgl.snapshot(paste(name, &#39;.png&#39;, sep = &#39;&#39;), fmt = &#39;png&#39;)
        return(paste(&#39;\\includegraphics{&#39;, name, &#39;}\n&#39;, sep = &#39;&#39;))
      }
    }
    )
    
    options(replace.assign = TRUE, width = 60)
    @ 
    \begin{document}
     
    &lt;&lt; label=packages &gt;&gt;=
    library(car)
    @
    &lt;&lt; label=rgl1, rgl=TRUE, fig.show=&#39;animate&#39; &gt;&gt;=
    scatter3d(prestige ~ income + education, data=Duncan)
    @
      
    \end{document}

I&#39;m not getting graph in my knitted documents.

Updated
------

I&#39;m still unable to get it work and getting the following warning:


    Warning messages:
    1: In rgl.snapshot(paste(name, &quot;.png&quot;, sep = &quot;&quot;), fmt = &quot;png&quot;) :
      RGL: Pixmap save: unable to open file &#39;D:\A B\C D UAF\Test\knitr\rglAnimation\figure\rgl1.png&#39; for writing
    2: In rgl.snapshot(paste(name, &quot;.png&quot;, sep = &quot;&quot;), fmt = &quot;png&quot;) :
      snapshot failed
    3: running command &#39;&quot;C:\PROGRA~2\MIKTEX~1.9\miktex\bin\x64\texi2dvi.exe&quot; --quiet --pdf &quot;rglAnimation.tex&quot; --max-iterations=20 -I &quot;C:/PROGRA~1/R/R-31~1.1/share/texmf/tex/latex&quot; -I &quot;C:/PROGRA~1/R/R-31~1.1/share/texmf/bibtex/bst&quot;&#39; had status 1 


My `sessionInfo()` is 

    R version 3.1.1 (2014-07-10)
    Platform: x86_64-w64-mingw32/x64 (64-bit)
    
    locale:
    [1] LC_COLLATE=English_United States.1252 
    [2] LC_CTYPE=English_United States.1252   
    [3] LC_MONETARY=English_United States.1252
    [4] LC_NUMERIC=C                          
    [5] LC_TIME=English_United States.1252    
    
    attached base packages:
    [1] tools     stats     graphics  grDevices utils     datasets  methods  
    [8] base     
    
    other attached packages:
    [1] mgcv_1.8-2    nlme_3.1-117  rgl_0.93.1098 car_2.0-21    knitr_1.6.15 
    
    loaded via a namespace (and not attached):
    [1] evaluate_0.5.5  formatR_1.0     grid_3.1.1      highr_0.3      
    [5] lattice_0.20-29 MASS_7.3-34     Matrix_1.1-4    nnet_7.3-8     
    [9] stringr_0.6.2  

**Edited**

Changing `fig.path = &#39;figure/&#39;`  to `fig.path = &#39;&#39;` in `opts_chunk$set` compiles the document with `png` graphs but without any animation. How can I get animated `rgl` graphs with `fig.path = &#39;figure/&#39;`.


All Knitr Solutions on Gang of Coders

Total of 39 Knitr Solutions