[ESS] Is there a simple newbie guide to using knitr in ESS

Steve Lianoglou mailinglist.honeypot at gmail.com
Sun Feb 10 17:18:59 CET 2013

Hi Vitalie,

On Sun, Feb 10, 2013 at 11:01 AM, Vitalie Spinu <spinuvit at gmail.com> wrote:
> Hi,
> As far as I am concerned, this is the only must-do for ESS 13.03. I have
> finally resumed working on a new literate programming system for
> ESS. Will do my best to get it into 13.03.

That would be really awesome. I'm sure lots of people would be looking
forward to that.


While babel might look a bit strange at first, I'm pretty sure it's
actually not *that* bad ... also, org mode is supposed to be really
quite amazing (though, still, I don't use it), so if you do dabble w/
babel, you might get the added benefit of being blown away at how cool
org mode is in the process.

In fact ... I might be convincing myself to give babel a go as we speak ;-)


>     Vitalie
>   >> Steve Lianoglou <mailinglist.honeypot at gmail.com>
>   >> on Sun, 10 Feb 2013 10:48:22 -0500 wrote:
>   > Hi Chris,
>   > Last I checked, I'm pretty sure that the only kintr support in ESS is
>   > to have Sweave (*.Rnw) be piped through knitr instead of sweave for
>   > compilation of the semi-tex -> tex -> output.
>   > I would love to be told that I'm wrong, but it's my impression that
>   > Rmarkdown files are not really supported.
>   > As an alternative, I believe others have suggested to use org/babel,
>   > which *should* get you pretty close to an Rmarkdown-like document:
>   > http://orgmode.org/worg/org-contrib/babel/
>   > If I were a better person, I would have gone that route myself, but
>   > I've been using a different editor (Sublime Text 2) to whip up
>   > Rmarkdown documents.
>   > -steve
>   > On Sun, Feb 10, 2013 at 10:36 AM, Chris Evans <chrishold at psyctc.org> wrote:
>   >> Dear all,
>   >>
>   >> I am very keen to switch to knitr and a better literate statistics way of
>   >> using R.  I have been a long term user of emacs though never emacs lisp and a
>   >> fairly long term (a decade?) user of ESS to handle R.  I have never managed
>   >> the switch two sweave both because I've equally never made the switch to TeX
>   >> mainly because in my substantive field sadly everyone uses M$ Word documents
>   >> and the learning curve for TeX on top R was just too much for me.
>   >>
>   >> KnitR seems much easier for me to use and the HTML output (or PDF) is OK if
>   >> not ideal for sharing with colleagues and collaborators so I started using it
>   >> in Rstudio but I have yearned to come back to ESS as Rstudio is clever but too
>   >> often left me feeling I really didn't know how to debug it and missing my
>   >> usual keyboard commands.
>   >>
>   >> I was very pleased to see that knitr support is now in ESS but I'm failing
>   >> hopelessly to use it.  I had, perhaps naively, assumed that I could take .Rmd
>   >> files that had worked in Rstudio, starting with its initial template one, open
>   >> it in emacs/ESS and be away but that's absolutely not the case!  I then
>   >> searched around and found correspondence here from last year including a
>   >> request from Pierre Kleiber from October last year that is really the same as
>   >> mine request now:
>   >>
>   >> "Being a long-time user of R and ESS but never having tried sweave or other
>   >> literate programing systems, I would like to try knitr. I'm searching for a
>   >> knitr tutorial that makes use of ESS rather than RStudio. Can anyone direct me
>   >> to such a tutorial?"
>   >>
>   >> I can't see any answer and most of what I find about ESS/knitR is about
>   >> technicalities of what has to be done internally in ESS to make it work
>   >> ... nothing (not that I can understand) on how I can use it.
>   >>
>   >> It seems clear to me that Vitalie and others have got things in ESS so that it
>   >> works for them with their expertise. Please would someone tell me how I could
>   >> take this default file from Rstudio (attached) and rename it or get ESS to
>   >> recognise that it is in a markdown form suitable to be parsed and knitted up
>   >> by knitR and R?  Questions:
>   >>
>   >> 1) ESS doesn't seem to recognise it as any special file at all.  Does ESS expect another file extension (.rnw?)
>   >> 2) I think I have to tell ESS to use knitr not sweave by setting a variable.  Is there a way I can make that a permanent instruction as I don't use sweave?
>   >> 3) I suspect there are other things I need to do?!
>   >>
>   >> TIA,
>   >>
>   >> Chris
>   >>
>   >>
>   >> ______________________________________________
>   >> ESS-help at r-project.org mailing list
>   >> https://stat.ethz.ch/mailman/listinfo/ess-help>

Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact

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