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

Chris Evans chrishold at psyctc.org
Sun Feb 10 16:59:36 CET 2013

Aha.  Thanks Steve. That would fit with my getting nowhere (noweb/nowhere: starting to feel ominously similar to me!)

I've just had a look at the paper at http://www.jstatsoft.org/v46/i03/paper which introduces org mode and it looks very clever but not what I, as someone in the overlap field of psychotherapy research, would call "literate".  I guess if that's what I've got to learn to stick with emacs/ESS/R and get "literate" and it helps me avoid learning TeX I might still give it a go.

Can anyone confirm and perhaps give a simple guide that might allow me to do some of what I was doing in Rstudio in ESS?

I'd hugely appreciate if someone can,


----- Original Message -----
> From: "Steve Lianoglou" <mailinglist.honeypot at gmail.com>
> To: "Chris Evans" <chrishold at psyctc.org>
> Cc: ess-help at r-project.org
> Sent: Sunday, 10 February, 2013 3:48:22 PM
> Subject: Re: [ESS] Is there a simple newbie guide to using knitr in ESS
> 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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