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

Vitalie Spinu spinuvit at gmail.com
Sun Feb 10 17:01:44 CET 2013


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.


  >> 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
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