[R-SIG-Mac] R code chunks

[Mollie Brooks]

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> 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
> --
> 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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>>> R-SIG-Mac mailing list
>>> R-SIG-Mac at r-project.org
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>> 
> 
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