https://yihui.org/en/2011/12/knitr-elegant-flexible-and-fast-dynamic-report-generation-with-r/
Guest *liyun* @ 2011-12-01 17:21:19 originally posted:
would like to be the lab rat :) Thank you for offering us this revolutionary tool.
yihui 2022-12-16 21:03:02I learned "guinea pig" last week and realized it actually means "lab rat".
Originally posted on 2013-01-27 20:45:09
Guest *Tal Galili* @ 2011-12-01 20:11:28 originally posted:
Dear Yihui,
Is an ongoing enthusiast of your work - I am very happy to hear about this new project of yours.
Two big tips that caught my eye:
p.s: install "subscribe to comments" or the likes for this blog - I would have been happy to know of other replies to this post :)
Cheers,
Tal
yihui 2022-12-16 21:02:36Thanks for the feedback, Tal.
Hmm... even Chrome is not consistent over different OS'es? It works well under Ubuntu. I need to reconsider HTML5.
Demos are not there yet, but the manual itself can be a ``killer app'': https://github.com/downloads/yihui/knitr/knitr-manual.pdf (source: https://github.com/yihui/knitr/blob/master/inst/examples/knitr-manual.Rnw; there are other examples under the examples directory too)
I will add a few demos to the website soon.
The feed link to comments is in the right column (see bottom): http://yihui.name/en/comments/feed/
Originally posted on 2011-12-01 21:16:29
yihui 2022-12-16 21:02:45Tal, the demos are up now: http://yihui.github.com/knitr/demos
Originally posted on 2011-12-04 01:46:50
Guest *Tal Galili* @ 2011-12-01 21:28:56 originally posted:
Hi Yihui,
A few more notes:
yihui 2022-12-16 21:02:37notes:
Sweave() (you may file a feature request to RStudio developers to support user-defined functions to run Sweave after knitr is mature enough); however, as I have been advertising for a long time, LyX is really the way to go if you want to be lazy and do not want to be buried in all kinds of raw LaTeX commands; see this short video to get a feel about how knitr works in LyX: http://vimeo.com/32948939 (the support for knitr in LyX is on the way: http://www.lyx.org/trac/ticket/7887 but you may want to spend a few days learning LyX first)Originally posted on 2011-12-02 07:48:34
Guest *randomas* @ 2011-12-01 21:47:13 originally posted:
Great effort and highly appreciated!
At the moment the top of my wish list for R is report generating features for tables comparable to SAS proc report and tabulate with export to rtf and odf files. This is actually a necessity for me and at the moment has me doing half my work in SAS and the other half in R. I work in the medical field and my co-workers with whom I have to share documents are all MS Office users so pdfs and Latex are out for me ...
Here's hoping!
yihui 2022-12-16 21:02:39I guess I'm not going to invest time in the rtf and odf format in the near future, but since other people have done the odfWeave package (http://cran.r-project.org/package=odfWeave), it should be possible for knitr to work with odf as well.
Have you ever tried http://www.tug.org/applications/tex4ht/mn.html? It might be easier to convert a tex document to odt than hacking at R's side.
Originally posted on 2011-12-02 08:49:14
Guest *Ali* @ 2011-12-02 05:18:20 originally posted:
Thanks alot Yihui! Your quick setup for lyx and pgfsweave helped me produce many dynamic reports since last year. This looks even more promising and user-friendly, and I am really exciting to get started with it.
But, how do I go about for getting to work on lyx? I went ahead and installed the libraries for R, using library(devtools); install_github('knitr', 'yihui'), but what else should I do? I cannot yet open and run your knitr-manual.lyx (error yields that it is not a readable document).
yihui 2022-12-16 21:02:38I have provided a patch to LyX and am waiting for LyX developers to test it: http://www.lyx.org/trac/ticket/7887 Actually I have been working with LyX+knitr for quite a few weeks now. The problem you met was because I'm using a devel version of LyX, which I compiled from the source checked out from SVN. That said, it is actually way easier than you imagined to get knitr working with LyX -- you do not have to apply the patch and compile LyX from source; what you need to do is to read FAQ2 in the manual: https://github.com/downloads/yihui/lyx/sweave.pdf then README https://github.com/yihui/lyx then download the script lyxknitr.R, rename it, put it in your user directory; then you are ready to go -- the Sweave module in LyX actually becomes a knitr module. Of course, you lose the real Sweave module (i.e. calling R's Sweave()).
To open my lyx document, you can open it with a text editor first, change 417 to 413 (this means cheating LyX as if the document were created with LyX 2.0.x), save it and you are done.
Originally posted on 2011-12-02 07:59:48
giscus-bot 2022-12-16 21:02:40Guest *Ali* @ 2011-12-02 10:57:17 originally posted:
Thanks Yihui! I am going to try this over the weekend. I am actually still using LyX 1.6.x because I had been using pgfsweave (through your great instructions) and didn't want to risk a change. The change now seems worthwhile!
yihui 2022-12-16 21:02:41It is not that dangerous to update LyX if you back up your LyX user directory first; even if anything screws up, you can go back by restoring the user directory. All your old configurations are there. The only thing you need to be careful is to make sure Rscript is in your PATH variable if you update R from 2.13.x to 2.14.0 (knitr requires R >= 2.14.0).
Originally posted on 2011-12-02 11:03:16
giscus-bot 2022-12-16 21:02:43Guest *Huang* @ 2011-12-03 16:18:02 originally posted:
The manual runs well in MAC without the lyx. I use my usual texlive under MAC to compile it.
yihui 2022-12-16 21:02:44Good to know. Thanks!
Originally posted on 2011-12-04 01:45:46
giscus-bot 2022-12-16 21:02:47Guest *Huang* @ 2011-12-10 06:57:28 originally posted:
A bit strange now, the manual and even the minimal Rnw files do not work now. I think I only reinstall qt 4.74 a few times but do not make any changes in my MAC these days. The errors are as belows in R.
Error in str_match(str_sub(input, loc[, 1], loc[, 2]), inline.code)[, :
incorrect number of dimensions
In addition: Warning message:
In theme_latex() :
unable to find LaTeX package 'framed'; will copy from the knitr package
sh: kpsewhich: command not found
yihui 2022-12-16 21:02:47I found this by myself this afternoon as well: yihui/knitr#46
The solution is to update knitr from GitHub. Thanks!
Originally posted on 2011-12-10 07:42:03
Guest *Eric* @ 2011-12-02 14:56:28 originally posted:
Yihui:
Thanks for your work, and I am keen to try out the package, but I am foiled right from the start as I cannot get the package installed (as you thought in your first request for feedback).
I've downloaded the .zip from Github, and attempted to ask R to install package from local zip. No success, renamed the zip to 'knitr' extracted the directory and placed in R/library all to no avail. Resorted to simply sourcing the files in the R directory and could not succeed either because of absence of package (evaluate) as in evaluate:::plot_calls in plots.R and function str_c() in header.R
But anxious to give this a go.
yihui 2022-12-16 21:02:42Great. Now I know not all my readers know how to deal with a source package. The correct way to install the package is to use library(devtools); install_github('knitr', 'yihui') as indicated in the website (http://yihui.github.com/knitr/) or the traditional R CMD INSTALL (tedious, not recommended).
After this package is released to CRAN, you will be able to use the normal approach install.packages('knitr'). For the devel version, you have to be sort of a hacker.
Originally posted on 2011-12-02 22:23:58
访客 *土木坛子* @ 2011-12-04 21:17:01 写道：
that is something very interesting, but it seems I have no any idea on R.
Guest *Songpants* @ 2011-12-05 21:01:06 originally posted:
Wow, that is REALLY cool! Thanks a lot for your effort and for providing this!!!
Best regards!
Guest *Kevin Wright* @ 2011-12-09 21:03:33 originally posted:
The "align" option is great! Was always tedious to use "centering" with Swevae.
I'm fine with background shading of code, but not for graphics. I use light gray for reference lines in graphics--hard to see when there is background shading.
yihui 2022-12-16 21:02:46This will be better explained in the knitr graphics manual, which is not finished yet: https://github.com/downloads/yihui/knitr/knitr-graphics.pdf
The default background of some graphical devices is transparent, and you need to explicitly set it to white (e.g. http://www.inside-r.org/howto/knitr-elegant-flexible-and-fast-dynamic-report-generation-r); you can also do this globally via the fig hook (so you do not need to write it in every single chunk), e.g. knit_hooks$set(fig = function(before, options, envir) {if (before) par(bg = 'white')}. This applies to base graphics, of course. For ggplot2, I do not see any problems since the background is white by default.
Originally posted on 2011-12-09 23:34:38
Guest *Huang* @ 2011-12-17 21:40:25 originally posted:
How to get pdf file directly from Rnw file?
Referring to the link below, some sh file can do this for Sweave. However, package knitr is not loaded by default like package utils. How can we do something similar for knitr? If possible, support for the bib file is appreciated.
#!/bin/bash
export PATH=$PATH:/usr/texbin:/usr/local/bin
#export SWEAVE_STYLEPATH_DEFAULT="TRUE"
R CMD Sweave "$1"
pdflatex -interaction batchmode "${1%.}"
pdflatex -interaction batchmode "${1%.}"
yihui 2022-12-16 21:02:48I told people for thousands of times that they should consider LyX, but it seems people barely believe me. For me, it is a waste of time to try to solve these LaTeX issues by myself, either through sh files or Makefile or Rscript... See http://yihui.github.com/knitr/demo/lyx/
The difficulty for beginners at the moment is that knitr is not yet officially supported by LyX (hopefully the next version will), so it may take a while to understand how it works. After that, everything becomes as easy as clicking a single button, and no worries about how knitr is loaded, and how/when bib files should be compiled. LyX does all the jobs intelligently. It almost makes no sense to me to hack at these LaTeX problem on R's side.
Originally posted on 2011-12-17 23:11:51
giscus-bot 2022-12-16 21:02:49Guest *Huang* @ 2011-12-18 05:11:17 originally posted:
Maybe I am a little old fashioned. I did try lyx for half a year but give up finally.
If you read the website above, the file did add an engine to the textshop GUI and there is a button there for you to click to compile the rnw file to pdf directly.
yihui 2022-12-16 21:02:50Yes I did read it long time ago when Cameron wrote it. The problem is, there are just too many gory details that you have to take care of if you deal with raw LaTeX code; like you requested, how about the compilation of bib files? When to compile them and should we run bibtex every time we compile a LaTeX file? (The answer is probably no; sometimes you do not need to run bibtex, and you need to check the *.aux file first)
I mean this is almost completely a LaTeX problem, and there has been a perfect solution to me, so I have no motivation on hacking at any other scripts. I often work hard to be lazy -- I spent an enormous amount of time on connecting LyX with R/Sweave/knitr. As a ``visual'' guy, I cannot resist the visual interface of LyX. I love seeing real figures instead of includegraphics{} and real section titles instead of section{}. I avoid typing source code whenever I can; LyX is only a visual wrapper, so I do not lose anything in LaTeX. Sorry if this sounds a little bit extreme :)
Originally posted on 2011-12-18 05:36:54
giscus-bot 2022-12-16 21:02:51Guest *Huang* @ 2011-12-18 07:18:06 originally posted:
Emm. Thanks for your explaination anyway. I hope someone else will do this after knitr is on CRAN.
yihui 2022-12-16 21:02:52If all you want is a script, you can quickly modify Cameron's like this (not tested; I do not have a Mac OS):
#!/bin/bash
export PATH=$PATH:/usr/texbin:/usr/local/bin
R -e "library(knitr);knit('$1')"
pdflatex "${1%.*}"
If you also want bibtex support, you can add more commands into it. It is not terribly hard.
Originally posted on 2011-12-18 07:43:12
giscus-bot 2022-12-16 21:02:53Guest *Huang* @ 2011-12-18 15:51:10 originally posted:
Thanks. It works. I got a button in my texshop.
Guest *zhonggai* @ 2012-01-21 14:05:37 originally posted:
Yihui,
Randomly ran into your blog today in searching for R animation. I am already excited about trying out your "knitr" package. I had used sweave before and recently tried org-mode as well, based on your manual, I already determined to try my next work on with "knitr".
I like simple and flexible tool, and more importantly, reliability.
Great vision and implementation.
Happy Chinese New Year 2012.
yihui 2022-12-16 21:02:54Thanks! I'm glad that you like it, and happy new year to you too :)
Originally posted on 2012-01-21 18:42:58
Guest *Subramanian* @ 2012-02-04 10:05:29 originally posted:
Hi Yihui
Knitr works perfectly for me in R Gui. However, while coding i use RStudio more that R Gui. If i try knitting the same document from RStudio i get an error.
sample Rnw file (it is in the home directory):
documentclass[a4paper]{book}
begin{document}
chapter{Downloading data with R}
In this chapter, I will show you how to download data with R
<>=
x=rnorm(10)
@
end{document}
The sample.tex file is produced in R Gui using knit(sample.Rnw), but if itry knitting from RStudio, i get an error (that says something like cannot change working directory). I wonder why because the file is in the home directory. Error msg:
processing file: trial.Rnw
|>>>>>>>>>>>>>>>>>>>>>> | 33%
ordinary text without R code
|>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> | 67%
chunk1:
Error in setwd(input_dir()) : cannot change working directory
output file: C:UsersSSDocumentstrial.tex
Any clues?
yihui 2022-12-16 21:02:55What is the value of opts_knit$get('input.dir') when the error occurs?
Originally posted on 2012-02-04 10:26:07
giscus-bot 2022-12-16 21:02:56Guest *Subramanian* @ 2012-02-04 10:31:27 originally posted:
That gives me Book:
opts_knit$get('input.dir')
[1] "/Book"
giscus-bot 2022-12-16 21:02:57Guest *subramanian* @ 2012-02-04 11:16:07 originally posted:
Hi, what to make out of it?..
yihui 2022-12-16 21:02:58This is weird. I do not know why it is "/Book"; it should be "C:UsersSSDocuments". Which versions of RStudio and knitr?
Originally posted on 2012-02-04 11:27:39
Guest *Subramanian* @ 2012-02-04 10:08:33 originally posted:
By the way, lest i confuse you, sample .Rnw and trial.Rnw are one and the same. and both are in the Home directory. Knit() doesn't work with both of them.
Guest *Subramanian* @ 2012-02-06 05:03:49 originally posted:
Thank you fr the reply..yes it works with RStudio daily build 0.96.12. i was using the current stable version 0.95.238.
Guest *Rod Alence* @ 2012-05-04 14:49:57 originally posted:
Hi Yihui,
I'm having a small problem running dotcharts using knitr and the Tikz device: the longer labels run over into the plotting area (and may be in a slightly larger font than they're supposed to be, compared to the document text). I don't have this problem using pgfSweave. I'm new to knitr and am not sure if I'm missing a setting somewhere. Here's a minimal example:
documentclass{article}
usepackage{tikz}
begin{document}
<<first,fig.keep="high",fig.width=5,fig.height=4,dev="tikz">>=
basic <- 1:2
names(basic) <- c("short label", "a slightly longer label")
dotchart(basic)
@
Some regular text.
end{document}
Rod
yihui 2022-12-16 21:02:58Thanks for reporting the issue. I can reproduce it. The reason is that the recording device (pdf() by default) is different with the rendering device (tikz), so that the metrics do not match, and the width of the long label in the pdf device does not apply to the tikz device.
I just tried ggplot2 and it worked fine, e.g.
basic <- 1:2
x <- c("short label", "a slightly longer label")
library(ggplot2)
qplot(x, basic) + coord_flip()
The ideal solution would be to use the tikz device to record plots, but I just tried and realized this device did not support plot recording, so I do not have a good solution in this case. Sorry.
Originally posted on 2012-05-04 16:39:48
giscus-bot 2022-12-16 21:02:59Guest *Rod Alence* @ 2012-05-06 12:31:01 originally posted:
Thanks for the tip on ggplot2. I also got it to work using the lattice "dotplot" function.
Guest *1dre* @ 2012-05-18 18:15:31 originally posted:
hi! I am new on this stuff, so I tried to use your package but is not working. I have a mac, both latex and r are installed. But unfortunately is not showing the output.
What should I do to have your package woking?
Sorry for bothering u
yihui 2022-12-16 21:03:00So what did you see when you knit() the file?
Originally posted on 2012-05-18 23:31:57
访客 *Puriney* @ 2012-09-28 06:23:52 写道：
有没有会打算把pandoc属性融入到knitr包里？我想，knitr既然能高亮R代码，加上pandoc类工具属性，实现对其他语言的高亮支持；同时勾芡上CSS，这样转换为html就更美观。新暗黑魔法，markdown->Rmarkdown->Html。“这样写报告的方法会不会更喜欢呢？”
yihui 2022-12-16 21:03:01有打算（ yihui/knitr#206 ），不过这事情没有太大的独特贡献，只是包装别人的工具而已，加上pandoc的用法太丰富了，所以我还是倾向于让用户自己去调用pandoc。
——原帖发布于 2012-09-29 21:57:21
访客 *LC Zhang* @ 2016-01-15 12:15:18 写道：
Yihui，你好，我想在lyx上使用R，在用knitr module的时候，不能顺利进行，弹出以下警告“
An error occurred while running:
Rscript --verbose --no-save --no-restore
"/Applications/http://LyX.app/Contents/Resources/scripts/lyxknitr.R"
"/var/folders/5z/6p_kh9b51s7cps7y2_g_4v_h0000gn/T/lyx_tmpdir.lTlHyVNlP795/ly...”，我看到网上有很多类似的问题，但是我尝试了一些解决方法后，并不能解决问题。我用sweave的时候，并没有这个问题。希望你能帮我看一下。如果问题过于naive，望谅。
yihui 2022-12-16 21:03:03菜单View - View Messages，看到底是什么错误。
——原帖发布于 2016-01-15 16:35:35
giscus-bot 2022-12-16 21:03:04访客 *LC Zhang* @ 2016-01-16 06:54:45 写道：
错误显示如下：
15:47:04.114: Previewing ...
15:47:04.115: (buffer-view: ⌘R)
15:47:04.393: Rscript --verbose --no-save --no-restore "/Applications/http://LyX.app/Contents/Resources/scripts/lyxknitr.R" "/var/folders/5z/6p_kh9b51s7cps7y2_g_4v_h0000gn/T/lyx_tmpdir.WOorMcYAA826/lyx_tmpbuf0/""newfile1.Rnw" "/var/folders/5z/6p_kh9b51s7cps7y2_g_4v_h0000gn/T/lyx_tmpdir.WOorMcYAA826/lyx_tmpbuf0/""newfile1.tex" ISO-8859-15 "/Users/behlab/Desktop/"
15:47:04.410: running
15:47:04.411: '/Library/Frameworks/R.framework/Versions/3.2/Resources/bin/R --slave --no-restore --no-save --no-restore --file=/Applications/http://LyX.app/Contents/Resources/scripts/lyxknitr.R --args /var/folders/5z/6
15:47:04.411: p_kh9b51s7cps7y2_g_4v_h0000gn/T/lyx_tmpdir.WOorMcYAA826/lyx_tmpbuf0/newfile1.Rnw /var/folders/5z/6p_kh9b51s7cps7y2_g_4v_h0000gn/T/lyx_tmpdir.WOorMcYAA826/lyx_tmpbuf0/newfile1.tex ISO-8859-15 /Users/b
15:47:04.411: ehlab/Desktop/'
15:47:04.411:
15:47:05.940:
15:47:05.941:
15:47:05.941: processing file: /var/folders/5z/6p_kh9b51s7cps7y2_g_4v_h0000gn/T/lyx_tmpdir.WOorMcYAA826/lyx_tmpbuf0/newfile1.Rnw
15:47:06.281: Warning: namespace 'formatR' is not available and has been replaced
15:47:06.281: by .GlobalEnv when processing object 'silent'
15:47:06.282:
|
| | 0%
|
15:47:06.298:
|...................... | 33%
15:47:06.299: ordinary text without R code
15:47:06.299:
15:47:06.299:
|
|........................................... | 67%
15:47:06.299: label: tile
15:47:06.492: Quitting from lines 11-13 (/var/folders/5z/6p_kh9b51s7cps7y2_g_4v_h0000gn/T/lyx_tmpdir.WOorMcYAA826/lyx_tmpbuf0/newfile1.Rnw)
15:47:06.493: Error in loadNamespace(name) : there is no package called 'highr'
15:47:06.493: Calls: knit ... tryCatch -> tryCatchList -> tryCatchOne ->
15:47:06.493:
15:47:06.493: Execution halted
support/Systemcall.cpp (292): Systemcall: 'Rscript --verbose --no-save --no-restore "/Applications/http://LyX.app/Contents/Resources/scripts/lyxknitr.R" "/var/folders/5z/6p_kh9b51s7cps7y2_g_4v_h0000gn/T/lyx_tmpdir.WOorMcYAA826/lyx_tmpbuf0/""newfile1.Rnw" "/var/folders/5z/6p_kh9b51s7cps7y2_g_4v_h0000gn/T/lyx_tmpdir.WOorMcYAA826/lyx_tmpbuf0/""newfile1.tex" ISO-8859-15 "/Users/behlab/Desktop/"' finished with exit code 1
Error: Cannot convert file
An error occurred while running:
Rscript --verbose --no-save --no-restore
"/Applications/http://LyX.app/Contents/Resources/scripts/lyxknitr.R"
"/var/folders/5z/6p_kh9b51s7cps7y2_g_4v_h0000gn/T/lyx_tmpdir.WOorMcYAA826/ly...
15:47:13.397: Error while exporting format: PDF (pdflatex)
15:47:22.404: (dialog-toggle progress)
请问改怎么破？谢谢。另外，我在mac air上用的时候，没有这个问题。
giscus-bot 2022-12-16 21:03:05Guest *LC Zhang* @ 2016-01-17 07:12:50 originally posted:
Hi, Yihui, I have fixed the problem and it appeared that I did not have package "highr" in R. Thanks for you time!
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