How to add new line in Markdown presentation?

I mean, something like `\newline` in TeX.

How to add new line in Markdown presentation?

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 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

So I want to insert a table AND a picture into R Markdown. In regular word document I can just easily insert a table (5 rows by 2 columns), and for the picture just copy and paste.

1. How do I insert a 5 row by 2 column table (and also type stuff into them)(and also adjust the table in terms of the 2nd column being wider than the first)?

2. How do I insert a picture? From my understanding, I should first save the picture as a png, then reference it into my document. Also, I want to automatically adjust the picture to the report, like not taking up more than a page, or less than a page.(Is there a way for me to adjust the size of the picture to my liking)?

3. If anyone knows anything cool/formatting about R Markdown could you also let me know? I know that `#` makes a big title for a paragraph, and `** **` bolds things. Thats about all I know though!

Insert picture/table in R Markdown

in markdown, `my_stock_index` is my*stock*index. But I want it to show `my_stock_index`. How can do that?

how to show underscores symbol in 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 wonder if one could simply use LaTeX `\newpage` command in R markdown v2 in a different way than this:

    ```{r, results=&#39;asis&#39;, echo=FALSE}
    cat(&quot;\\newpage&quot;)
    ```

I produce pdf_output.
If any1 has any idea please do not hesitate to comment :) ! 
Thanks

I create pdf like this:

    ---
    title: &quot; &quot;
    author: &quot; &quot;
    date: &quot;2014&quot;
    output: 
       pdf_document:
          includes:
             in_header: naglowek.tex
          highlight: pygments
          toc: true
          toc_depth: 3
          number_sections: true
          keep_tex: true
    ---

How to add \newpage in Rmarkdown in a smart way?

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

I am using RStudio for writing markdown documents and want to add Table of Contents (TOC) at top of the documents so that the user could click the relevant section for reading. There were some relevant examples on rpubs but now I can&#39;t seem to find them. Please note that I don&#39;t use `pandoc` and am quite new to `Rmd` &amp; `knitr`. Is there any way to add TOCs without using `pandoc`? If using `pandoc` is must then which functions are relevant?

# EDIT

Here&#39;s a small sample page:

    ---
    title: &quot;Sample Document&quot;
    output:
      html_document:
        toc: true
        theme: united
    ---

    Header 1
    ---------------
    This is an R Markdown document. Markdown is a simple formatting syntax for authoring HTML, PDF, and MS Word documents. For more details on using R Markdown see &lt;http://rmarkdown.rstudio.com&gt;.
        
    ## Header 2
    When you click the **Knit** button a document will be generated that includes both content as well as the output of any embedded R code chunks within the document. You can embed an R code chunk like this:
        
    ```{r}
    summary(cars)
    ```
    
    You can also embed plots, for example:
    
    ```{r, echo=FALSE}
    plot(cars)
    ```
    ### Header 3
    Note that the `echo = FALSE` parameter was added to the code chunk to prevent printing of the R code that generated the plot.

I tried running this in RStudio v 0.98.864 and it worked! but sadly it didn&#39;t work on 0.98.501 and 0.98.507. I am working on my thesis in 0.98.501 and after updating RStudio, some of my analyses didn&#39;t work. So, I reverted back to 0.98.501.
What should I do now? I really want TOCs but without harming the outputs of other analyses.


How to add table of contents in Rmarkdown?

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 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

In RMarkdown is there a way to specify the font color? 

There doesn&#39;t seem to be an option while browsing through the [chunk options][1] 




  [1]: http://yihui.name/knitr/options/#chunk_options

RMarkdown: How to change the font color?

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

**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

I want to center an image and/or text using R Markdown and knit a PDF report out of it.

I have tried using:

    -&gt;Text&lt;-

    -&gt;![](image1.jpg)&lt;-

That does not do the trick! Any other way of getting this done?

Centering image and text in R Markdown for a PDF report

***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

When I use the render{rmarkdown} to produce pdf file from .Rmd file on my Mac, an error message says

`pandoc: pdflatex not found. pdflatex is needed for pdf output.
Error: pandoc document conversion failed` 

However when I check with 

    pdflatex -v
I got

    pdfTeX 3.1415926-2.4-1.40.13 (TeX Live 2012)
    kpathsea version 6.1.0
    Copyright 2012 Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
    There is NO warranty.  Redistribution of this software is
    covered by the terms of both the pdfTeX copyright and
    the Lesser GNU General Public License.
    For more information about these matters, see the file
    named COPYING and the pdfTeX source.
    Primary author of pdfTeX: Peter Breitenlohner (eTeX)/Han The Thanh (pdfTeX).
    Compiled with libpng 1.5.10; using libpng 1.5.10
    Compiled with zlib 1.2.7; using zlib 1.2.7
    Compiled with xpdf version 3.03
The pdflatex is installed in my machine.

Can anyone help to tell how can I tell R where to find the pdflatex?

Many thanks!


rmarkdown: pandoc: pdflatex not found

I&#39;m trying to follow [this pandoc example](http://johnmacfarlane.net/pandoc/demo/example9/pandocs-markdown.html#yaml-metadata-block) to add multiple authors to an Rmarkdown file in the [yaml metadata block](http://rmarkdown.rstudio.com/authoring_pandoc_markdown.html#yaml-metadata-block). The pdf will generate in RStudio (Version 0.98.932), but there is no author information. 

    ---
    title:  &#39;This is the title: it contains a colon&#39;
    author:
    - name: Author One
      affiliation: University of Somewhere
    - name: Author Two
      affiliation: University of Nowhere
    date: &quot;`r format(Sys.time(), &#39;%d %B %Y&#39;)`&quot;
    tags: [nothing, nothingness]
    abstract: |
      This is the abstract.
    
      It consists of two paragraphs.
    output: pdf_document
    ---

I&#39;d also like to customize the heading a bit more and add a subtitle. Possible?

multiple authors and subtitles in Rmarkdown yaml

I have a problem generating a pdf report from my app shiny which is hosted on a server. 

the app works fine but when I press the button to download the report, I get this error :

     pandoc version 1.12.3 or higher is required and was not found.

The proble is that if I type `pandoc -v` I get:

     pandoc 1.12.3.3
     Compiled with texmath 0.6.6, highlighting-kate 0.5.6.1.
    Syntax highlighting is supported for the following languages:
        actionscript, ada, apache, asn1, asp, awk, bash, bibtex, boo, c, changelog,
        clojure, cmake, coffee, coldfusion, commonlisp, cpp, cs, css, curry, d,
        diff, djangotemplate, doxygen, doxygenlua, dtd, eiffel, email, erlang,
        fortran, fsharp, gnuassembler, go, haskell, haxe, html, ini, java, javadoc,
        javascript, json, jsp, julia, latex, lex, literatecurry, literatehaskell,
        lua, makefile, mandoc, markdown, matlab, maxima, metafont, mips, modelines,
        modula2, modula3, monobasic, nasm, noweb, objectivec, objectivecpp, ocaml,
        octave, pascal, perl, php, pike, postscript, prolog, python, r,
        relaxngcompact, restructuredtext, rhtml, roff, ruby, rust, scala, scheme,
        sci, sed, sgml, sql, sqlmysql, sqlpostgresql, tcl, texinfo, verilog, vhdl,
        xml, xorg, xslt, xul, yacc, yaml
     Default user data directory: /home/daniele/.pandoc
     Copyright (C) 2006-2013 John MacFarlane
     Web:  http://johnmacfarlane.net/pandoc
     This is free software; see the source for copying conditions.  There is no
     warranty, not even for merchantability or fitness for a particular purpose.

So I suppose I have the right version for that. TexLive is also installed and the path is in `$PATH`.

**Server.R**

    library(shiny)
    library(drsmooth)
    library(shinyBS)
    library(knitr)
    library(xtable)
    library(rmarkdown)

    shinyServer(function(input, output,session) { 
   
     output$downloadReport &lt;- downloadHandler(
    filename = function() {
      paste(&#39;report&#39;, sep = &#39;.&#39;,&#39;pdf&#39;)
    },
    
    content = function(file) {
      src &lt;- normalizePath(&#39;report.Rmd&#39;)
      
      # temporarily switch to the temp dir, in case you do not have write
      # permission to the current working directory
      owd &lt;- setwd(tempdir())
      on.exit(setwd(owd))
      file.copy(src, &#39;report.Rmd&#39;)
      
      library(rmarkdown)
      out &lt;- render(&#39;report.Rmd&#39;)
      file.rename(out, file)
    })

    output$tb &lt;- renderUI({
                 p(h4(&quot;Report&quot;)),
                &quot;Dowload a the report of your analysis in a pdf format&quot;,
                tags$br(),downloadButton(&#39;downloadReport&#39;,label=&quot;Download report&quot;),
                tags$em(&quot;This option will be available soon&quot;)
         })
    })

*** report.Rmd*** does not contain any sort of calculation, it&#39;s only text.
The pdf generation works fine on my local version (MacOS) but not on the server.

I&#39;m here to give other information if needed.



pandoc version 1.12.3 or higher is required and was not found (R shiny)

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?

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 am putting together an R Markdown HTML page for some new R users at my work to give them an introduction and walk them through some simple demos.

While showing off things like `head` and `tail`, it ends up looking messy and long because it prints out each output one after the other. I would like them as long as other sections of my .Rmd to be split into two columns.

In my research, I came across this [question](https://stackoverflow.com/questions/19237190/2-column-report-in-r-markdown-render-html-aside-data-frame). There was some discussion of workarounds with HTML code I did not understand.

I did try including:
```
&lt;div class=&quot;columns-2&quot;&gt;   
&lt;/div&gt;
```
from the official `rmarkdown` documentation, but it did not have any effect.

As I was ready to give up, there was a comment on the Stack Overflow question by @Molx saying that you can separate columns with `***`, but it did not give any further explanation. I tried it out in a few ways: I included the `***` in the middle of my R code chunk, I separated my R code chunks and put the `***` between the two. When I did the latter, the `***` simply became a horizontal rule and did nothing with columns.

I am hoping to avoid tables and CSS if possible.

How to export RMarkdown file to HTML document with two columns?

**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;ve got an Rmarkdown template that works well, and I&#39;ve parameterized it so I can generate variants of the same report from different data sources. However, I&#39;d like to change the title of the report in each case. How do I do that? 

Here&#39;s the YAML header I have so far:

    ---
    title: &quot;My Title&quot;
    author: &quot;Me, Inc.&quot;
    date: &quot;August 4, 2015&quot;
    output: pdf_document
    params:
      title: default
    ---

I&#39;ve tried using `params=list(title=&quot;ASDF&quot;)` in the call to `rmarkdown::render`, and although my code can see that variable, it doesn&#39;t change the title. I&#39;ve also tried using `r params$title` in the YAML, but that gives a syntax error.

Is there something else I should be trying? Thanks!


Setting document title in Rmarkdown from parameters

for some reason no link in my R markdowns (rmd) is formatted blue. knitting the simple rmd below to pdf is leaving the text color black. only when hovering over it does one realize that it&#39;s actually a link. knitting it to html will make the link blue. of course I can use a latex wrapper but I wonder why that is?

&gt; sessionInfo()
R version 3.3.0 (2016-05-03)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
loaded via a namespace (and not attached):
 knitr_1.15

RStudio 1.0.44

    ---
    title: &quot;R Notebook&quot;
    output:
      pdf_document: default
      html_notebook: default
    ---

    ```{r, echo=F}
    # tex / pandoc options for pdf creation
    x &lt;- Sys.getenv(&quot;PATH&quot;)
    y &lt;- paste(x, &quot;E:\\miktex\\miktex\\bin&quot;, sep=&quot;;&quot;)
    Sys.setenv(PATH = y)
    ```

    [link](www.rstudio.com)

[![enter image description here][1]][1]
  [1]: https://i.stack.imgur.com/awos7.png

R markdown link is not formatted blue when knitted to pdf

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

Is there a way to configure Emacs so that it recognizes (and allows execution of) R code chunks within R markdown (.Rmd) files similar to the way it recognizes code chunks in .Rnw (Sweave) or .org (org-mode) files?

How can I use Emacs ESS mode with R markdown?

I have a quite long title in a rmarkdown document and I would like to force a line break in a specific position.

Minimum example:

    ---
    title: &quot;Quite long title want the * line break at the asterisk&quot;
    output: html_document
    ---

I have tried: \n, \newline, \\\\ and a manual line break. None of them seem to work.

I believe it has to be quite straightforward but I haven&#39;t been able to find a solution.





How can I force a line break in rmarkdown&#39;s title?

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 am trying to create a report in R markdown that has sections ordered

1. Section 1 Header
    
    1.1 sub section 1

    1.2 sub section 3

2. Section 2 Header

    2.1 

    2.2 sub section 

          2.2.1 another sub section

Is there a way get R markdown to generate an ordered list like this?
 

Automatically number sections in RMarkdown

Is there a way to do it by adding latex code in the text or does the solution lie in (R)Markdown?

No sign of a solution here: http://rmarkdown.rstudio.com/pdf_document_format.html

At present I&#39;m bodging a solution by adding my `monospace` signature to the bottom of the 1st page, to force the next section to start on page 2: https://github.com/Robinlovelace/Creating-maps-in-R/blob/master/intro-spatial-rl.pdf


How to add whitespace to an RMarkdown document?

`setwd` in an Rmd file in RStudio does not appear to change the directory in subsequent chunks.  Is there a way to set the working directory for good?

Example:

    ```{r}
    setwd(&quot;/tmp&quot;)
    getwd()
    ```
    
    ```{r}
    getwd()
    ```

Output:

    setwd(&quot;/tmp&quot;)
    getwd()
    ## [1] &quot;/private/tmp&quot;

    getwd()
    ## [1] &quot;/Users/me/src&quot;

This is on Mac OS 10.8.5 using RStudio 0.97.551, R version 3.0.2 and knitr version 1.5.

I wish to set the directory once for all subsequent chunks.



In RStudio/RMarkdown, how to setwd?

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. 




All R Markdown Solutions on Gang of Coders

Total of 45 R Markdown Solutions