knitr is an R package for dynamic report generation based on the concept of literate programming.

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25
votes
2answers
13k views

How to include LaTeX package in R Markdown?

I am writing a report with Rmd in RStudio via knitr package. I want to write a indicator variable symbol in the report, like How do you get \mathbb{1} to work (characteristic function of a set)?. ...
15
votes
2answers
3k views

Building TeX file from knitr Rnw as child of larger parent TeX file to use R objects and output

Here's my general problem: I'm writing my dissertation using a LaTeX template (http://www.latextemplates.com/template/masters-doctoral-thesis). The template is a parent file with multiple chapters as ...
14
votes
1answer
3k views

How to build Knitr document from the command line

I would like to compile a knitr document from the command line. With Sweave, the sequence R CMD Sweave my_sweave_file.Rnw latex my_sweave_file.tex latex my_sweave_file.tex dvips my_sweave_file.dvi ...
14
votes
0answers
400 views

How to write an arara rule for knitr

I've been trying to write a rule for invoking knitr via arara, but I don't seem to know what I'm doing, apparently. The arara manual explains how to define custom rules. To do so, it is necessary to ...
13
votes
2answers
9k views

Suppress library comments from ouput with knitr

I noticed that some library comment manage to pass through the knitr options, with R 3.0.1 and knitr 1.5 running on Mac OSX 10.8.5. The following MWE \documentclass{article} \begin{document} ...
13
votes
5answers
4k views

knitr and biblatex

I'd like to create a PDF report with knitr with LaTeX-code in RStudio with biblatex for citations. However, the in-text-citations are always undefined and no bibliography is printed. The same ...
13
votes
1answer
4k views

Two column layout with text and knitr chunk

When making presentations (with latex beamer class), I often go for a frame layout with text and equations on the left and a corresponding figure on the right. My standard solution has been to wrap ...
13
votes
1answer
2k views

knitr & xcolor: incompatible color definition

I'm using knitr and RStudio to compile LaTeX. In my real project I'd like to use some options from the LaTeX package 'xcolor', but when I do include \usepackage[options]xcolor, I get the error message ...
11
votes
1answer
2k views

R+LaTex to HTML5 better than pdf?

I use R together with ggmap, ggplot2, Rstudio, knitr, and beamer to produce presentations in pdf. Soon I hope to have time to learn TikZ too. I have not moved to Markdown because I appreciate the ...
10
votes
2answers
560 views

Appending an empty row after every 5 or 10 rows in LaTeX table

I wonder how to append an empty row after every 5 or 10 rows in LaTeX table. Here is my MWE in .Rnw format. Any help will be highly appreciated. Thanks! \documentclass{article} ...
10
votes
1answer
2k views

Best Practice for nice layout with tikzDevice

R+tikDevice+LaTex+knitr is (as I understand it) the most efficient way to get relly nice looking publications from R, with maximum layout-support from LaTeX. I'm using R+LaTex+knitr now, but would ...
9
votes
3answers
1k views

What do Sweave/knitr offer that make doesn't?

I use LaTeX to write papers and R for data analysis and visualization, so I've been looking into Sweave and knitr. The Sweave website says: The purpose is to create dynamic reports, which can be ...
9
votes
1answer
2k views

Command already defined

I came across an odd problem compiling LaTeX exam.cls document producing with knitr. Pasted below is minimal reproducible code. knitr compiles fine, but pdflatex terminated with: Command \framed ...
9
votes
1answer
9k views

Knitr and rmarkdown will not add figure captions to the output

I am writing a report on Rmarkdown and knitr using RStudio, and cannot find a way to get figure captions on my document. My code for the chunk where I try to plot is like: ```{r ...
9
votes
1answer
623 views

Is it possible to get Sweave/knitr in RStudio to output the .tex file without typesetting it?

I would like to know if it is possible to tell Sweave or knitr in RStudio to create the .tex file without trying to typeset it. I want to be able to run my .Rnw file and produce a .tex file which I ...
9
votes
1answer
533 views

Different colors for default and language-specific listings

I'm generating pdf documents using knitr and pandoc. The conversion is mostly automated from R markdown -> markdown -> latex -> pdf. However, my documents combine R source code and its output, and I ...
8
votes
2answers
1k views

tikzDevice is not getting sizes right (knitr)

I am using OSX, pdflatex, R (cran), tikz/tikzDevice and knitr to create my documents. My problem is that the font sizes of the produced tikZ-file do not match the LaTeX document font sizes. Result / ...
8
votes
1answer
3k views

knitr how to label and call a figure number in a text

As a knitr beginner I don't know how to label a figure and call it. For my first figure I've tried the following code witouth succes... <<fig.cap="Dendrogram of GDP ...
8
votes
2answers
158 views

Encrypt and decrypt parts of text in a LaTeX source file

Assume that you have some text in parts of your LaTeX document that you only want people with a password to see. A reason could e.g. be a case with an guiding answer. You want to make the case public ...
8
votes
0answers
997 views

How to keep ggplot font size constant when varying figure width

I have different figures across my document with different width. I set the the font size for all ggplots globally with theme_set(theme_bw() + theme(text=element_text(family="Palatino", size=20))) but ...
7
votes
2answers
5k views

Vertical aligning text and vertical height of rows in longtable environment

I have now been working on fixing this problem for some time and I have read through some forums on the Internet and tried different things, but I can't solve this problem. I am looking to have some ...
7
votes
4answers
271 views

tikz has probably problems with czech babel when compiling .Rnw

Problem Tikz seems to have a problem with \usepackage[czech]{babel}. I had a moderately big .Rnw document written in czech with some plots via knitr chunks. When I set dev = 'tikz' the TeXmaker ...
7
votes
2answers
3k views

R-code linebreaks AND code highlighting in knitr

I used the great answer from @Sharpie on 19 Jan 2012 Getting Sweave code chunks to stay inside page margins? to get linebreaks in the R-code, but how can there be code highlighting (colors) too? ...
7
votes
1answer
2k views

Howto: Set up knitr (*.Rnw compilation) from in TexStudio

How do I set up TeXstudio to compile xxx.Rnw files? I am using the TeX-Editor TeXstudio 2.7, on Windows 7, and R 3.01 64-bit. I would like to write a xxx.Rnw-file in TeXstudio and then from ...
6
votes
1answer
6k views

Plot two figures side by side in knitr without changing mfrow?

I would like to plot 2 figures side-by-side using knitr. I know I could use par(mfrow=c(1,2)), but I've done a lot of work making the figures just right as they are. I've seen this (Two column layout ...
6
votes
1answer
719 views

Beamer (with style) to Html5?

My organization require the use of a standardized powerpoint template for how slides should look, so I've written my own Beamer .sty (style file). Then I write .Rnw-files in RStudio that I knit ...
6
votes
1answer
672 views

Using knitr, beamer, and /foreach to produce unique section titles in pdf from R string variable

Using R, knitr, and beamer, I have created a pdf that contains a graph for each school in our district. I read in each graph using the \includegraphics command within a /foreach loop. I want to ...
6
votes
1answer
4k views

no tex installation detected on RStudio after OS X 10.10 yosemite upgrade

I upgraded my MAC to OS X 10.10 yosemite today. Now, when I run RStudio and try to use Knitr to compile pdf, it says no text installation detected. So, I did the following steps sequentially. ...
6
votes
1answer
2k views

Error compiling .Rnw in TeXstudio (knitr with PdfLaTeX)

I´ve been trying to get the minimal Demofile for knitr running and compiling in TeXstudio, but I keep getting errormessages. Here´s the info, mybe somebody can help me out about what I´m doing wrong: ...
6
votes
0answers
398 views

Arguments of R Functions in Beamer with knitr

I'm using helpExtract.R function (can be obtained from here) to get arguments of R functions in Beamer with knitr. My (.Rnw) MWE is \documentclass{beamer} \usepackage{ragged2e} %new code ...
5
votes
1answer
1k views

Using Greek letters in LaTeX tables

I have the following Rnw document which I intend should produce a small table with "a b c" and "α β γ". At the moment, the encoding seems to be causing problems. The funny thing is that the output in ...
5
votes
1answer
2k views

knitr problem after update to R 3.0.0

I just updated R to 3.0.0. I couldn't compile PDF from my .Rnw file, which I could do with R 2.15. Here is the error I got: ! Undefined control sequence. l.192 \SweaveOpts ...
5
votes
1answer
3k views

Using knitr, how can I rotate page to landscape and fit the figure to full extent?

LaTeX newbie here, so please be gentle. I'm working with knitr to generate pdf report. The document consists of quite few large maps, with a lot of details or small multiples. Ideally, whenever such ...
5
votes
1answer
875 views

Math mode in knitr

How do one use a math-mode in knitr? For example as a label for X-Y axis: <<fe, echo=FALSE, sanitize=TRUE, dev="tikz">>= plot(1:10, main="${}^{57}Fe$", xlab="$\\\\lambda$", ...
5
votes
1answer
233 views

minitoc package adds extra page when used with float and lastpage packages

The minitoc package adds extra page when used with float and lastpage packages. I figured out that this problem can be resolved by loading minitoc package before float and lastpage packages. In LyX ...
5
votes
2answers
219 views

Create pdf with subset of slides

I use knitr and RStudio with XeLaTeX to create a presentation with many slides. But sometimes not all of the slides should appear in the final pdf. Is it possible to have a variable that I change ...
5
votes
3answers
74 views

How to extract a series of text not in an environment, but with defined commands enclosing them

Under Windows 8, I am using R and the knitr package in RStudio with an .Rnw script. My regex skills are passable, but only in R. My document has about thirty pages with a different text section at ...
5
votes
1answer
379 views

Insert a TeX file created with knitr into a main TeX file [duplicate]

I want to insert a knitr output file (created in RStudio as .rnw file, then I compiled, it creates the .tex file) into my main .tex file. But I got an error, how we can do this? Knitter Tex file: ...
5
votes
1answer
604 views

knitr and font style consistency in graphics

I am starting to use knitr to print graphics from R in my document. So far what I have been doing (I don't know if this is the best approach, but it is working) is to load the my R workspace with ...
5
votes
0answers
148 views

What are the advantages of switching to Emacs for TeX/knitR work? [closed]

Currently, I am using TeXStudio. Now, I am considering to switch to Emacs because I heard that is has its advantages when it comes to R and knitR. But what are the specific advantages? Yet, I am still ...
5
votes
0answers
845 views

Color first row in a xtable generated table

I am trying to color the FIRST row of my table. But if I add \rowcolor[gray]{0.95} to the FIRST row the colored row will be the SECOND. Indeed it is quite straight forward to modify from the second ...
5
votes
0answers
168 views

How to mantain consisten font size in different plots

I usually embed numerous R plots in my TeX documents. knitr is very handy in helping me producing plots using the same font family of the TeX document. But a different problem of consistency is given ...
4
votes
1answer
961 views

Texstudio and Rnw Files

Is there any way in Texstudio, for the document tree to detect Rnw files called within a knitr chunk? For example, the following would be ignored: <<MYCHUNK,child='./Myfile.Rnw'>>= @ ...
4
votes
1answer
315 views

Memory issue when producing dense TikZ figure (14500 points scatterplot) with knitr

I have a series of plots in my document which are correctly drawn by knitr with dev=tikz. Yet figure number 7, which is much more dense than the others in terms of data points, foo, doesn't: label: ...
4
votes
1answer
387 views

display \Sexpr{} in Latex without evaluation

I am working on a tutorial for the knitr package using the beamer class. I was able to display latex code and knitr chunks inside my presentation without evaluation but I additionally want to add ...
4
votes
1answer
96 views

Input Tex file in knitr file

I am showing a simple example here just to frame the question. \documentclass{article} \begin{document} <<>>= library('ggplot2') dataset <- diamonds @ \begin{table}[htbp] ...
4
votes
3answers
214 views

knitr. Splitting a function into several blocks

Is it possible with knitr to split an R function across several blocks (for documentation reasons)? Here is a MWE: \documentclass{article} \begin{document} Part1 gives salutation. ...
4
votes
2answers
365 views

TikzDictionary slow and blocking in knitr

I need to knit presentations with many slides and Tikz-plots. Knitr is fantastic for this, but it takes very long time and I cant knit two reports in parallel. I have isolated the problem to the ...
4
votes
1answer
622 views

Dynamically format labels/columns of a LaTeX table generated in R/knitr/xtable

I have some tables coming from the statistical package R that I want to export in LaTeX markup. I would like to make every column large as the longest word of its label (assuming for simplicity the ...
4
votes
1answer
287 views

Robust processing of autogenerated LaTeX files that contain many errors

I use knitr to generate pretty reports, with pdflatex as backend. Everything works fine if the R code runs without error. However, if the R code fails, the autogenerated file is sometimes invalid in ...