[knitr] Code Externalization: Use an external R script with your document | /knitr/demo/externalization/

There is no read_source(); there is only read_chunk(). This function only reads the code; it does not evaluate the code as source() does.

Originally posted on 2012-06-04 14:25:13

It is language agnostic, meaning you can use any format including LaTeX, HTML, Markdown, ...

writeLines(readLines("path-to-r-script.R")) only reads and writes the code; it is not really read into knitr -- you have to use read_chunk() to read code chunks into knitr and reference them later.

Originally posted on 2012-07-13 19:20:49

Guest *mrdwab* @ 2012-07-14 05:18:32 originally posted:

Ok. Got it working.

Perhaps it would be useful to mention that the title and author declarations in markdown should come before set-options for proper PDF generation.

% title
% author

```{r set-options, echo=FALSE, cache=FALSE}
read_chunk(...)
```

That is the pandoc syntax. The original markdown syntax does not support that.

Originally posted on 2012-07-14 17:36:06

I just tested a python script and it worked.

read_chunk('[test.py](http://test.py)')  

In test.py I have

@knitr abc

print(1)

Originally posted on 2012-09-24 05:20:47

Guest *Phil* @ 2012-09-27 05:42:12 originally posted:

Cheers Yihui, I thought I'd need engine='py' in the read_chunk settings. That doesn't make sense now...

Great package btw.

Did you see the links to Rnw source files?

But isn't that the default style in knitr? I did use tikz with external=TRUE. The syntax highlighting is a little bit different now, though.

Originally posted on 2012-11-30 07:17:30

Guest *ADPowers* @ 2012-11-30 12:26:40 originally posted:

Yeah, but all I get is plain text, indistinguishable from the rest of the document. Got no idea what is going on here. Tried to use the knit_hooks, but doesn't do anything.

I'm not really sure exactly what you want -- a minimal example? https://github.com/yihui/knitr-examples/blob/master/059-tikz.Rnw

Originally posted on 2012-11-30 16:32:14

Guest *ADPowers* @ 2012-12-01 00:34:04 originally posted:

Thanks almost got to the bottom of it. It seemed that by moving some of my standard preamble from a reference text file [which I call using include(./standard_preamble.tex)] it made the problem go away, specifically, the document class line needed to be in the actual document.This surprised me as I really didn't think that this would have been a problem, since the contents of the reference file contained no chunks, knitr settings or anything generally knitr related.

The next problem, and I'm not entirely sure this is a knitr issue, nonetheless, is that on my PC, many versions of R have been installed, knitr appears to be calling version 2.14.2, which is leading to issues with tikzDevice (built under R version 2.15.1 and not available for 2.14.2) how can I instruct latex to refer to R2.15.1?

UPDATE >> Dont worry, I worked it out.... Duh.

UPDATE >> Getting pages of errors when trying to typeset. Appears that the source is the xcolor package, since, usepackage{xcolor} works fine but usepackage[svgnames]{xcolor} or usepackage[x11names] both cause errors to be thrown.

UPDATe >> Everythings broken. Something to do with getMetricsFromLatex(TexMetrics).

UPDATE >> So finally go things sorted. Have to say, no criticism but debugging and problem solving is a hell of a lot easier in some of the OOP languages like C# or Java. Trying to work out whats going wrong in LaTeX, which is calling R, is like tying to decipher the Rosetta stone. ... All good.

UPDATE >>.On a more serious note, is there a way to control how the R output is formatted in the LaTeX Doc? Things are much better for me now, however, lines of R code are running off the page. Ie line breaks seem to be ignored???

That error dialog box is not helpful; see this manual on how to debug Sweave or knitr in LyX: https://github.com/downloads/yihui/lyx/sweave.pdf

Originally posted on 2012-12-10 06:19:59

Guest *Karlpolen* @ 2012-12-10 14:19:39 originally posted:

thanks for responding

here are 2 screen shots of the detailed message logs

I've also attached a third message I frequently get about inability to delete tmp files -- in case it's relevant to how LyX and windows 7 are dealing with each other.

Guest *Karl Polen* @ 2012-12-10 14:35:44 originally posted:

figured it out!

"" instead of "/" in file path name

Can you paste the full message log please? e.g. use pastebin.com

Originally posted on 2013-01-08 22:40:40

library(knitr)

Originally posted on 2013-01-08 06:14:31

1. I do not know what is your desired output. I use GIT to check if my output has changed since last run, e.g. https://github.com/yihui/knitr-examples In this case I only need to guarantee my first run generates the desired output.

2. see the purl() function (to extract R script from *.Rrst)

Originally posted on 2013-01-12 19:15:54

.. {r setup, echo=FALSE}
opts_chunk$set(echo = FALSE)
..

Originally posted on 2013-01-12 19:16:41

What error did you see? I just ran the two examples and I did not find any problems.

Originally posted on 2013-05-25 07:14:13

Guest *Karl* @ 2013-05-31 05:30:17 originally posted:

Guessing here: It may be related to the fact that tikzDevice has been pulled from CRAN, so he's probably missing that package..

Guest *Miguel A.* @ 2013-06-01 15:57:06 originally posted:

Hi,

I had this probleem and the problem was the one that Karl pointed out. I solved it installing tikzDevice, following the instructions that can be found in http://lightonphiri.org/blog/r-graphical-representation-installing-tikzdevice-package

Regards,

I do not quite recommend you to put too much code into the document. I think it is legitimate to simply source() the script. There is no need to read_chunk().

Originally posted on 2013-08-22 04:19:21