Guest *MartinInFfm* @ 2012-03-23 11:13:32 originally posted:

When I use xtable in a chunk, I  get a grey shaded empty line.
What can I do to suppress it?
I have tried already the options : warning=FALSE,message=FALSE,error=FALSE

Example:
<<print,echo=false,results='asis',warning=false,message=false,error=false>>=
print(xtable(data.frame(x=1)))
@

Guest *Bastien Ferland-raymond* @ 2012-04-03 17:26:32 originally posted:

Hello Yihui,

First, thanks a lot for your work, this package is great!

I have a problem adding a figure using the layout() function and was wondering if you could help me.

An exemple code:

<<virees, results="hide" ,echo="F,fig=T,dev="png",dpi=150,fig.height=6,fig.width=10,fig.keep="high"," fig.align="center" ,fig.height="6,fig.width=10">>=
for(i in c("g4564", "g4167")){
windows(10,6)
layout(matrix(c(1,2),1,2), widths=lcm(c(25.4-15.24,15.24)), heights=lcm(c(15.24,15.24)))
par(mar=c(0,0,0,0))
plot(1,1); text(1.1,1,i)
plot(2,1, col="red"); text(2.1,1,i)
dev.off()
}

If I use that, my figures include only the left plot in the layout.  Any idea why?

I actually want to print in a report with multiple figures (~250) where each one is the result of a special layout format.

Thanks a lot

Bastien

Guest *Morales* @ 2012-04-08 08:21:02 originally posted:

Hi Yihui, congratulations for your work with knitr. I am using it a lot, but I am having problems when I try to supress some lines in the output. It's fine when I use i.e. "echo=2", but I am not able to get "echo= 1:3" . Try this example please:
 begin{document}
<<p1,echo=f,comment=na>>=
rendimiento = c(30,34,25,21,24,11,25,12,9)
metodo = factor(c(1,1,1,2,2,2,3,3,3),
labels= c("A","B","C"))
mod=aov(rendimiento~metodo)
@
<<p2,echo=1:3,comment=na,tidy=f, results="asis">>=
library(multcomp)
tuk1 = glht(mod, linfct= mcp(metodo="Tukey"))
res=summary(tuk1)
x1a=res$test$coefficients
x2a=res$test$tstat
x3a=res$test$sigma
x4a=res$test$pvalues
a1=round(data.frame(x1a,x3a,x2a,x4a),3)
colnames(a1)=c("Estimación","Std","T","P")
library(xtable)
print(xtable(a1,caption="Comparaciones: Método Tukey"),caption="top",floating=T)
@
end{document}

Guest *Morales* @ 2012-04-08 08:36:53 originally posted:

Hi Yihui,forget my previous post. I forgot the quotation marks in results= "asis" . Thanks for your fine work

Guest *jamiefolson* @ 2012-05-15 14:47:45 originally posted:

What is the best practice for chunks where you only want the figures?  I can turn off all of the output, but that still leaves a colored, framed box around all the chunks, even if it's just an includegraphics.  I also end up with lots of stuff added to the main document header that's never used.  Is there any way you could just put that stuff in a latex package and include it like framed is?

I can turn off the highlighting, but I still get the framed colorbox.

Guest *Eric Nord* @ 2012-05-15 18:01:54 originally posted:

Does anyone have nice example of using chunk options in markdown with knitr? I'm lost.
 

Guest *Florian Oswald* @ 2012-05-25 01:51:30 originally posted:

hi yihui!
I recently updated to the latest knitr version (along with R 2.15). I had a very nice (and fast) running setup with lyx before the upgrade. now knitr complains that i am using old Sweave options and I should visit this page. I'm having a hard time figuring out which options are outdated and which ones are not. Is there a kind of list for this somewhere? I guess it's slower because of this. Thanks for your help!
Florian

Guest *Eugene* @ 2012-05-30 19:52:55 originally posted:

Hi Yihui,

I am running Lyx 2.0.3 on Windows XP with loaded module Knitr and have following error popping up while trying to convert R code to TeX:

"An error occurred while running>
Rscript --verbose --no-restore "C:/Program Files/LyX20/bin/../Resources/scripts/lyxknitr.R" "C:/Documents and Settings/me/Local Settings/Temp/lyx_tmpdir.Hp3588/lyx_tmpbuf2/""Paper2.Rnw""C:/Documents and Settings/me/Local Settings/Temp/lyx_tmpdir.Hp3588/lyx_tmpbuf2/""Paper2.tex" ISO-8859-15"M:/CODE/Paper2/" 

"Do you have a clue what it might be?My document have an empty preamble. I only use the following options in the beginning of the document"
<<set-options, include="FALSE," echo="FALSE," cache="FALSE">>=options(replace.assign=TRUE,width=90)knit_hooks$set(par=function(before, options, envir){if (before) par(mar=c(4,4,.1,.1),cex.lab=.95,cex.axis=.9,mgp=c(2,.7,0),tcl=-.3)})read_chunk('Paper2.R')opts_chunk$set(fig.path='figure/', cache.path='cache/', dev='tikz', external=TRUE, fig.width=7, fig.height=4, fig.align='center', fig.show='hold',cache=FALSE, par=TRUE) at "
If i run the document with R chunks without bold options, it seems to work, although output needs aligning and sizing.

In R i have loaded both knitr and tikzDevice packages. I wrote "at" instead of a symbol only here due to mail autocompletion...

Best regards,
Eugene

Guest *Rafik Margaryan* @ 2012-07-04 07:45:13 originally posted:

Hi Yihui,
I've got confused with references and it seems does not work for me. If I put chunck label for plot fig1, how shoud referre to that figure by default : fig:fig1 or just fig1?
And how should I refer to tables( I use Hmisc summary.formula for creating tables)?
Many thanks

Guest *Chris Okugami* @ 2012-07-09 20:48:45 originally posted:

Hi, Yihui, 

I got a problem using kintr and markdown on ubuntu. x64

here is my markdown code. 
mytest.Rmd 

this code generates animation buttons but it doesn't play on web browser. 

{r echo=FALSE,fig.path='figure/fig2',fig.keep='all',[fig.show](http://fig.show)='animate'}  plot(rnorm(100))plot(rnorm(100))
yes, i have mp4 support on ubuntu, with internet connection.

Any idea? 

Guest *Chris Okugami* @ 2012-07-09 21:00:55 originally posted:

animation option. 

Currently, support animation.fun ="hook_ffmpeg_html". 

Is it possible to use animated gif as  output? instead of mp4? 

It will be very nice to make animated PDF from markdown so that we can space in our report!! 

My motivation behind this is that 
I work with large dataset, many sampling points, very tiring of scrolling down!!

Thank for your help
Chris  
 

Guest *Donlumor* @ 2012-07-10 08:32:49 originally posted:

senic ¡- read.table(”pdata.txt”, header = FALSE) colnames(senic) ¡- c(”y”, ”x1”, ”x2”, ”x3”, ”x4”,
”x5”, ”x6”, ”x7”, ”x8”, ”x9”, ”x10”) attach(senic) pairs(senic, pch = 21, bg = c(”red”, ”yellow”, ”blue”,)

I used this code for the above result
<<echo=true,fig=true,comment="", eval="TRUE">>=senic<-read.table("pdata.txt",header=FALSE)colnames(senic) <- c("y","x1","x2","x3","x4","x5","x6","x7","x8","x9","x10")attach(senic)pairs(senic, pch=21, bg=c("red","yellow","blue","black"))

My output does not execute line by line
I used <- to store  read .table but i get  ¡- in output

I use Rstudio for my reports

Guest *Sebastian Campbell* @ 2012-07-13 04:49:10 originally posted:

testfun.Rmd:

summary(cars)  

I'm not sure if this is a bug (and it doesn't cause knitting a document to stop), but this causes and error:

options(encoding=''); require(knitr); knit('testdash.Rmd');
Loading required package: knitr

processing file: testdash.Rmd
Error in parse(text = str_c("alist(", params, ")")) :
1:20: unexpected ','
1: alist( car-function,
^
Warning in parse_params(params) :
(*) NOTE: I saw options " car-function, eval=FALSE"
are you using the old Sweave syntax? go http://yihui.name/knitr/options

Guest *Gurix* @ 2012-07-17 16:49:01 originally posted:

Good work bro. That's indeed a significant step forward in R history.

Guest *wegelinjacob* @ 2012-07-18 19:45:13 originally posted:

At http://jacobwegelin.net/tmp/XieYihui/, in the 
20120718Wed151045-foo.Rhtml example, I specified "echo=FALSE" to try to show only the results. But when the resulting html file (also on the website) is displayed in a browser, a bunch of pound or number signs (#) are displayed in place of the R source code. Is there a clean automatic way to get rid of all traces of the R code in the displayed html, so that one only sees (in this case) the displayed table? 

The pertinent documentation (from http://yihui.name/knitr/options) is: 

echo: (TRUE; logical or numeric) whether to include R source code in the output file

In the same place a 2nd html file can be found which contains the lines from the prevous html that are necessary to display the table, without the preamble that starts the first html file.  What is the function of those pound signs?  

Guest *wegelinjacob* @ 2012-07-18 20:37:25 originally posted:

knitr issues a warning about my chunk options, accusing me of Sweave thinking, when (as far as I can tell) I am using the very options specified in this page, http://yihui.name/knitr/options. What am I missing?

See "20120718Wed163809-knit01.Rnw.txt example" on the following page:

http://jacobwegelin.net/tmp/XieYihui/

knitr says

Warning in parse_params(params) :
  (*) NOTE: I saw options "echo=TRUE, results=asis"
 are you using the old Sweave syntax? go http://yihui.name/knitr/options

See the url above for the details and a reproducible example.

Guest *wegelinjacob* @ 2012-07-18 21:24:59 originally posted:

I have tried to convert a *.Rnw which works in Sweave, into knitr. Using Sweave and xtable, I can display a table in a pretty format within a LaTeX-created pdf. You can find a link to the Sweave success, and my attempt to make this work in knitr, at http://jacobwegelin.net/tmp/XieYihui/ under "20120718Wed171457 example." 
If I'm reading the knitr options correctly on this page, to convert to knitr one must eliminate chunk header such as "results=tex" and replace it with something like "results=asis" or "results=markup". But I'm running into two problems. (1) Even with the above change in header specification, knitr still issues a warning.(2) The table does not display in the pdf file as a proper table. See http://jacobwegelin.net/tmp/XieYihui/ for details.

Thanks for any insights.

Jake

Guest *Gary4IR* @ 2012-07-26 04:49:31 originally posted:

Yi Hui, Thanks for your great contribution to the UseR community with this package. I am new to LaTeX and LyX. I have built a substantial report using R and LyX with knitr, and I love the way it looks. There is one thing I'm stuck on, however. One page of the report has a wide table taking up the top half of the landscape document, and another smaller table takes up less than half of the bottom half of the page. I want to have a ggplot2 graphic appear in the lower right hand corner using a chunk, but no matter what I try, I can't keep it from bumping down to the next page. Is there a way to force an image created in a chunk to appear adjacent to a table? Thanks for any help you can offer.
-Gary

Guest *HLM* @ 2012-07-26 11:44:18 originally posted:

Hi YiHui,

Thanks again for creating knitr its amazing!

Is there a way to set the chunk options (and specifically fig.width and fig.height) mid chunk?Also is there an issue about plotitng the same graph in the same chunk. e.g. I would expect two very different size graphs to appear when running the following:

{r}opts_chunk$set(fig.width=3)plot(1:1000)opts_chunk$set(fig.width=10)plot(1:1000)

the image attached is what I got

Guest *Gary4IR* @ 2012-07-30 19:14:26 originally posted:

How does one turn off all caching? I'm stuck on this despite reading the section on Cache in the user's guide.
For example, I'd like the following chunk to return a different value each time:
<<ch1,echo=false>>=
rnorm(1, 6, 1.1)
@          

Feel free to yell at me - I know this must be very basic.
-Gary

访客 *97m423* @ 2012-08-13 13:50:47 写道：

Hi 谢大侠,

using caption[Example]{blahblahblah} in LaTeX allows two different captions of a graphic, [Example] will be showed in List of Figures and {blahblahblah} will be showed directly as caption under the graphic. How could I use this []{} in fig.cap in knitr?Best regard,Schorschi

Guest *Akshay* @ 2012-08-26 20:27:28 originally posted:

Hi, 

I am trying to input a yacas expression in a knitr file. 

The output of this

{r }fmt <- sprintf("TeXForm(%s)", cost)yacas(fmt, retclass = "unquote")

is a latex expression  as follows : 

$ mu  + frac{2 lambda }{mu  - lambda } $

But I'd like knitr to understand that it is a latex statement and write it in latex form ( as it would do if I had written seperately : $$ mu  + frac{2 lambda }{mu  - lambda } $$

Any ideas? Thx!

Guest *Donelle* @ 2012-09-13 02:45:28 originally posted:

I am trying to use R to do some matrix calculations and then display
using Latex,  I cannot seem to find any help online that tells me how I
would go about doing this.  I briefly looked at Xtable, but it does not
perform to the specifications I need.  Please let me know if there
currently is an option.  

Guest *Mark80305* @ 2012-09-13 22:04:31 originally posted:

Thanks again for this wonderful package.

How do I change the default font size for my tikz plots?

Guest *wellermatt* @ 2012-10-17 23:20:54 originally posted:

I can't stress enough how good this package is.  It really is magnificant.  Dumping my analysis to an HTML page is so simple, shame the same cannot be said for the LaTex creation, but that's due to the steep learning curve with that form of output rather than limitations of knitr.

I have a specific question regarding the sizing of plots.  I have a routine which generates 120 plots in a list [1..30] of lists [1..4] for later output.  I wish to be able to dump these out, but apply some resizing depending on which plot I am outputting. 

print(x)  

Currently every plot is outputted within a single code chunk using a single height x width, but I need the flexibility for every 4th plot to be much smaller.  So the question is whether I can set the size parameters WITHIN the chunk.  I really want to avoid having to write 60 chunks of code, such as:

print(x[[1]][[1:3]])  

print(x[[1]][[4]])  

etc for element of the outer loop.

My apologies for not explaining myself extremely clearly here but I hope I've got my question over well enough for somebody to advise.  Thanks.

Guest *Feizai060* @ 2012-10-20 00:02:47 originally posted:

Hi Yihui,

It is a fantastic package, which I like so much. One problem when I want to generate animation is:

I set chunk option: fig.show='animate'. But there is no mp4 file generated in the Figure Folder. Therefore no animation displayed in the knitted html. Any help or suggestion? Thanks.

Best,

Guest *Guangyu Zhu* @ 2012-10-29 16:12:48 originally posted:

Hi Yihui,
This is a great package. It helps me a lot in writing notes. 
I meet a problem, I want to make the output in two columns, then I tried 
usepackage{multicol}
 begin{multicols}{2}
<<>>=
@
end{multicols}

but it did not work. Do you have any solution?

Guest *Matt Bannert* @ 2012-11-05 13:54:26 originally posted:

Thanks sooo much for the cairoPDF option... googlers read this: http://www.stat.auckland.ac.nz/~paul/R/PDF/pdfEncoding.html

Guest *Matt Bannert* @ 2012-11-05 14:00:12 originally posted:

afaik the cairo function is called dev='cairo_pdf', not dev='CairoPDF'.  Hell of an option though. Thanks sooo much. Googlers might want to read this note by Paul Murrell, too: http://www.stat.auckland.ac.nz/~paul/R/PDF/pdfEncoding.html

Guest *Akshata Udyavar* @ 2012-11-07 06:50:47 originally posted:

Hi - When I try to echo R code, it gives me a message in compile PDF such as this e.g. : "Overfull hbox (148 pt too wide) in paragraph at lines 204--204". 
How do I resize the output text in the R output?

Guest *Jesus_Gaby* @ 2012-12-02 01:25:04 originally posted:

Hi Yihui,

Below I showed you the result of using R Mardown [I select that data from database]. I dont need the ##, ##1, ##",..., ##19, and another one is the result Setúbal = Setúbal [not recognized portuguese characters like ú, é, ç, etc...] How would I solved it?

region_id name total_users

1 2735941 Porto 573

2 2742610 Aveiro 288

3 2267056 Lisboa 121

4 2740636 Coimbra 48

5 2742031 Braga 46

6 2262961 Setúbal 10

7 2732437 Vila Real 8

8 2267094 Leiria 8

9 2732264 Viseu 4

10 2593105 Madeira 4

11 2732772 Viana do Castelo 4

12 2263478 Santarém 3

13 2268337 Faro 3

14 3411865 Açores 3

15 2269513 Castelo Branco 3

16 2268404 Évora 2

17 2270984 Beja 2

18 2742026 Bragança 1

19 2738782 Guarda 1

Guest *Jesus_Gaby* @ 2012-12-02 03:39:56 originally posted:

I'm using RStudio. These caracters are saving on database, like in database table is Évora but when I select using SQL queries thru RPostgreSQL, return me Évora.

Are there any settings on RStudio to solve this problem?

Thanks in advance,

Guest *Jesus_Gaby* @ 2012-12-02 18:32:35 originally posted:

The caracter in database is en_US.UTF-8. I see, maybe it used english US that's why didnt recognize portuguese caracter. Thanks for suggestions. Let me see how to solve it.

Thanks,

Guest *JoAnn Alvarez* @ 2012-12-11 20:07:04 originally posted:

Hi Yihui,

I noticed that if I have multiple plots within one chunk that will run over more than one page in my output file, adding a fig.cap in the chunk header will cause only the first page to display on the output document. If I leave out the fig.cap, all the plots will display on the pages. This could be problematic.

Thanks!

Guest *Rafik Margaryan* @ 2013-01-04 12:45:21 originally posted:

Hi Yihie,
I have to ask an advice. I write it here , because I could not find better place tho ask.
Here is a code that I have written for my personal use for article writing and it expresses mean +/- sem.
Here is the code:

m.se <- function (x, na.rm = TRUE) {  
if (na.rm)  
x <- x[![is.na](http://is.na)(x)]  
n <- length(x)  
if (n == 0)  
return(c(mean = NA, sem = NA))  
xbar <- sum(x)/n  
se <- sqrt(sum((x - xbar)^2)/(n - 1))/sqrt(n)  
ret = c(mean = xbar, sem = se)  
class(ret) ="m.se"  
ret  
}

print.m.se = function(x, digits = getOption("digits"),...){  
print(paste(format(x["mean"],digits=digits), "pm",format(x["sem"],digits=digits)))  
invisible(x)  
}  

R output gives me "2.35 pm 0.35",
I was expecting from knitr to return with Sexpr {} like example of 2.35 pm 0.34 or so, but it returns in latex file as
2.35, 0.34 when I use Sexpr{}, "2.35 pm 0.35" when I use it inside the chunk. I have no idea how I can fix it.
Could you give some suggestion on this?
Many thanks beforehand.

Guest *JoAnn Alvarez* @ 2013-01-16 21:29:11 originally posted:

Is there a different default highlighting color (highlight option) for different types of chunks? I am using the framed package to highlight some latex text outside of the chunks. A side effect is that, while most of my r code has the default gray background color, the code from one chunk has blue highlighting.

Guest *Dave Matthews* @ 2013-01-18 14:02:53 originally posted:

My first attempt at Rmarkdown.

rnorm(10)  

I am getting this error when I Knit HTML
Quitting from lines 28-29 (test.rmd)
Error in evaluate(code, envir = env, new_device = FALSE, stop_on_error = if (options$include) opts_knit$get("stop_on_error") else 2L) :
unused argument(s) (new_device = FALSE, stop_on_error = if (options$include) opts_knit$get("stop_on_error") else 2)

Guest *Carl* @ 2013-02-13 18:09:18 originally posted:

We can selectively turn on/off chunk execution with eval=TRUE and eval=FALSE within the source.
But is there a way to call knit() and select execution of chunks without changing the source?

Guest *guest* @ 2013-02-20 20:38:04 originally posted:

Dear Yihui, I am using Knitr to make weekly reports. I was wondering is there a way to set a test chunk in the middle of the file, so that if returned FALSE, Knitr will not run the rest of the report? Thank you !

Guest *JoAnn Alvarez* @ 2013-03-13 16:07:02 originally posted:

What up, Yihui. I have a question about caching. Suppose you have 2 .Rnw files in the same directory, and both of them have a chunk with the same chunk label, but the code inside is different. By default, if caching is used, there will be one cache directory that both files will try to access. Will the caching work correctly for both files?

Guest *Doi* @ 2013-03-30 07:49:45 originally posted:

Hi Yihui, a command in a chunk has been printed out too long that goes beyond the margin. How can I limit the width of it?

Guest *Brett Longworth* @ 2013-04-22 20:21:36 originally posted:

Knitr seems to not embed png figures in the html output if the chunk name includes spaces (I know, bad practice). Is this a bug, or am I missing something? This is almost certainly a FAQ, but I couldn't find it mentioned. Thanks for knitr!

Guest *Harold C.* @ 2013-05-25 11:38:27 originally posted:

Excellent work, you have made my computing life much easier, thank you! I am also reporting an error in documentation: „highlight: (TRUE; character)“ should be logical.

Guest *Shima* @ 2013-05-30 12:02:26 originally posted:

Hello Yihui,

How can I change the font size of the values in my table to prevent it to exceed from the margin?
I used "size=footnotesize" but it does not work.

<<make the="" table,="" echo="F,tidy=TRUE," results="markup" ,="" size="footnotesize">>=
library(psych)
Duration_TimeByRoute<-describeBy(CopReadingDataFrame$Duration_Time,
CopReadingDataFrame$Route, mat =
TRUE)[,c("group1","n","mean","sd","min","median","max")]
@
<<print table,="" echo="F," tidy="TRUE" ,results="asis" ,="" size="footnotesize">>=
xtable(as.matrix(Duration_TimeByRoute), floating=FALSE)
@

It seems also that the ”floating=FALSE” does not work either.

I have another question,
Is there any way to prevent running all the R codes when I only change one chunk option?

Thanks for your reply in advance.

Yours Sincerely,
Shima.

Guest *astralth* @ 2013-06-07 09:18:55 originally posted:

Hi,

I found a minor glitch in the fig.scap option : is you enter captions with decimal numbers like ${0.12}$ without specifying the fig.scap option, you get an error because the subcaption is ${0 . Specifying the scap solves the issue but I guess it should be automatic not to break the caption in math mode :)

Thanks again for the great work !

Guest *Peng Zhang* @ 2013-07-17 02:19:27 originally posted:

Hi Yihui,

Is that possible to put "opts_chunk$set(message = FALSE)" into some config files (like .Rprofile) so one doesn't have to put it into every single Rnw file? Thanks!

Peng

Guest *Brandon* @ 2013-07-28 18:37:22 originally posted:

I'm using the setspace package with doublespacing in RStudio/knitr. However, I would not like the R output to be affected by this change in spacing. Is this possible?

If you want to hide everything, use include=FALSE; if you want to hide the messages, use message=FALSE. See http://yihui.name/knitr/demo/output/

Originally posted on 2012-05-26 05:55:38

Please read the documentation ?print.xtable carefully. There are no arguments named tabular.environments. I can only see tabular.environment, and I do not see it can take a vector of length 2 in its documentation.

The only relevant piece for knitr is you need to set the chunk option results='asis' for that chunk.

Originally posted on 2012-06-19 14:39:27

Guest *yesraj* @ 2015-03-10 23:39:11 originally posted:

how to align the output to the left using knit options

Guest *dhduncan* @ 2015-06-11 15:28:13 originally posted:

Yihui, thanks again for this page, I keep coming back.

I've just distributed an assignment to students in spanish using a knitted html doc, but when my colleague opens it the international characters aren't recognised. (ó, ñ, etc). The view settings in his browser look right (unicode) to me. I imagine there must be a way to encode instructions for the browser in the file itself, is there?

Guest *Guilherme Parreira* @ 2015-08-20 01:07:52 originally posted:

Hi Yihui!

How can I make the output from kable() to be like the first image?

When I use kable() I only get the second table.

I don't want this large space between columns...

(I realized that it has to deal with templates, but how can I control it?)

Guest *Hao Zhu* @ 2015-09-04 20:23:26 originally posted:

@disqus_JgnwJRdXiJ:disqus You can try the vignette template.

访客 *peter* @ 2015-10-14 06:11:41 写道：

目前knitr除了R之外,只支持python和awk,希望下一步能支持scheme.

访客 *🐉®γσ ξηg* @ 2016-01-08 21:03:12 写道：

感谢分享哦，俺差不多每天都得与RMarkdown打交道，呵呵～

Guest *Paulo Mah* @ 2016-03-24 23:42:07 originally posted:

Hello,
Please, I am a beginner using knitr. I am using RStudio and Texnichcenter and trying to format a plot (graphic) in my latex document. The figure only appears at the top of the page. I have already change some chunk options, but they didn't work.

My global chunk is

<<setup, include="FALSE">>=
opts_chunk$set(dev="pdf", fig.path = "graphics/plot",

fig.lp = "",

out.width=".05textwidth",
fig.pos="b",
fig.keep="high",
fig.show="hold",
fig.align="center",

comment=NA)

knit_hooks$set(inline = function(x) {
if (is.numeric(x)) return(knitr:::format_sci(x, 'latex'))
x = as.character(x)
h = knitr:::hilight_source(x, 'latex', list(prompt=FALSE, size='normalsize', highlight=FALSE))
h = gsub("([_#$%&])", "1", h)
h = gsub('(["'])', '1{}', h)
gsub('^begin{alltt}s*|end{alltt}s*$', '', h)})
par(las = 1)
options(width = 30, scipen = 4, digits = 3)
@

So as to test, a specific chunk in my document would be:

<<model, echo="FALSE," fig.pos="b">>=
x1=c(1:10)
plot(x1, type="p")
@

Please, Does someone have any tip for me?

Thanks!!

Guest *Mason Garrison* @ 2016-03-25 18:06:59 originally posted:

You have a typo:

knit_patternss$get('document.begin') should read

knit_patterns$get('document.begin')

Guest *herz* @ 2016-04-30 01:22:50 originally posted:

I have put the following (and various variations of it where I load tidyr and/or formatR; try cache=FALSE, etc) in my first chunk.

library(knitr)  
opts_chunk$set(tidy.opts=list(width.cutoff=60))  

Yet it does not wrap code/comments in the rest of the document! I'm wondering if the version of RStudio, Rmarkdown, or of the packages it relies on matters (I have 0.99.484, rmarkdown - I deleted markdown, formatR is v1.3, knitr v1.12.3 I am able to fix by adding to the beginning of chunks as you suggested. However, I have a very large document that needs fixing so fixing this would be wonderful. Any other ideas? Thanks!

I can say that adding: ```{r, tidy=TRUE, tidy.opts=list(width.cutoff=60)} to the top of each chunk in the file works, but that will not help with my long document.

Guest *Aleza Wallace* @ 2016-05-09 23:37:04 originally posted:

is there a way to slide numbers to my beamer output

Guest *Joseph Powers* @ 2016-06-15 18:24:28 originally posted:

I am trying to control the size of pdf figures when knitting word documents from R Markdown, but the figures ouput as the same size in my word output (2" x 2") regardless of the fig.width and fig.height settings I write in the chunk options. All that fig.width and fig.height are changing is the proportions within the 2" x 2" figure output.

All help is greatly appreciated.

title: "Controlling PDF figure size in MS Word output"
output: word_document

knitr::opts_chunk$set(fig.path='02_Figs/', [fig.show](http://fig.show)='asis', dev = 'pdf',  
include=FALSE, warning=FALSE, message=FALSE)  

Fig. 1. Small Plot

with(mtcars, plot(mpg～wt))  

Fig. 2. Big Plot

with(mtcars, plot(mpg～wt))  

Guest *Shilpa Deshmukh* @ 2017-01-12 05:35:35 originally posted:

What should I do if I want to halt the execution of running code chunk in Rstudio (.Rmd file)?

Guest *George* @ 2017-04-26 22:28:09 originally posted:

Thank you for your work. This is very helpful.

I am wondering how I can suppress "intermediate" plots. The code below generate a histogram although the 'hist' command is only used to get counts from hist(). Thanks in advance for any idea.

George

See the code below:

min_ct<-min(hist(myfdata[myfdata$slope>low, ]$dy, breaks = bi)$counts)

Guest *Juan* @ 2017-05-31 18:25:06 originally posted:

Yihui It is possible to write an article in the Spanish language with R markdown. Example "Table = Tabla", "Figure = Figura", ....
Gracias.

Guest *Marius Bottin* @ 2017-06-05 14:42:34 originally posted:

I am wandering whether there is a simple way to automatically insert the name of the engine (R, python, bash,sql) as a title of the chunk in the final document (html and pdf through pdflatex).
It is because I am writing documents using different engines, and it is sometimes confusing for my readers...
I imagine it is possible through css classes for html, but since I like to make output document in both pdf and html...

Guest *fboehm* @ 2017-11-08 21:07:54 originally posted:

Is it possible to create a html file in which the user can "expand" or "collapse" an R code chunk to view (or not view) the code in the chunk?

Guest *Henrik* @ 2017-12-14 18:49:52 originally posted:

is it possible to create a new empty python chunk (in rmarkdown in Rstudio) using a short cut like we can do to create a new r code chunk?

Guest *Henrik* @ 2017-12-19 08:58:40 originally posted:

Yihui, I love how I can work with Rmarkdown and knitr in Rstudio.

On the other hand, I love writing in my favorite text editor Atom.

I can execute both R and Python code chunks in Atom but the Python implementation is better in Atom (with packages) because e.g. the variables are not lost as in RStudio between code chunks. Also, I just like writing in Atom more.

But the problem is that I cannot convert e.g. the final .md file that contains markdown and R&Python chunks into such a nice looking output as Rstudio can do with rmarkdown.

Is there a way to basically use rmarkdown/knitr in Atom and especially in such a way that I can run Python code chunks just like I use R code chunks? Currently I can run Python but not between code cells...

访客 *Shixiang Wang* @ 2018-02-12 07:53:19 写道：

Yihui，我有一个问题，怎么样可以在knit输出md文档时，自定义图片的名称和路径。 比如![plot of chunk test_plot](./2018-02-12-new_test/test_plot-1.png) 我怎么在rmd文档设定方括号内和圆括号内的内容呢？
我使用hexo写博客有点小忧伤，它识别图片既不是机器的相对路径，也不是绝对路径；而是根据它自己内在设定的目录层级识别的。所以我希望能在rmd文档自定义knit导出后的效果。

Guest *Matthias* @ 2018-02-23 15:46:40 originally posted:

Dear Yihui,
Great work!
I am using knitr in combination with Rnw. Is there a possibility to highlight only certain elements of syntax and/or to change the color of certain elements of syntax highlighting.
Thanks a lot!

Guest *Esteban Cervetto* @ 2018-02-23 18:01:28 originally posted:

cómo hago funcionar un prompt interactivo dentro de un chunk

promptGuardar <- menu (c ("Si", "No"), title="¿Actualizar caché de tablas?")  
if (promptGuardar == 1) {  
save.image()  
}  

me sale

Error in menu(c("Si", "No"), title = "¿Actualizar caché de tablas?") :
menu() cannot be used non-interactively
Calls: ... withCallingHandlers -> withVisible -> eval -> eval -> menu
Ejecución interrumpida

Guest *Jan Spörer* @ 2018-06-03 16:45:29 originally posted:

Is it possible to fit the size of a plot to the size of a beamer slide?

Guest *George Flynn* @ 2018-08-18 08:01:12 originally posted:

Yihui - hello - I am new to knitr and am trying to create a PDF document for an assignment, I am getting the following error:
processing file: Cars.Rmd
|...... | 9%
ordinary text without R code

|............ | 18%
label: setup (with options)
List of 1
$ include: logi FALSE

|.................. | 27%
ordinary text without R code

|........................ | 36%

Quitting from lines 25-32 (Cars.Rmd)
Error in eval(x, envir = envir) : object 'False' not found
Calls: ... process_group.block -> call_block -> eval_lang -> eval -> eval
Execution halted

Lines 25 -32 are:

library(knitr)  
library(ggcorrplot)  
library(ggplot2)  
data(mtcars)

corr <- round(cor(mtcars), 2)  
ggcorrplot(corr, hc.order = TRUE, type = "lower",lab = TRUE)  

I am assuming it has something to do with the chunk options?
Thanks George

Guest *Matthias* @ 2019-03-23 15:43:16 originally posted:

Yihui, great work - I love to use knit, actually with .Rnw to write a textbook.

One question: Is there a way to remove the empty line between the function call and the respective output of the function?

Thanks a lot for your support!

Guest *Pedro Torres* @ 2020-02-06 01:01:10 originally posted:

Whenever i print a large vector or a frame, i always get part of my R output out of the margins... ¿Is it possible to adjust the output margins?

Guest *Jon Wakefield* @ 2020-07-06 22:14:51 originally posted:

I use beamer slides extensively, as created by Rmarkdown, and always have problems with R output being too wide.
Can you help me with the following simplified file:

---  
title: "Test File"  
author: |  
| Jon  
| University of Washington  
date: "`r Sys.Date()`"  
output:  
beamer_presentation:  
theme: "AnnArbor"  
colortheme: "dolphin"  
keep_tex: yes  
slidy_presentation: default  
---

```{r setup, echo=FALSE, message=FALSE, warning=FALSE}  
library(knitr)  
opts_chunk$set(collapse=TRUE, fig.align='center', tidy=TRUE, tidy.opts=list(blank=TRUE, width.cutoff=20,strip.white=TRUE), warning=FALSE,message=FALSE,cache=TRUE)  
```  
## test

```{r, message=FALSE, collapse=TRUE, tidy=TRUE,tidy.opts=list(width.cutoff=30)}  
seq(1,100)  
```

Guest *ERWIN LARES* @ 2021-02-20 19:30:43 originally posted:

Hello Smart People!

Here with a question about cross-referencing. I am successfully using @ref(tab:my-table) and @ref(fig:my-figure) to cross reference tables and figures that I created inside R chunks. Yay for me.

Then I started writing numbered linguistics examples with code like this:

begin{exe}  
exlabel{stm-01}  
hfil  
begin{tikzpicture}[baseline=0pt]  
Tree [.{textbf{Aspectual Classes}} [.textbf{Statives} textit{States} ][.textbf{Dynamic} [.textbf{Atelic} textit{Activities} ][.textbf{Telic} [.textbf{Instantaneous} textit{Achievements} ][.textbf{Durative} textit{Accomplishments} ]]]]  
end{tikzpicture}  
hfil  
medskip  
end{exe}  

When I was trying to cross reference my example I was stuck. I trying adding a name to the chunk and captioning the chunk, but no avail. Then by chance I wrote this ref{stm-01} and it work like a charm.

So my question is, what is the difference between @ref(tab:my-table) and ref{my-label}

Much appreciative!

Guest *Ale Campoy* @ 2021-03-07 00:51:18 originally posted:

Why is this happening? I cannot find the proper argument. My Rmd is:

title: |
| Title
output:
pdf_document: default
html_document: default
always_allow_html: 'true'

knitr::opts_chunk$set(fig.pos = 'H' )  
knitr::opts_chunk$set(echo = TRUE)  

Paquetes que vamos a usar en alguno de los ejercicios:

library(rio)  
library(rknn)  
library(kknn)  

0. Análisis exploratorio y transformación de los datos

Primero cargamos el archivo con los datos

setwd("P:/MDS/AEM/Entrega 2") # Mi Working directory, cambiar para que funcione  
dataset_raw <- import("khantrainadd.csv")  
dataset_raw$V1 <- NULL # esta columna con el indice no nos interesa  
head(dataset_raw)[,1:5]  
table(dataset_raw$class) # Mi variable objetivo  
dim(dataset_raw)  

and I get inverted order of the chunks, no matter what I do the following pdf knit https://uploads.disquscdn.com/images/e716a777b15a9bbe91aea5ebb629b1f485af61922031eeaffb6eea31453ecc8b.png

Guest *Ming* @ 2021-04-11 12:33:57 originally posted:

Hi Yihui, in R notebook inline display, the real plot size in the chunk display is consistently about 2.5-3 times larger than the specified fig.width and fig.height in the chunk options. Any comments on what might be causing this issue? Plus, the font size in the chunk display is about 50% larger than the specified font size, when compared with ggsave output. I have tried updating my Rstudio, R, didn't change anything. I also tried to use external monitors, same behavior. I use R notebook as a workhorse and having the right size plot in the chunk display is really important to me. Any insight would be appreciated!

Guest *rt* @ 2021-11-08 06:12:46 originally posted:

~ code chunks are related to links on a page while r relates to data packages

Guest *Mike Gilchrist* @ 2021-11-10 05:29:16 originally posted:

I'm using knitr with emacs and ESS. My console output is getting truncated with with the text "[TRUNCATED]". I believe this is the result of knitr. Is there a setting I can change to remove this?

Guest *peacecop kalmer:* @ 2022-05-11 18:29:04 originally posted:

How can i include LaTeX-package declarations for HTML output? For instance, if i choose PDF as output format, i can write "usepackage{...}" into a separate TEX-file that i reference in RMD-file by "template: ...". However, if i don't use a separate TEX-file and only want HTML-output then the built-in LaTeX-packages work fine and i can use equations using them but if i want to use a non-buil-in-package then what should i do? There are so many examples out there for primitive things but once it gets complicated i seldom find a solution.

Guest *MrDJR* @ 2017-04-25 14:33:21 originally posted:

Sorry for the poor formatting. I can't seem to preview, edit, or delete. I'll try once more with escape characters:
Hi! I'm trying to append a custom class to a figure div by supplying class.output='myClass' to my chunk options as follows:

plot(1:10)  

I expect the page element to be <div class="figure myClass" ="">; but instead it remains <div class="figure" ="">. I'm rendering the page with bookdown::html_document2. What am I doing wrong?

FYI: in

size: ('normalsize'; character) Font size of the chunk output from .Rnw documents. See this page for possible sizes.

The URL link is broken. Perhaps this is temporary(?), in the meantime, here is another page covering the topic: https://latex-tutorial.com/changing-font-size/

Hello yihui

I am rendering a pdf document from within Shiny app and at one instance I need to include a png plot previously saved. The Rmd file is placed in the root directory of the shiny app along with global.R, server.R and ui.R. Function includegraphics() works fine if I use it inline but not so inside code chunk:

Inline, but with no caption (caption throws a "float" error in this case):

knitr::include_graphics('./src/coverage001.png', dpi = 72, auto_pdf = TRUE)

Inside code chunk preferably with caption:

```{r covPlot, fig.align='center',  fig.ncol = 1, fig.sep = '\\par', fig.width = 9, fig.show = 'asis', fig.keep = 'all', fig.cap = sprintf('Protein %s: Coverage', names(chain))}
# coverage plot
knitr::include_graphics('./src/coverage001.png', dpi = 72, auto_pdf = TRUE)
```

When I run the chunk in RStudio, the figure appears under the chunk but not so inside the rendered document. No latex error either in the log file. I am using graphicx package without any success and all R packages are at their latest version. I have also `tlmgr_reinstalled tinytex and updated, to no avail. Please advise, thank you!

@yihui Thank you for the prompt reply!
Is not about where the figure appears in the pdf document. My question was referring to why the figure only appears in the pdf document when include_graphics is used inline and why it does not appear at all in the pdf document when include graphics is used inside the code chunk.

In other words, what should I add to the chunk options to have the figure appear when I use include_graphics inside the code chunk (please see chunk options in example 2).

This is what I mean by inline (example 1):

`r knitr::include_graphics('./src/coverage001.png', dpi = 72, auto_pdf = TRUE)`

and this is what I mean by code chunk (example 2):

```{r  fig.align='center',  fig.ncol = 1, fig.sep = '\\par', fig.width = 9, fig.show = 'asis', fig.keep = 'all', fig.cap = "A00B10"}
knitr::include_graphics('./src/coverage001.png', dpi = 72, auto_pdf = TRUE)
```

This is part of my document header, including latex packages (the indents are stripped by the browser - they are correct in the Rmd):

output: 
  pdf_document: 
    latex_engine: xelatex
    df_print: paged
    fig_caption: yes
    toc: yes
    extra_dependencies: float
    highlight: tango
lof: yes
lot: yes
fontawesome: yes
fig.align: center
graphics: yes
header-includes:
 \usepackage{fontspec} \usepackage{graphicx} \usepackage{pdflscape} \usepackage{rotating} \usepackage{titling} \setlength{\droptitle}{-1cm} \usepackage{float} \let\origfigure\figure \let\endorigfigure\endfigure \renewenvironment{figure}[1][2] {\expandafter\origfigure\expandafter[H]} {\endorigfigure} \usepackage{mdframed} \usepackage{subfig} \usepackage{fancyhdr} \setlength{\headheight}{42.45442pt} \addtolength{\topmargin}{-1.3pt} \usepackage{graphicx} \usepackage{booktabs,xcolor} \usepackage{lastpage} \usepackage{longtable} \pagestyle{fancy} \fancyhf{} \fancyfoot[R]{\thepage} \setlength\footskip{14.5pt} \fancypagestyle{plain}{\pagestyle{fancy}} \lhead{\today}  \rhead{\includegraphics[width=2.5cm]{./www/logo.png}}
mainfont: Palatino Linotype
geometry: margin = 0.75in
fontsize: 11pt

Regarding latex packages: where can I find some succinct information on what latex package(s) to call with \use{} for various tasks?

Thank you!

I had a render pdf problem when my images had multiple dots in the filename, knitr.include.graphics.ext not run?