I'm writing a book in R Sweave, as long as the document is becoming larger I use the \include LaTeX command to include files. When I PDF-Compile the main file the files with R chunks are not included. What extension they must have .tex or .Rnw?
From the Sweave User Manual, p. 7
Latex files can include others via \input{} commands. These can
also be used in Sweave files, but the included files will be included by
Latex and are not processed by Sweave. The equivalent if you want
the included files to be processed is the \SweaveInput{} command.
Included files should use the same Sweave syntax (see below) and
encoding as the main file.
Related
I would like to get the Latex source for the PDF that is built when executing
R CMD Rd2pdf /path/to/mypackage
for building the R package documentation.
It would be very nice if I could get the documentation as a latex document such that I could easily include it in another latex document as an appendix and have a continuous page numbering.
I have only seen the possibility to compile the files one by one from .Rd to .tex:
How to create R documentation file (.Rd) in latex?, which points to the function tools::Rd2latex and the question How do I convert Rd files to pdf for a package that I am creating in R? which points to the command
R CMD Rdconv -o x.tex --type=latex man/x.Rd
Both commands only work on single .Rd files. The created files lack the header/definitions. So I would have to sort and include each file manually in the final latex file. It would be nice if there is some way to get the latex document in a simpler way.
You can do:
R CMD Rd2pdf path/to/package/man --no-clean
In addition to the PDF file, this creates a folder containing the auxiliary files, including the tex source file.
This is probably documented somewhere, but I cannot find it ...
I have an .R file which can be used as a read_chunk() file and call from an .Rnw latex template or in a .Rmd file for primary review.
This design worked well for the first part of our project, but since the .R file will change, it's not 'reproducible research'.
Since I already have a 'template' with the named chunks referring to chunks in the read_chunk() file, is there any way to interleave the R into the .Rnw for posterity?
You want the reverse operation of purl(), I believe. I don't know any such function, but technically it doesn't seem too hard; all the pieces are there:
chunks <- knitr:::knit_code$get()
for(k in names(chunks))
cat(c(sprintf("<<%s>>=", k), chunks[[k]], "#\n"), sep = "\n")
would return all the chunks in a format suitable for inclusion in the Rnw file.
I have a file for my thesis, which include the chapters.
A few weeks ago, I worked with R-Statistic and *.rnw files to produce a *.tex paper.
Now, I want to include these *.tex paper in my thesis. However, every time I get several errors.
Structure
/home/UserName/R-files/Dokumentation5.rnw
/home/UserName/tex-Files/Dokumentation5.tex // from Dokumentation5.rnw files
In the following folder, I put the TeX and the figures (*.pdf).
/home/UserName/Documentation/chapter/
Edit the Dokumentation5.tex, remove the beginning and "end document"
In thesis file, I added the following commands:
\usepackage{Sweave} \include /home/UserName/Documentation/chapter/
run latex
If I run LaTeX, I got several errors like:
File `Dokumentation5-004' not found.
\begin{document} ended by \end{Schunk}.
Too many }'s
File `Dokumentation5-033' not found.
Create a file master.Rnw that contains nothing but the LaTeX setup (packages to be used, geometry, title, begin/end document, bibliography style and file......)
If you need to use R functions in various places in your paper, create a file func.Rnw where you create these functions. Make this file the first to \SweaveInput{func.Rnw} in your master.Rnw - see here for details
Now create one file for each "unit" of your paper (chapter, section, whatever you like). Make them all chapX.Rnw files, whether they contain R code or not.
\SweaveInput{chapX.Rnw} them in the desired order in your master.Rnw file.
At any time during the process, run Sweave("master.Rnw") in R and then pdflatex master.tex from the console to see what you have produced.
I have a master file master.tex containing the preamble and which inputs (via
\input{chapter01}, \input{chapter02}, ...) chapters. The chapters are .Rnw
files. My goal is to use patchDVI::SweavePDF to compile the chapters (say,
chapter.Rnw) individually (each chapter starts with sourcing Sweave preliminary
settings but [of course] does not have a preamble). When I execute
Rscript -e "patchDVI::SweavePDF('chapter.Rnw')
I obtain
Error: ‘chapter.Rnw’ is not ASCII and does not declare an encoding
Normally one uses \usepackage[utf8]{inputenc} to solve this problem. However, I
can't put this into chapter.Rnw since it is only allowed in the preamble, so in
master.tex. But there it has no effect. The question is how to solve this.
I found this but I couldn't figure out how to adjust it to make it work with patchDVI::SweavePDF.
I am writing my thesis in LaTeX and because things got a bit long for my taste, I had split it into several files. Let's call them thesis.tex, intro.tex, mat_n_met.tex, rslts.tex and discsn.tex. I have linked intro.tex, mat_n_met.tex, rslts.tex and discsn.tex through thesis.tex with \include{intro} (and so on...).
I have also created a separate file called r_crunching.Rnw (that I run through Sweave) that holds a chunk that runs the R script with data analysis and chunks that produce pdf outputs of graphs that I embed via \includegraphics (in e.g., rslts.tex). Still following?
If I run a Rnw (i.e. I renamed rslts.tex to rslts.Rnw) without "a link" to the chunk with the R script, you will get a Sweave() error saying the reference in \Sexpr{} doesn't exist. Is there a way, without merging all the files into a single .Rnw, to call \Sexpr{} in say rslts.Rnw?
Other methods how to accomplish this are welcome.
I recommend using RStudio (http://www.rstudio.com/ide/). Sweave is nicely integrated into that IDE and it supports multi-file documents. Even Synctex and TeX error log navigation still work when working with multi-file documents.
From the master file you can include child files using
\SweaveInput{Child.Rnw}
You can link a child file back to the master file by including the directive
% !Rnw root = Master.Rnw
in the child file. That way when working on a child file and typesetting it, RStudio know to typeset the master file.
The details are explained in the RStudio documentation at http://www.rstudio.com/ide/docs/authoring/multiple_rnw_files
Forget for a second that you are dealing with Sweave and just think of the latex problem -- for which \include and \includeonly offer solutions. Try that with a few simple test files.
Once you have that figured out, fold Sweave back into the mix and it just work as Sweave is after 'merely' a pre-processing step, albeit a very clever one.
To expand Dirk's and mjm's answer, I would suggest using \include's and Makefiles.
Suppose you have a master file: master.tex. In that file, you include some .tex and .Rnw files, i.e.
\include chapter1
\include chapter2
\include chapter3
....
Now the following Makefile provides functions for creating the .tex, .R and .pdf files:
.SUFFIXES: .tex .pdf .Rnw .R
MAIN = master
##List your your .Rnw includes
RNWINCLUDES = chapter1 chapter2 chapter3
TEX = $(RNWINCLUDES:=.tex)
RFILES = $(RNWINCLUDES:=.R)
RNWFILES = $(INCLUDES:=.Rnw)
all: $(MAIN).pdf
$(MAIN).pdf: $(TEX) $(MAIN).tex
R: $(RFILES)
.Rnw.R:
R CMD Stangle $<
.Rnw.tex:
R CMD Sweave $<
.tex.pdf:
pdflatex $<
bibtex $*
pdflatex $<
pdflatex $<
Essentially, the .SUFFIXES provide a set of rules for convert from one file format to another. For example, to convert from .Rnw to .R, we use the command
`R CMD Stangle $<`
one fairly obvious answer is to use a makefile, possibly using package cachesweave, to process the relevant files in the right order.
My solution to multi-file projects in Sweave (under Rstudio) is the following:
1) Create a master file, say master.Rnw, in which you have the calls to the subfiles intro.Rnw, matmet.Rnw, etc:
\documentclass[11pt]{book}
% \usepackage{blah, blah} as you wish
\graphicspath{ {./figs/}
\begin{document}
\SweaveOpts{concordance=TRUE}
\include{intro} % a call to 'intro.Rnw'
\include{matmet} % a call to 'matmet.Rnw'
\include{results} % a call to 'results.Rnw'
\include{discuss} % a call to 'discuss.Rnw'
\end{document}
2) Create the subfiles. I'm giving here only the first one, intro.Rnw. Please note that in the subfiles you do not use preambular commands such as \documentclass or \begin{document}
\chapter{Introduction}\label{ch:intro}
\section{This is section 01}
In section 01 we are concerned about whether \texttt{Sexpr} could possibly work. The chunk below creates a variable \em{a} which will be referred to by this command later on.
<<>>=
a <- 1+2
#
Ok, if it is working, we shall see number 3 right here: \Sexpr{a}.
3) After saving modifications in 'intro.Rnw', simply go to 'master.Rnw' and compile it using Ctrl+Shift+K and... voilá:
Screenshot of the file created by the above command.