Using graphicspath in latex/sweave - r

I have an Sweave file, where I need to embed a png and pdf from another folder. This is how I tried it
\usepackage{graphicx}
\graphicspath{{inst/extdata/}}
\DeclareGraphicsExtensions{.pdf,.png}
\begin{document}
\begin{figure}
\includegraphics[scale=0.7]{image.png}
\caption{captionA}
\label{fig:labelA}
\end{figure}
I also tried like this, but this didn't work:
\graphicspath{{filePath}}
filePath = "C:/path"
\begin{figure}
\includegraphics[scale=0.7]{image.png}
\caption{captionA}
\label{fig:labelA}
\end{figure}
I have googled a lot, and look up https://en.wikibooks.org/wiki/LaTeX/Importing_Graphics#Compiling_with_latex, but this is the error I get.
LaTeX Warning: File `image.png' not found on input
line 613.
! Package pdftex.def Error: File `image.png' not found.
See the pdftex.def package documentation for explanation.
Type H <return> for immediate help.
...
l.613 ...]{image.png}

I expand my comment with three different ways of achieve your goal; Suppose you want to include a file image named IMG_7254.JPG (note that I do not write the file extension in the following code because I use the \DeclareGraphicsExtensions{.JPG}), You can do it in three ways:
to put the file to compile (the .tex one) and the image to include in the same folder. LaTeX searches (by default) for pictures to include in documents in the same directory where the file to be compiled is. In this case the code is just:
\includegraphics[width=0.7\textwidth]{IMG_7254}
Have pictures and file to compile in very different folders, in this case you must specify the complete path of the file (it can be found in different ways), example with Mac OS read here. In this case the code is:
\includegraphics[width=0.7\textwidth]{/Users/SabDeM/Pictures/IMG_7254}
to put the file to compile in a folder (say File_to_com), then put all pictures to include in a sub folder, say, File_to_com/picturesToInc, and then specify the path. In this latter case the code is:
\includegraphics[width=0.7\textwidth]{picturesToInc/IMG_7254}
As you can see in all ways (one way or another) LaTeX (which render the PDF) must to know where the pictures are located in your computer.

Related

Adding XeTeX to ess-swv-PDF

I am working with an .Rnw file with Hebrew in it, and I would like to compile the resulting .tex file using XeTeX. I work in Emacs, so I am using the Emacs Speaks Statistics (ESS) package, which allows a few options for compiling the .tex file. However, using XeTeX is not currently among the possible selections of ess-swv-PDF, accessed via M-n P.
I would like to add XeTeX to this list. Ideally, this added option would allow me to not only compile the .tex file using XeTeX but also run, as needed, BibTeX on the same file—all from a buffer displaying the .Rnw file. This would be similar to texi2pdf, one of the current options of ess-swv-PDF.
This can be customized if you have ESS already installed: M-x customize-group select ess-sweave and edit ess-swv-pdflatex-commands to add "xelatex" to them. If you want to use xelatex or xetex as the default TeX engine, like I do, you can put that in front (see screenshot below).
Then press Apply and save this should save code into your .init.el or .emacs.el, depending on your setting.
Now when you go to your .Rnw file and hit M-n P you will see xelatex as default since you put it ahead of other commands. That is all to it.

Latex and Sweave, cannot include figure

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.

R, Sweave: How to pass file encoding to patchDVI::SweavePDF?

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.

How to make sweave copy generated graphics to a subfolder?

I would love to use some shell script based pdfcrop on all the graphics.pdf created from my Sweave report. Hence i'd be nice if all the graphics were stored to a subfolder instead of being dropped where all the latex stuff like .aux .log files (and so on) is located. If I just had to use the crop script on ALL files in a particular directory it would be much easier.
Here's my Sweave chunk:
\begin{figure}[htbp]
\begin{center}
<<fig=true,echo=false>>=
print(mygraph)
#
\caption{my graph}
\end{center}
\end{figure}
If I run the sweave code mygraph.pdf is stored in the same directory as the report.tex file itself.
Is there a way to store this file in an existing subfolder like /graphics ?
Insert this:
\SweaveOpts{prefix.string=foo/bar}
into your Sweave source file, preferably up the top in the preamble. The above line is taken from the Sweave FAQ, and indicates that the created figures will be stored in the subdirectory (of the directory where the Sweave source is) foo, and each image filename will begin with bar. This, and a whole lot more is discussed in the Sweave FAQ.
Okay RTFM, ran2.
Here's how:
\SweaveOpts{prefix.string=graphics/report}
See also: the manual.
graphics is directory and report is a substring you might wanna use. At least you'll find SO better on google :)
EDIT:
For the sake of completeness I'll add my several lines of shell script here:
#!/bin/sh
R CMD Sweave report.Rnw
for file in `ls graphics`;
do pdfcrop "$file" graphics/"$file"
done
pdflatex report.tex
open report.pdf
Maybe some of you want to use $1 as a directory argument.

How do I Sweave a multiple-file project?

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.

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