[knitr] Minimal examples: Examples for Rnw, GFM, HTML and LaTeX | /knitr/demo/minimal/

Guest *idrisr* @ 2012-04-09 04:54:06 originally posted:

I'm struggling to see how to create a  .markdown file and convert it to html? Point me in the right direction?

Guest *Rich* @ 2012-05-06 01:16:54 originally posted:

Your comments about not breaking other languages are interesting!  Do you think you will extend this thinking to a file format where R is the protected format?  What I mean is that all the documentation is in comments, and the file remains valid R code if you were to copy it in.  

Something like

My analysis## ===========#### Text describing the analysisset.seed(1121)(x <- rnorm(20))

Guest *Remko Duursma* @ 2012-05-08 02:28:13 originally posted:

Excellent package. 
I ran the knitr-minimal.Rnw example, and noticed that in your pdf output (knitr-minimal.pdf), the figures are placed inside the grey code box, but in my pdf output they are not (they are placed below). I also noticed on your websites some examples of both.

What is the problem you think? (I have the newest version of knitr, as well as highlight, and R).

Guest *Remko Duursma* @ 2012-05-08 02:34:25 originally posted:

And I just noticed that when I include a figure produced by rgl (with rgl=TRUE, and the rgl hook), it does place the figure in the grey code box.

Guest *datapixie* @ 2012-06-26 19:48:38 originally posted:

The knitr-minimal.Rnw example doesn't work for me from inside RStudio when I click on "Compile PDF". If I add the line "library(knitr)" inside the first code block, then at least it will compile, but then the pictures do not show up, and the displayed code does not have syntax coloring.

If I do knit("knitr-minimal.Rnw"), and then LaTex the resulting file elsewhere, it becomes clear that I have to add the line "usepackage{alltt}" to the .Rnw file. Once I do that, then LaTexing elsewhere produces the proper PDF. But even after this change, I still get no pictures from the "Compile PDF" button in RStudio.

Sorry if this is an RStudio question and not a knitr question... but I'll be really happy if I can get this all to work within RStudio.

Guest *AJ Rossini* @ 2012-10-25 13:00:12 originally posted:

actually, you got it a bit wrong.  The original noweb syntax (thanks to Norman Ramsey) was to have code chunks and doc chunks interspersed, with means to have code chunks in other code chunks, but left the doc chunks unlabelled.  From this, you could use any doc language(but needed to be consistent, no facility for switching)  and any code language (which could be inconsistent, since there was a facility for switching and annotation.  You should read Norman's tech report (and I think he had a publication that is citable) for that.
Sweave broke the noweb syntax by mixing up code in the doc chunks, but this wasn't a bad idea in theory, since Fritz wanted to do reporting.  
If I had started with nuweb (which was a cleaner but trickier code-language agnostic language), we'd have made a bit more progress..

best,
-tony

Guest *Bastiaan Quast* @ 2012-10-27 11:53:52 originally posted:

Thank you very much for this, I tried to replicate your minimal.Rmd example and upload it to Github, but the pictures won't display. I guess this is because they are in the figure folder, is there a way to avoid this?

Guest *Marcus R* @ 2013-02-01 18:50:54 originally posted:

Hi. I am about to write my masters thesis. I am right now setting up my software environment with git, R, latex etc within a Ubuntu 12.04 installation. I used Sweave for my Bachelors thesis but I will now give knitr a try. But I have some problems.

I decided to first try try replicate the 002-minimal.Rnw above with the commands:
Rscript -e "library(knitr); knit('002-minimal.Rnw')"
pdflatex 002-minimal.Rnw.tex

But then I get a error that says:
! Undefined control sequence.
l.59 SweaveOpts
{concordance=TRUE}

And in the resulting pdf there is this text above that says:
concordance=TRUE

I know you have a guide for R Studio to output PDF (even though I still have trouble with it). But do you have, or know about, some guide that how to use command line to get a good PDF-output. I know there are pdfLatex, knit2pdf and a lot of different programs but there is so much to get into.

And also, I almost forgot, thanks a a lot for this package, when I get hold of it it really going to turn my thesis studies from frustration to Euphoria! :)

Guest *Honza* @ 2013-06-04 15:07:24 originally posted:

I completely agree with you on the advantage of the LaTeX example with R codes written in comments. But unfortunately Emacs ESS does not support it. Or does it?

Guest *hcheng* @ 2013-10-22 03:43:57 originally posted:

Hi, I am very confused why the results are different when I use markdown and just run in Rstudio. In your markdown example, there are two lines: set.seed(123) rnorm(5). I get quite different results by running markdown and rstudio. For markdown, the results are what you provide in the output but in rstudio the results are 0.1870696 1.9960295 2.2993699 1.1274577 1.0811140. As I need to generate some simulated dataset, If i use the markdown, the results are far too different. Could you give me any clue?? Thanks!

Guest *David States* @ 2015-02-04 00:21:21 originally posted:

Would like to use LyX to edit knitr .Rnw files but having some problems getting started. Have R version 3.1.1 installed with the knitr library installed on a Mac running OS X 10.10.2 (Yeosemite).

First, LyX will not open .Rnw files directly, only .tex files. I guess this is by design, but it would be very useful if LyX could load .Rnw files directly and autoload the knitr module in the process.

Second issue, if I follow the description on this website, open a new file in LyX, load the knitr module and then try to import an existing .Rnw file (knitr-minimal.Rnw from this website), I get an error message from R:

An error occurred while running:

Rscript --verbos --no-save --no-restore
"Applications/http://LyX.app/Contents/Resources/scripts/lyxknitr.R"
"/Users/dstates/Documents/""knitr-minimal.Rnw"
"/Users/dstates/Documents/""knitr-minimal.tex" "/Users/dstates/Documents"

Sorry if I am missing something really basic here. Newby :(

Guest *Xing* @ 2015-03-31 14:24:20 originally posted:

Hi, Yihui, Can I just the R markdown Beamer-Presentation in Chinese?
I cannot make it

Guest *Stefano Lombardi* @ 2015-05-22 08:20:12 originally posted:

Hi Tihui,
I have a basic question. I am trying to replicate your 002-minimal.Rnw example.
After changing the weaving option to "knitr", I tried to compile the pdf, but I get this:

Quitting from lines 9-13 (knitr_minimal.Rnw)
Errore in data.frame(..., check.names = FALSE) :
arguments imply differing number of rows: 3, 0

Note that if I delete the chunk of R code the pdf is compiled correctly.
Actually, whenever I try to embed any chunk of R-code the above error is reported.
Do you have any idea why this happens?

Thank you very much fro your work!
best,

Stefano

Guest *Paul Burger* @ 2015-06-12 15:50:00 originally posted:

Hi, Using RStudio Version 0.99.441 on Win8.1 (x32) with Miktex and RMarkdown; I cannot get your minimal PDF example to compile. Knitr cannot find inputnc.sty but everything seems to indicate that inputnc was superceded by inputenc.sty and that exists in Miktex. Can you explain the problem?

Here is the output log:
processing file: test.Rmd
|............. | 20%
ordinary text without R code
|.......................... | 40%
label: unnamed-chunk-1
|....................................... | 60%
ordinary text without R code
|.................................................... | 80%
label: unnamed-chunk-2 (with options)
List of 1
$ echo: logi FALSE
|.................................................................| 100%
ordinary text without R code

"H:/program files/RStudio/bin/pandoc/pandoc" test.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output test.pdf --template "h:PROGRA～1RR-32～1.0libraryRMARKD～1rmdlatexdefault.tex" --highlight-style tango --latex-engine pdflatex --variable "geometry:margin=1in"
output file: test.knit.md

! LaTeX Error: File `inputnc.sty' not found.

Type X to quit or to proceed,
or enter new name. (Default extension: sty)
Enter file name:
! Emergency stop.
<read *="">
l.79
pandoc.exe: Error producing PDF from TeX source
Error: pandoc document conversion failed with error 43
In addition: Warning message:
running command '"H:/program files/RStudio/bin/pandoc/pandoc" test.utf8.md --to latex --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash-implicit_figures --output test.pdf --template "h:PROGRA～1RR-32～1.0libraryRMARKD～1rmdlatexdefault.tex" --highlight-style tango --latex-engine pdflatex --variable "geometry:margin=1in"' had status 43
Execution halted

Guest *Young* @ 2015-07-09 19:55:27 originally posted:

@yihui:disqus Hi, I am trying to learn knitr. I started with your basic example "knitr-minimal.Rnw"; however, the pdf file I get does not include the figures. I am running exactly what you have included without any modeification. What is the problem?

Guest *🐉®γσ ξηg* @ 2015-10-15 10:59:07 originally posted:

paragraph 1...

gc(reset=TRUE)  

paragraph 2...

I got a question about recall chunk. May I know how do I recall the chunk reset after paragraph 2?

Guest *ManiA* @ 2015-11-30 08:46:38 originally posted:

Hi, I have a question which I asked here http://stackoverflow.com/questions/33983298/run-an-r-markdown-check-rmd-and-an-r-knitr-test-rnw-file-together
do you have any hint for me please?

Guest *joe* @ 2015-12-29 00:37:41 originally posted:

when will it be possible to use ggvis on Rnw knitr documents to produce pdf? (With Windows, where it's not possible to get a working Vega)

Guest *Khagay Na* @ 2016-12-04 19:46:47 originally posted:

is there any way to use bash syntax in Rrst documents? I thought .. {bash name} would be a replacement but, it's not.