[knitr] Elegant, flexible and fast dynamic report generation with R | /knitr/

[yihui]

knitr: Elegant, flexible and fast dynamic report generation with R

https://yihui.org/knitr/

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Guest *Kihoro* @ 2012-03-02 08:38:03 originally posted:

Thanks for your good work. We are following and using the tools innovatively. Here at  JKUAT (KENYA) .  We are now able to dynamically generate exams in LYX.  

[yihui]

 That sounds super cool! Do you have any examples that I can see online? If not, I'm wondering the brief idea behind these dynamic exams. Thanks!

Originally posted on 2012-03-02 20:28:48

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Guest *Kihoro* @ 2012-03-22 18:47:32 originally posted:

System not yet hosted but the concept is simple.

Write all questions (with their answers/solutions) as child documents and have the main file to input them only if knitr code allows (random or systematic) selection. Knitting allows not manages the file/question selection but also sweaves the child files before a  standard exam draft with appended marking scheme thanks to answers.sty package.

Two questions

1. With the appended exams it would be nenessary to access the lyx/latex file containing the solutions. Is this possible. In other words, how can one access lyx temporary files immediately after compilation.

2. With Knitr, character zero (0) is displayed in scientific notation. How can I alter this?

[yihui]

2 is a bug and has been fixed in the latest version on CRAN; for 1, take a look at the object .cmdargs when you compile the lyx document -- it contains information about the temp directory (e.g. dirname(.cmdargs[1]) might be what you want).

Originally posted on 2012-03-22 20:01:12

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Guest *astaines* @ 2012-03-31 20:20:16 originally posted:

Very impressive, thank you very much!
Anthony Staines

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Guest *idrisr* @ 2012-04-09 03:52:44 originally posted:

I'm about to dig in to knitr, thanks in advance for your effrots.

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Guest *Timm Danker* @ 2012-04-10 10:16:25 originally posted:

Thank you so musch for this excellent work!

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Guest *MartinInFfm* @ 2012-04-11 02:14:48 originally posted:

I use the lyx/knitr  for dataset validation reporting in population pharmacokinetic modeling and simulation.
The new code externalization is superb.
What could improved is that

• framed chunks (you use them in your demos) appear to work differently than unframed chunks.
  The frame of a chunk is a pain because on the screen you do not see whether the surrounding format is "standard" as you most certainly want it or "chunk". Framed chunks embedded in a chunk environment are not executed without warning.
  The benefit of the frame around a chunk is still unclear to me as it has no properties menu.
  One feature that would come in handy would be collapsability of the frame at a mouse click.
  Another would be mobility so that the chunk label needs no update if I cut and paste it somewhere else.
• The cache function could be simplified. At the moment I create a new filename everytime I want to preview. Cache=FALSE does not help somehow. There appear pdf in the same folder where the lyx file is kept.
  Is there a global option to switch off all caching?

[yihui]

1. I guess you mean the TeX ERT (Ctrl+L)  is the framed chunk, and the Chunk ERT is the unframed chunk ( https://github.com/downloads/yihui/lyx/sweave.pdf ). The former is more stable because it is a whole unit and the Chunk ERT is not, e.g. you cannot easily paste code into a Chunk ERT, and when you copy and paste a Chunk ERT, you can lose the indentation information. It is strongly recommended to use the TeX ERT only. You can collapse it by right click and "Close Inset".

2. I do not understand your situation, but you can turn off cache by SweaveOpts{cache=FALSE} which is the default of the cache option, so you do not really need to do it.

Originally posted on 2012-04-11 04:00:10

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Guest *MartinInChemnitz* @ 2012-04-23 04:13:07 originally posted:

Thank you for the helpful clarification Yihui.

1. I did have ERT-frames in chunk formatted paragraphs that did not evaluate. Now I know what caused the problem.

2. The caching and the overwriting of figures by reused chunks are still my biggest stumbling blocks:
   a) If I make a little change to a chunk in a lyx file that I have compiled, like inserting a line with a "1" at the   end, I need to save the file under a different name or the output of the chunk will remain unchanged in the necxt compilation - in spite of an ERT-box at the very top with the command "SweaveOpts{cache=FALSE}" that you recommended above.  One filename one compilation is my work around routine fight against caching.
   b) I reuse a chunk that displays descriptive statistics for various columns in a data frame.
   like (ERT boxes not shown)
   SweaveOpts{cache=FALSE}
   <>=
   require(ggplot2)
   a<- data.frame(X=c(1,2,3),Y=c(4,5,6),Z=c(7,8,9))
   VarName<- 'Y'
   (at)
   <<displayvar,cache=f,results='asis',echo=f,fig.width=4,fig.height=3>>=
   d <- a[,c('X',VarName)]
   names(d)<-c('x','y')
   ggplot()+geom_point(data=d,mapping=aes(x=x,y=y))
   (at)
   <<2>>=
   VarName<- 'Z'
   (at)
   <<displayvar,cache=f,results='asis',echo=f,fig.width=4,fig.height=3>>=
   (at)

And the second call of the chunk overwrites the figure produced by the first call so that I get twice the same figure.
No idea why I cannot remove the following from this comment:

[yihui]

You need to convert < to < when writing comments; I'm using Disqus and this annoys me a lot (they should be able to automatically encode HTML entities).

For caching, you are recommended to use the ref.label option: http://yihui.name/knitr/demo/reference/

It will not work if you use the same label for two chunks which generate cache and figure files, because these filenames are from the chunk label. The latter will certain overwrite the former if they have the same name.

Originally posted on 2012-04-23 04:30:52

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Guest *Klebyn* @ 2012-04-29 20:30:14 originally posted:

knitr+Lyx don't compile if I set my language for 'Portuguese (Brazil)'. Someone have a tip? thanks.

[yihui]

I recommend you to use the UTF-8 encoding for your LyX document; before trying knitr, you need to make sure this LyX document compiles successfully without R code. Besides, Windows is difficult to work with non-ASCII documents.

Originally posted on 2012-04-29 21:29:29

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Guest *Klebyn* @ 2012-04-29 22:30:57 originally posted:

Every examples (in ... Rlibraryknitrexamples) compile very fine, no errors! :-). But when I put characters with accents, like áéíóú in normal text, not in R chunk, I get the error message:

File ended while scanning use of Hy@scantitle.  
<*> knitr-listings.tex  
                       
*** (job aborted, no legal end found)  

neither convert to plain latex, works.
In Lyx, I set to utf8, but don't work anyway... Thanks for your attention.

Cleber Borges

[yihui]

knitr 0.5 has been submitted to CRAN this morning, and if it passes R CMD check, it will be on CRAN in two days.

Originally posted on 2012-04-30 01:25:31

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Guest *Klebyn* @ 2012-04-30 01:42:22 originally posted:

 I used the suggestion:library(devtools); install_github('knitr', 'yihui')and I get the version 0.5. I get the same behaviour :-( .

[yihui]

Then it is real hacking time for you -- the R script used to call knitr is lyxknitr.R under the "scripts" directory of your library directory (see Help -- About). Open that script and tweak it to see if you can make it. I guess it may have something to do with options(encoding = ...).

Originally posted on 2012-04-30 01:51:26

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Guest *Klebyn* @ 2012-04-30 02:44:25 originally posted:

 o/o/o/

Now it works!!! :-)

I just comment the line (in lyxknitr.R)
####options(encoding = .cmdargs[3])

I don't understand why, but works!

Thanks for your attention and patience

[yihui]

Good to know. I will update the web page accordingly. Thanks!

Originally posted on 2012-04-30 03:01:45

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Guest *Bastien Ferland-Raymond* @ 2012-05-01 12:34:59 originally posted:

If I can allow myself a simple comment and suggestion, I would love to have a 'silent=T' option with the knit function.  Seeing the code compile is nice at the beginning, but when it's working fine, I found it neater without.  Anyway, it's not a big deal, just my 2 cents.

Thanks.

[yihui]

Thanks. That makes sense, and you can set opts_knit$set(progress = FALSE) before you knit() to suppress the progress bar. See http://yihui.name/knitr/options

Originally posted on 2012-05-01 15:09:58

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Guest *Bastien Ferland-Raymond* @ 2012-05-01 18:37:24 originally posted:

 Thanks, it works great.  Sorry I didn't notice the option, I still new in sweave/knitr and I not there yet in my self teaching schedule...
Keep up the good work, your package is amazing.

[yihui]

No problem. I know there are too many options :)

Originally posted on 2012-05-01 18:43:39

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Guest *Shmil T* @ 2012-05-20 17:33:53 originally posted:

OK, no worries.

I think that what can actually solve the problem is to hook a TeX command which forces LTR in the beginning of the R code, and cancel it (meaning to return to the previous writing direction) in the end of the code. 

As you can see, the whole document is right aligned (which happens only when I use knitr)
I tried to write Pi several times.
Attached is the output of this syntax:

% Preview source code

%% LyX 2.0.3 created this file. For more info, see http://www.lyx.org/.
%% Do not edit unless you really know what you are doing.
documentclass[english,hebrew]{article}
usepackage[T1]{fontenc}
usepackage[latin9,cp1255]{inputenc}
usepackage{fixltx2e}

makeatletter
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Textclass specific LaTeX commands.
usepackage{theorem}
theorembodyfont{upshape}
newtheorem{theorem}{R{משפט}}[section]
AtBeginDocument{make@lrthetheorem}

makeatother

usepackage{babel}
begin{document}
שלום, רציתי לומר מהו הערך של המספר האהוב עליי, פי: Sexpr{pi} . ואני
שואל אתכם, האין זה מספר יפה?

<<>>=
pi
@

inputencoding{latin9}Now, lets take a look of an english expression
such as Sexpr{pi}. Ain't it beautiful? %

end{document}

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Guest *Shmil T* @ 2012-05-20 03:36:30 originally posted:

Hi, Thanks for the wonderful work. Knitr is a very powerful tool.
I have a problem working with knitr through Lyx in Hebrew -  when I activate the module it crashes.
I tweaked it as You said, and I got it to work together with the FixLatex package.
But now, I can't see graphs and the alignment is LTR! 
Which means that all is in the opposite direction.

I'd be happy to know if there's a solution for this situation.

Thanks in advance!

[yihui]

I'm afraid it is difficult for me to help in this case, because I know nothing about Hebrew. Can you provide an example to me? What is your OS and what is the version of your LyX as well as its LaTeX backend?

Originally posted on 2012-05-20 15:55:48

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Guest *Shmil T* @ 2012-05-20 16:23:52 originally posted:

Hi, and thanks for the reply!
Using windows 7, Lyx 2.0.3, MikTeX 2.9.Using also the TEWAKED version of knitr (solution taken from other post in this site), as it is the only way to get it working.The attached code gave me 2 words in hebrew and a reversed R output (RTL).FYI, I don't get it to draw plots either.Thanks again!Shmulik% Preview source code

%% LyX 2.0.3 created this file. For more info, see http://www.lyx.org/.
%% Do not edit unless you really know what you are doing.
documentclass[english,hebrew]{article}
usepackage[T1]{fontenc}
usepackage[latin9,cp1255]{inputenc}
usepackage{fixltx2e}

makeatletter
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% Textclass specific LaTeX commands.
usepackage{theorem}
theorembodyfont{upshape}
newtheorem{theorem}{R{משפט}}[section]
AtBeginDocument{make@lrthetheorem}

makeatother

usepackage{babel}
begin{document}
שלום

<<>>=
1+1
@

%
תודה!
end{document}

[yihui]

I do not even know how to compile a normal Hebrew document with LaTeX; at least pdflatex fails under my Ubuntu system...

Originally posted on 2012-05-20 17:19:38

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Guest *Shmil T* @ 2012-05-21 13:33:41 originally posted:

Sorry, I replied to the next thread by mistake :

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Guest *zhangym* @ 2012-05-25 02:28:44 originally posted:

How to use knitr in the file with ctex?

[yihui]

An Rnw document is basically a LaTeX document, so just write whatever you write with ctex, and make sure the R code is marked up appropriately. If you are not familiar with Sweave, see this example: https://github.com/yihui/knitr/blob/master/inst/examples/knitr-minimal.Rnw

Originally posted on 2012-05-25 02:40:54

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Guest *Aloy* @ 2012-05-31 18:30:46 originally posted:

I am trying to make a beamer presentation with knitr in Rstudio and am running into some problems when I use cite(...) for references. Commenting out the cite(...) commands avoids errors when knitting, and I can open the .tex file and bibtex and latex the file twice to produce the citations. Is there a way to do all of this within Rstudio?

[yihui]

Sounds like a pure RStudio problem (so better report to them: http://support.rstudio.org/help/ ). What is your RStudio version? I thought RStudio should be intelligent enough to solve the bib problem; if you could provide a reproducible example, they should be glad to help you.

Originally posted on 2012-06-01 20:40:12

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Guest *Kevin Goulding* @ 2012-05-31 21:16:22 originally posted:

Hi Yihui -- I'm considering learning either "Rapport" or "Knitr".  Could you give a rundown on how knitr is different (...better!) than rapport, or why someone might gravitate to one versus the other?  Many thanks!

[yihui]

rapport is based on templates, and knitr is based on literate programming; programming allows you to do anything, including using templates. There are just too many features to describe, but I do not know your background, so it is hard to list the points that may interest you most. Anyway, one thing that I can sell to you is that you can easily get started with this R Markdown example in RStudio: https://raw.github.com/yihui/knitr/master/inst/examples/knitr-minimal.Rmd

Originally posted on 2012-06-01 20:36:57

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Guest *JMol* @ 2012-06-03 10:32:50 originally posted:

Hello Yihui;
First thank you very much, you have done a great job.
How can I decrease the distance between the knitrout environment and the normal text?

[yihui]

This is a LaTeX question; you can redefine the knitrout environment, and here is an example: https://gist.github.com/2760395#file_knitrout_vspace.rnw

Originally posted on 2012-06-03 13:41:50

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Guest *JMol* @ 2012-06-04 18:24:54 originally posted:

Thank you very much. Originally in what file is defined for first time the knitrout environment?. I have been looking for in knitr.sty and other files with out luck.

[yihui]

It was defined as an empty environment which allows you to redefine later: https://github.com/yihui/knitr/blob/master/inst/misc/knitr.sty

Originally posted on 2012-06-04 18:47:37

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Guest *JMol* @ 2012-06-04 18:54:54 originally posted:

Thank you again for your great job.

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Guest *Chris* @ 2012-06-04 21:33:47 originally posted:

Hi Yihui,

Thank you very much for knitr, it has together with RStudio become a very important component of my R-work.

One question: I use LaTex because of its powerful layout capabilities, especially for creating advanced slides (beamer) with graphs, maps and text layouted together, that can be recreated many times with different indata. I see a lot of focus on Markdown, both here and with RStudio. It is good for fast and simple production, but for me it is too limited. Have I misunderstood Markdown? Can I continue using LaTex with knitr for my more advanced layout-needs?

Again, thanks a lot for knitr and all the supporting documentation and examples.

/Chris

[yihui]

Hi,

This is pretty simple to decide: the two formats have different goals. Markdown aims to be simple, so it has to be very limited; LaTeX is a comprehensive typesetting toolset, which allows you to do anything but requires more efforts too. If you need advanced layouts, you definitely should go with LaTeX.

Originally posted on 2012-06-04 23:29:38

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Guest *Chris* @ 2012-06-05 08:01:02 originally posted:

Ok, good. I hope knitr will continue to support LaTex. Thanks again for it.

[yihui]

Absolutely! I worked much harder on LaTeX than Markdown. You can compare the amount of code on them respectively: https://github.com/yihui/knitr/blob/master/R/hooks-md.R and https://github.com/yihui/knitr/blob/master/R/hooks-latex.R There is not much to do with markdown now, and there may still be issues to fix/improve with LaTeX.

Originally posted on 2012-06-05 15:10:40

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Guest *JMol* @ 2012-06-05 17:48:53 originally posted:

Hello again, Yihui;

There is a problem with the R output, it produces a overfull hbox warning.
Example:
<<codigo1, size="small">>=
str(Orange)
@

[yihui]

That is because the output is too wide; you should either make the page margin smaller, or cut the output width somehow (may not be possible with str()).

BTW, you should use size='small' instead of size=small; see http://yihui.name/knitr/options

Originally posted on 2012-06-05 17:55:26

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Guest *JMol* @ 2012-06-05 18:33:01 originally posted:

I am a newbie both in R and LaTeX, so, please, excuse my insolence, but is it not possible to find a solution. For example, redefining knitrout environment

ifdefinedknitrout
  renewenvironment{knitrout}{
    parnoindentbegin{minipage}{textwidth}
  }{
    end{minipage}
  }
else
fi

Generating new problems, it resolves partially the overfull problem.

Nevertheless, I can break the line manually.

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Guest *Jefe_goode* @ 2013-02-16 12:53:25 originally posted:

I have just tried running the example 'knitr-minimal.Rnw from the code:
https://raw.github.com/yihui/knitr/master/inst/examples/knitr-minimal.Rnw

then tried > knit2pdf('knitr-minimal.Rnw')
and got the following error message:

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet, :
pdflatex is not available

where do I get pdf2latex from?

[yihui]

Why not google for it?

Originally posted on 2013-02-16 16:40:26

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Guest *Jeffrey Erlich* @ 2013-02-20 19:26:29 originally posted:

when i put two read.table in one chunk, the second read fails. If I put them in separate chunks it succeeds.

This works:

fof=read.table("<http://brodylab.princeton.edu/clicks/data/fof_musc_uni.dat>")  

ppc=read.table("<http://brodylab.princeton.edu/clicks/data/ppc_musc_uni.dat>")  

This fails:

fof=read.table("<http://brodylab.princeton.edu/clicks/data/fof_musc_uni.dat>")  
ppc=read.table("<http://brodylab.princeton.edu/clicks/data/ppc_musc_uni.dat>")  

Thoughts?

[yihui]

All three chunks work for me. Maybe an Internet connection problem?

Originally posted on 2013-02-21 00:42:44

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Guest *Jeffrey Erlich* @ 2013-03-15 16:33:10 originally posted:

Did you check that the number of rows returned was the same in both conditions. It often would not fail with an error, but just not return the whole table

[yihui]

Yes, I did check it. The objects are identical, so again I do not see any problems.

fof=read.table("http://brodylab.princeton.edu/clicks/data/fof_musc_uni.dat")  

ppc=read.table("http://brodylab.princeton.edu/clicks/data/ppc_musc_uni.dat")  

fof2=read.table("http://brodylab.princeton.edu/clicks/data/fof_musc_uni.dat")  
identical(fof, fof2)  
ppc2=read.table("http://brodylab.princeton.edu/clicks/data/ppc_musc_uni.dat")  
identical(ppc, ppc2)  

Originally posted on 2013-03-15 19:49:51

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Guest *Christian Ponce* @ 2013-03-21 10:38:07 originally posted:

I'm having some issues when a child file in a folder different from project root folder calls to another child ('grandchild') file in the same subfolder. Is this a common issue?

In my main file I call the first child in a chunk:
<<label1, child="somefolder/foo1.Rnw">>=
@

In the child file I call the second child (in the same subfolder) with another chunk:
<<label2, child="foo2.Rnw">>=
@

Whenever I do this, I receive an error message like this:
(this is my actual output)

Process started

processing file: ResolucionTarea5_EST-601.Rnw

processing file: ./Ejercicios/primeraparte.Rnw

Warning in readLines(if (is.character(input2)) { : cannot open file '1.1.Rnw': No such file or directory

Quitting from lines 2-2 (./Ejercicios/1.1.Rnw)

Quitting from lines 15-NA (./Ejercicios/1.1.Rnw) Error in readLines(if (is.character(input2)) { : cannot open the connection Calls: ... process_group.block -> call_block -> lapply -> FUN -> knit -> readLines Execution halted

Process exited with error(s)

If all three files are in the same folder, this does not happen. Any idea of what I'm doing wrong?

[yihui]

Using sub directories can make things really complicated in knitr. If possible, please write child documents in the same directory.

Originally posted on 2013-03-21 17:59:48

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Guest *Tom Ravalde* @ 2013-03-26 17:04:25 originally posted:

Hi Yihui,
I'm using the vim-latex plug-in. If I write a *.Rnw file in vim and try to insert a '<' so I can write a code-chunk, vim gives me the error ;E117: Unknown function: RwriteChunk'.
Am I missing something? Any idea what I might be doing wrong.
Thanks
Tom

[yihui]

Sorry I do not know much about vim; perhaps you can try http://stackoverflow.com/questions/tagged/knitr

Originally posted on 2013-03-26 18:26:27

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Guest *Tom Ravalde* @ 2013-03-27 14:05:11 originally posted:

Thank you. I have now resolved the problem. I just copied the Vim-R runtime file from "~/.vim/ftplugin" into "/usr/share/vim/vim73/ftplugin".

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Guest *John Maindonald* @ 2013-04-23 10:54:50 originally posted:

Earlier today, I suddenly started getting the error 'tikzDevice not available', or the equivalent, when I tried to compile my .Rnw file.

Upgrading from knitr_1.1 to knitr_1.2 made no difference. The error was identified as occurring from code 'library(p, ...)', where ... stands for text that I did not record. Unfortunately I wiped the log file in the process of experimenting with what turned out to be a fix. It turned out that placing the .Rnw file in a different directory (I was running under RStudio) allowed the compilation to proceed. Removing the cache directory from the initial location turned out to fix the problem. Clearly something in the cache was triggering the demand for 'tikzDevice', which I do not have on my R_3.0.0 installation (running under OS X10.8.3). I am posting this for the record.

[yihui]

That is because knitr caches the package names as well, to make sure the required packages are loaded before code chunks are re-evaluated. You can find the package names in cache/__packages (by default) and remove tikzDevice from the list if you do not need it.

Originally posted on 2013-04-24 09:09:38

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Guest *ADPowers* @ 2013-05-09 11:12:04 originally posted:

Tikz is chewing up too much memory in a plot I am trying to make, is there any way to externalize the plotting,whilst still having the convenience of using chunks?

[yihui]

The plots are already externalized (chunk option external = TRUE by default). What you can do at best is cache=TRUE. Other than that, there are no solutions.

Originally posted on 2013-05-25 07:17:13

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Guest *Peng* @ 2013-05-20 21:25:53 originally posted:

Hi, I am new to the package. Do you have any suggestion about learning it?

[yihui]

Perhaps the video above helps. Or wait for my book: http://bit.ly/knitr-book

Originally posted on 2013-05-25 06:54:24

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Guest *Thibaut Jombart* @ 2013-05-21 12:25:41 originally posted:

Hi there,
congrats on knitr, this is awesome! Glad to be able to use it for package vignettes too.
Cheers
Thibaut

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Guest *Shima* @ 2013-05-27 18:54:18 originally posted:

Hello Yihui,

First of all thanks for this good video,

Second, I have some questions:
Can I use this package without installing Rstudio and with only using RGui or with using Revolution R enterprise?
If so, is there any tutorial for a beginner to do that?

As far as I have understood, in Rstudio, I can create an R Sweave document and then compile Pdf for a document with Rnw extension. How can I make a Sweave document in Revolution R Enterprise or in RGui?

Best,
Shima.

[yihui]

You can use any R front-end and you are not restricted to RStudio, but RStudio has made things much easier. If you use RGui (I suppose you are talking about Windows), you simply call

library(knitr)
knit('yourfile.Rnw')

That will be very tedious when you want to compile your documents again and again.

Originally posted on 2013-05-27 20:43:54

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Guest *Vathy M.K* @ 2013-06-10 01:09:42 originally posted:

Hi Yihui,
There are very few packages I find more useful than knitr. Thank you.

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Guest *Ann* @ 2013-06-17 17:32:55 originally posted:

Is this published in a journal article or other publication that is indexed in PubMed? If yes, can you send the PubMed id? If not, I hope you will consider writing a short applications note to Bioinformatics (or other suitable journal) so that I can cite it. Thank you for creating a very useful great tool I use nearly every day! Yours, Ann Loraine

[yihui]

You can cite either the package or the book: http://cran.r-project.org/web/packages/knitr/citation.html

Originally posted on 2013-06-18 00:07:37

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Guest *David Arnold* @ 2013-07-27 22:58:07 originally posted:

Yihui,

Brand new to knitr, awaiting the arrival of your new book. Meanwhile, what do folks do now about installing tikzDevice when they are using R version 3.0.1?

David

[yihui]

Just for future reference: http://r.789695.n4.nabble.com/tikzDevice-td4672523.html

BTW, I always recommend asking questions on StackOverflow or in the mailing lists. I do not read the comments here very often.

Originally posted on 2013-07-31 20:27:32

[yihui]

Hi, I think you can try the latest development version:

install.packages('markdown', repos = 'http://rforge.net')
install.packages('knitr', repos = c('http://rforge.net', 'http://cran.rstudio.org'), type = 'source')

The stable version 1.2 on CRAN has some known problems for the SAS engine.

Originally posted on 2013-07-21 22:30:34

[bgrieger]

Many thanks for this really nice work. I use it lot, it's great fun.
I have one question: Is there any way to avoid the expansion of included chunks in echoed source code and rather see only the labels of the included chunks?

[yihui]

If you need to evaluate the code chunk, there is no way to avoid the expansion. If you don't, you can write a verbatim code chunk.

[bgrieger]

Thanks for this very quick reply!
I think the original idea of literate programming was to explain how a big program is constructed out of large code chunks which are in turn constructed out of smaller code chunks and so on. And the explanation can go top down or bottom up or start somewhere in between. It can follow human logic and not the program flow. In this respect, it would be very useful if one could have a code chunk echoed in the document like it looks in the source code (ideally with syntax highlighting). But I would also like to execute it.
Anyway, don't worry, it's a great tool.

[yihui]

I see. I think it's a good idea, but doesn't appear to be straightforward enough for me to implement. I can think more about it at a later time. Thank you!

[Shari2k20]

Hi, I am unable to update knitr in my R and the error comes from updating xfun whose version is 0.43 whereas latest is 0.46. Is there any way I can copy the latest folder of xfun and replace it in my folder. Thanks