    eval = FALSE

Checkout The R Markdown Cheat Sheet http://blog.rstudio.org/2014/08/01/the-r-markdown-cheat-sheet/

It summarizes the options for code chunks

I&#39;ve uploaded my website to a webhosting and this error came up; &lt;br/&gt;
&#39;**Error occurred during a cryptographic operation**.&#39;.&lt;br/&gt;
&lt;br/&gt;
I&#39;ve done some research and it seems that the formauthenticated cookie is bound to the MachineKey (which differs when using webhost).&lt;br/&gt;

&lt;br/&gt;
I&#39;ve found a method that should fix this problem but the error remains.&lt;br/&gt;
&lt;br/&gt;
**CODE:**&lt;br/&gt;

    /// &lt;summary&gt;
        /// This method removes a cookie if the machine key is different than the one that saved the cookie;
        /// &lt;/summary&gt;
        protected void Application_Error(object sender, EventArgs e)
        {
            var error = Server.GetLastError();
            var cryptoEx = error as CryptographicException;
            if (cryptoEx != null)
            {
                FederatedAuthentication.WSFederationAuthenticationModule.SignOut();
                Global.Cookies.FormAuthenticated Cookie = new Global.Cookies.FormAuthenticated();
                Cookie.Delete();
                Server.ClearError();
            }
        }

&lt;br/&gt;
**STACKTRACE:**&lt;br/&gt;

    
    [CryptographicException: Error occurred during a cryptographic operation.]
       System.Web.Security.Cryptography.HomogenizingCryptoServiceWrapper.HomogenizeErrors(Func`2 func, Byte[] input) +115
       System.Web.Security.Cryptography.HomogenizingCryptoServiceWrapper.Unprotect(Byte[] protectedData) +59
       System.Web.Security.FormsAuthentication.Decrypt(String encryptedTicket) +9824926
       Archive_Template.Main.resolveLoginUser(String sessionKey) in f:\Archive_Template\Archive_Template\Main.aspx.cs:481
       Archive_Template.Main.OnPreInit(EventArgs e) in f:\Archive_Template\Archive_Template\Main.aspx.cs:52
       System.Web.UI.Page.PerformPreInit() +31
       System.Web.UI.Page.ProcessRequestMain(Boolean includeStagesBeforeAsyncPoint, Boolean includeStagesAfterAsyncPoint) +335



&quot;Error occurred during a cryptographic operation&quot; when decrypting Forms cookie

Has anyone been able to load an app preview video in iTunes connect?  I receive an error every time, saying &quot;Your file could not be loaded.  Please try again.&quot;

Any workaround to this, that you&#39;re aware of?

Unable to load app preview in iTunes connect

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 am using <code>Rmarkdown</code> and <code>Knitr</code> using Rstudio.
The following both print script and output to html.
<pre><code class="hljs language-go">```{r}
summary(cars)
```
</code></pre>
However the following will only print the output, that is embedded plot.
<pre><code class="hljs language-go">```{r, echo=FALSE}
plot(cars)
```
</code></pre>
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.
<pre><code class="hljs language-go">```{r}
#summary(cars)
```
</code></pre>
But I need a better way to do this - Is there any better way presenting script without running it.

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 received one of these errors.  

    Error: unexpected symbol in &quot;&lt;my code&gt;&quot;    
    Error: unexpected input in &quot;&lt;my code&gt;&quot;
    Error: unexpected string constant in &quot;&lt;my code&gt;&quot;  
    Error: unexpected numeric constant in &quot;&lt;my code&gt;&quot;   
    Error: unexpected SPECIAL in &quot;&lt;my code&gt;&quot;         
    Error: unexpected &#39;&lt;some punctuation&gt;&#39; in &quot;&lt;my code&gt;&quot; 
    Error: unexpected &#39;&lt;reserved word&gt;&#39; in &quot;&lt;my code&gt;&quot;        

**What does the error mean, and how can I fix it?**

Some simple examples that reproduce the errors, and common variants:

    a a
    ## Error: unexpected symbol in &quot;a a&quot;
    a\
    ## Error: unexpected input in &quot;a\&quot;
    a&quot;&quot;
    ## Error: unexpected string constant in &quot;a&quot;&quot;&quot;
    &quot;&quot;1
    ## Error: unexpected numeric constant in &quot;&quot;&quot;1&quot;
    %%
    ## Error: unexpected SPECIAL in &quot;%%&quot;
    ,
    ## Error: unexpected &#39;,&#39; in &quot;,&quot;
    =
    ## Error: unexpected &#39;=&#39; in &quot;=&quot;
    )
    ## Error: unexpected &#39;)&#39; in &quot;)&quot;
    else
    ## Error: unexpected &#39;else&#39; in &quot;else&quot;



Error: unexpected symbol/input/string constant/numeric constant/SPECIAL in my code

I have a data frame (&quot;data&quot;) with lots and lots of columns. Some of the columns contain a certain string (&quot;search_string&quot;).

How can I use `dplyr::select()` to give me a subset including only the columns that contain the string?

I tried:

    # columns as boolean vector
    select(data, grepl(&quot;search_string&quot;,colnames(data)))
    
    # columns as vector of column names names 
    select(data, colnames(data)[grepl(&quot;search_string&quot;,colnames(data))]) 

Neither of them work.

I know that `select()` accepts numeric vectors as substitute for columns e.g.:

    select(data,5,7,9:20)

But I don&#39;t know how to get a numeric vector of columns `ID`s from my `grepl()` expression.

Select columns based on string match - dplyr::select

I have data from an online survey where respondents go through a loop of questions 1-3 times. The survey software (Qualtrics) records this data in multiple columns—that is, Q3.2 in the survey will have columns `Q3.2.1.`, `Q3.2.2.`, and `Q3.2.3.`: 

    df &lt;- data.frame(
      id = 1:10,
      time = as.Date(&#39;2009-01-01&#39;) + 0:9,
      Q3.2.1. = rnorm(10, 0, 1),
      Q3.2.2. = rnorm(10, 0, 1),
      Q3.2.3. = rnorm(10, 0, 1),
      Q3.3.1. = rnorm(10, 0, 1),
      Q3.3.2. = rnorm(10, 0, 1),
      Q3.3.3. = rnorm(10, 0, 1)
    )

    # Sample data

       id       time    Q3.2.1.     Q3.2.2.    Q3.2.3.     Q3.3.1.    Q3.3.2.     Q3.3.3.
    1   1 2009-01-01 -0.2059165 -0.29177677 -0.7107192  1.52718069 -0.4484351 -1.21550600
    2   2 2009-01-02 -0.1981136 -1.19813815  1.1750200 -0.40380049 -1.8376094  1.03588482
    3   3 2009-01-03  0.3514795 -0.27425539  1.1171712 -1.02641801 -2.0646661 -0.35353058
    ...

I want to combine all the QN.N* columns into tidy individual QN.N columns, ultimately ending up with something like this:

       id       time loop_number        Q3.2        Q3.3
    1   1 2009-01-01           1 -0.20591649  1.52718069
    2   2 2009-01-02           1 -0.19811357 -0.40380049
    3   3 2009-01-03           1  0.35147949 -1.02641801
    ...
    11  1 2009-01-01           2 -0.29177677  -0.4484351
    12  2 2009-01-02           2 -1.19813815  -1.8376094
    13  3 2009-01-03           2 -0.27425539  -2.0646661
    ...
    21  1 2009-01-01           3 -0.71071921 -1.21550600
    22  2 2009-01-02           3  1.17501999  1.03588482
    23  3 2009-01-03           3  1.11717121 -0.35353058
    ...


The `tidyr` library has the `gather()` function, which works great for combining *one* set of columns:

    library(dplyr)
    library(tidyr)
    library(stringr)

    df %&gt;% gather(loop_number, Q3.2, starts_with(&quot;Q3.2&quot;)) %&gt;% 
      mutate(loop_number = str_sub(loop_number,-2,-2)) %&gt;%
      select(id, time, loop_number, Q3.2)


       id       time loop_number        Q3.2
    1   1 2009-01-01           1 -0.20591649
    2   2 2009-01-02           1 -0.19811357
    3   3 2009-01-03           1  0.35147949
    ...
    29  9 2009-01-09           3 -0.58581232
    30 10 2009-01-10           3 -2.33393981

The resultant data frame has 30 rows, as expected (10 individuals, 3 loops each). However, gathering a second set of columns does not work correctly—it successfully makes the two combined columns `Q3.2` and `Q3.3`, but ends up with 90 rows instead of 30 (all combinations of 10 individuals, 3 loops of Q3.2, and 3 loops of Q3.3; the combinations will increase substantially for each group of columns in the actual data):

    df %&gt;% gather(loop_number, Q3.2, starts_with(&quot;Q3.2&quot;)) %&gt;% 
      gather(loop_number, Q3.3, starts_with(&quot;Q3.3&quot;)) %&gt;%
      mutate(loop_number = str_sub(loop_number,-2,-2))


       id       time loop_number        Q3.2        Q3.3
    1   1 2009-01-01           1 -0.20591649  1.52718069
    2   2 2009-01-02           1 -0.19811357 -0.40380049
    3   3 2009-01-03           1  0.35147949 -1.02641801
    ...
    89  9 2009-01-09           3 -0.58581232 -0.13187024
    90 10 2009-01-10           3 -2.33393981 -0.48502131


Is there a way to use multiple calls to `gather()` like this, combining small subsets of columns like this while maintaining the correct number of rows?

Gather multiple sets of columns

My plot is showing values on the y-axis in the form of e notation. Which command should I use to get the values in the numeric form. The values in the file used are in the numeric form?
Thanks

How to prevent scientific notation in R?

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 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?

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;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

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 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?

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

Content Type	Original Author	Original Content on Stackoverflow
Question	SHRram	View Question on Stackoverflow
Solution 1 - R	Hernando Casas	View Answer on Stackoverflow

preventing a chunk run in rmarkdown

R Problem Overview

R Solutions

Solution 1 - R

Unable to load app preview in iTunes connect

"Error occurred during a cryptographic operation" when decrypting Forms cookie

Attributions