R help - Nov 2015 - conditionally disable evaluation of chunks in Rmarkdown...

I do have an Rmd where I would like to conditionally evaluate the second part.

So far I am working with :

```{r}
if(length(specLibrary at ionlibrary) ==0){
  library(knitr)
  opts_chunk$set(eval=FALSE, message=FALSE, echo=FALSE)
}
```

Which disables the evaluation of subsequent chunks.

However my RMD file contains also these kind of snippets : `r `

How do I disable them?

regards



-- 
Witold Eryk Wolski

Strictly speaking, wrong email list.

Markdown is R Studio software, and you should post on their support site.

Cheers,
Bert


Bert Gunter

"Data is not information. Information is not knowledge. And knowledge
is certainly not wisdom."
   -- Clifford Stoll


On Tue, Nov 10, 2015 at 2:40 AM, Witold E Wolski <wewolski at gmail.com>
wrote:
> I do have an Rmd where I would like to conditionally evaluate the second
part.
>
> So far I am working with :
>
> ```{r}
> if(length(specLibrary at ionlibrary) ==0){
>   library(knitr)
>   opts_chunk$set(eval=FALSE, message=FALSE, echo=FALSE)
> }
> ```
>
> Which disables the evaluation of subsequent chunks.
>
> However my RMD file contains also these kind of snippets : `r `
>
> How do I disable them?
>
> regards
>
>
>
> --
> Witold Eryk Wolski
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.

Well, strictly speaking knitr and rmarkdown are a contributed packages and the
official contact for any contributed package is found via the maintainer()
function. The Posting Guide indicates that R-help should only be used as a
backup if that avenue is a dead end.

To be fair to the OP, there are a lot of useful contributed packages that get
discussed here anyway. But Bert is right that if there is a forum more
appropriate for a contributed package then it should be preferred and any
question posed here should mention any dead ends encountered and good netiquette
would be to link to any publicly-visible record of those attempts.
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Sent from my phone. Please excuse my brevity.

On November 10, 2015 6:44:16 AM PST, Bert Gunter <bgunter.4567 at
gmail.com> wrote:
>Strictly speaking, wrong email list.
>
>Markdown is R Studio software, and you should post on their support
>site.
>
>Cheers,
>Bert
>
>
>Bert Gunter
>
>"Data is not information. Information is not knowledge. And knowledge
>is certainly not wisdom."
>   -- Clifford Stoll
>
>
>On Tue, Nov 10, 2015 at 2:40 AM, Witold E Wolski <wewolski at
gmail.com>
>wrote:
>> I do have an Rmd where I would like to conditionally evaluate the
>second part.
>>
>> So far I am working with :
>>
>> ```{r}
>> if(length(specLibrary at ionlibrary) ==0){
>>   library(knitr)
>>   opts_chunk$set(eval=FALSE, message=FALSE, echo=FALSE)
>> }
>> ```
>>
>> Which disables the evaluation of subsequent chunks.
>>
>> However my RMD file contains also these kind of snippets : `r `
>>
>> How do I disable them?
>>
>> regards
>>
>>
>>
>> --
>> Witold Eryk Wolski
>>
>> ______________________________________________
>> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>> https://stat.ethz.ch/mailman/listinfo/r-help
>> PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>> and provide commented, minimal, self-contained, reproducible code.
>
>______________________________________________
>R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
>https://stat.ethz.ch/mailman/listinfo/r-help
>PLEASE do read the posting guide
>http://www.R-project.org/posting-guide.html
>and provide commented, minimal, self-contained, reproducible code.

The short answer is you cannot. Inline R code is always evaluated.
When it is not evaluated, I doubt if your output still makes sense,
e.g. "The value of x is `r x`." becomes "The value of x is
." That
sounds odd to me.

If you want to disable the evaluate of inline code anyway, you may use
a custom function to do it. e.g.

cond_eval = function(x) {
  if (isTRUE(knitr::opts_chunk$get('eval'))) x
}

Then `r cond_eval(x)` instead of `r x`.

Regards,
Yihui
--
Yihui Xie <xieyihui at gmail.com>
Web: http://yihui.name


On Tue, Nov 10, 2015 at 4:40 AM, Witold E Wolski <wewolski at gmail.com>
wrote:
> I do have an Rmd where I would like to conditionally evaluate the second
part.
>
> So far I am working with :
>
> ```{r}
> if(length(specLibrary at ionlibrary) ==0){
>   library(knitr)
>   opts_chunk$set(eval=FALSE, message=FALSE, echo=FALSE)
> }
> ```
>
> Which disables the evaluation of subsequent chunks.
>
> However my RMD file contains also these kind of snippets : `r `
>
> How do I disable them?
>
> regards
>
>
>
> --
> Witold Eryk Wolski

On Tue, Nov 10, 2015 at 9:00 AM, Yihui Xie <xie at yihui.name>
wrote:
> The short answer is you cannot. Inline R code is always evaluated.
> When it is not evaluated, I doubt if your output still makes sense,
> e.g. "The value of x is `r x`." becomes "The value of x is
." That
> sounds odd to me.
>
> If you want to disable the evaluate of inline code anyway, you may use
> a custom function to do it. e.g.
>
> cond_eval = function(x) {
>   if (isTRUE(knitr::opts_chunk$get('eval'))) x
> }
>
> Then `r cond_eval(x)` instead of `r x`.
>
> Regards,
> Yihui
> --
> Yihui Xie <xieyihui at gmail.com>
> Web: http://yihui.name
>
>
> On Tue, Nov 10, 2015 at 4:40 AM, Witold E Wolski <wewolski at
gmail.com> wrote:
>> I do have an Rmd where I would like to conditionally evaluate the
second part.
>>
>> So far I am working with :
>>
>> ```{r}
>> if(length(specLibrary at ionlibrary) ==0){
>>   library(knitr)
>>   opts_chunk$set(eval=FALSE, message=FALSE, echo=FALSE)
>> }
>> ```
>>
>> Which disables the evaluation of subsequent chunks.
>>
>> However my RMD file contains also these kind of snippets : `r `
>>
>> How do I disable them?
Just a FYI and maybe/maybe not a option for you; this is one of the
use cases where RSP (https://cran.r-project.org/package=R.rsp) is
handy because it does not require that code snippets (aka "code
chunks" as originally defined by weave/tangle literate programming) to
contain complete expressions.  With RSP-embedded documents, you can do
things such

    <% if (length(specLibrary at ionlibrary) > 0) { %>

    [... code and text blocks to conditionally include ...]

    <% } # if (length(specLibrary at ionlibrary) > 0) %>

or include from a separate file, e.g.

    <% if (length(specLibrary at ionlibrary) > 0) { %> <%@include
file="extras.md.rsp"%> <% } %>

You can also use loops over a mixture of code and text blocks etc.

Depending on when 'specLibrary at ionlibrary' gets assigned, you could
preprocess you R Markdown file with RSP, but for this to work out of
the box you basically need to know the value
length(specLibrary at ionlibrary) before your R Markdown code is
evaluated, i.e. before you compile the Rmd file.  Your build pipeline
would then look something like:

    rmd <- R.rsp::rfile("report.rmd.rsp")
    rmarkdown::render(rmd)

/Henrik
(author of R.rsp)
>>
>> regards
>>
>>
>>
>> --
>> Witold Eryk Wolski
>
> ______________________________________________
> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide
http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.