[R-SIG-Mac] R code chunks

[Ivan Calandra]

Thank you Mollie and all,

So it looks like there's no way to properly use chunks within the Mac R 
GUI.
I will have to decide whether I completely switch to RStudio, or develop 
in the R GUI and then run in RStudio.

Still, until now I was a great fan of the R GUI on Mac so I'm a bit 
frustrated. It would be great if this feature were integrated to the R 
GUI some day! Alternatively, a better GUI for RStudio allowing for 
multiple screens would be fine too (but that's for another list!).

Bests,
Ivan

--
Ivan Calandra, PhD
University of Reims Champagne-Ardenne
GEGENAA - EA 3795
CREA - 2 esplanade Roland Garros
51100 Reims, France
+33(0)3 26 77 36 89
ivan.calandra at univ-reims.fr
--
https://www.researchgate.net/profile/Ivan_Calandra
https://publons.com/author/705639/

Le 12/04/2016 15:05, Mollie Brooks a écrit :
> Hi Ivan,
>
> Using the R GUI and the built-in editor, you should be able to format 
> your document in the standard Rmarkdown or knitr way and save it with 
> the appropriate extension (Rmd or Rnw), but only run lines within 
> chunks in the console (using command + enter in the normal way). You 
> can make sure all the chunks are working in that way. Then to format 
> the whole document you can use a command in the Terminal as described 
> in the links Tom sent or reopen the document in Rstudio.
>
> Somehow my R GUI can’t find the right pieces to make the pdf, so I 
> have to use the Terminal. render("EstObsErr.Rmd") produces the error
> /usr/local/bin/pandoc EstObsErr.utf8.md --to latex --from 
> markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures 
> --output EstObsErr.pdf --template 
> /Library/Frameworks/R.framework/Versions/3.2/Resources/library/rmarkdown/rmd/latex/default-1.14.tex 
> --highlight-style tango --latex-engine pdflatex --variable 
> 'geometry:margin=1in'
> pandoc: pdflatex not found. pdflatex is needed for pdf output.
> Error: pandoc document conversion failed with error 41
>
> cheers,
> Mollie
>
> ------------------------
> Mollie Brooks, PhD
> Postdoctoral Researcher, Population Ecology Research Group
> Department of Evolutionary Biology & Environmental Studies, University 
> of Zürich
> http://www.popecol.org/team/mollie-brooks/
>
>> On 12Apr 2016, at 12:57, Ivan Calandra <ivan.calandra at univ-reims.fr 
>> <mailto:ivan.calandra at univ-reims.fr>> wrote:
>>
>> Thank you for your answer.
>>
>> I don't usually use the Terminal, so I'm not sure how to do it.
>> But do you mean to start it from the Terminal and then use the R GUI 
>> or do everything in the Terminal? In the latter case, I would prefer 
>> using RStudio... My question was about using the R GUI Editor rather 
>> than RStudio.
>>
>> Ivan
>>
>> --
>> Ivan Calandra, PhD
>> University of Reims Champagne-Ardenne
>> GEGENAA - EA 3795
>> CREA - 2 esplanade Roland Garros
>> 51100 Reims, France
>> +33(0)3 26 77 36 89
>> ivan.calandra at univ-reims.fr <mailto:ivan.calandra at univ-reims.fr>
>> --
>> https://www.researchgate.net/profile/Ivan_Calandra
>> https://publons.com/author/705639/
>>
>> Le 12/04/2016 11:41, Tom Hopper a écrit :
>>> Ivan,
>>>
>>> You need to run knitr manually from the terminal (RStudio automates 
>>> this with the “knit” button). See
>>>
>>> http://joshldavis.com/2014/04/12/beginners-tutorial-for-knitr/
>>> http://kbroman.org/knitr_knutshell/pages/Rmarkdown.html
>>>
>>> for short tutorials on using knitr from the terminal.
>>>
>>> Regards,
>>>
>>> Tom
>>>
>>>> On 201604 12, at 05:15, Ivan Calandra <ivan.calandra at univ-reims.fr 
>>>> <mailto:ivan.calandra at univ-reims.fr>> wrote:
>>>>
>>>> Dear Mac useRs,
>>>>
>>>> A colleague of mine have introduced me to rmarkdown and knitr to 
>>>> produce nice reports. The other interesting thing here is to have 
>>>> so-called chunks of code, which I find very practical to organize 
>>>> scripts.
>>>>
>>>> I have found that it works well within RStudio. But is there a way 
>>>> to enable chunks within the R GUI (and its great editor)?
>>>> What I don't like with RStudio (except that I need to install still 
>>>> another software, and place is limited on the 256GB SSD of my 
>>>> MacBook Air) is that it is not able to work on multiple screens.
>>>>
>>>> Thank you in advance for your help.
>>>> Ivan
>>>>
>>>> -- 
>>>> Ivan Calandra, PhD
>>>> University of Reims Champagne-Ardenne
>>>> GEGENAA - EA 3795
>>>> CREA - 2 esplanade Roland Garros
>>>> 51100 Reims, France
>>>> +33(0)3 26 77 36 89
>>>> ivan.calandra at univ-reims.fr <mailto:ivan.calandra at univ-reims.fr>
>>>> --
>>>> https://www.researchgate.net/profile/Ivan_Calandra
>>>> https://publons.com/author/705639/
>>>>
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>>>
>>
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