I would like to be able to use knitr to produce a structured PDF file. I did not see anything unless the input file is Sweave format. This question may be too vague but I really like to know right from knitr, is it possible to create a structured PDF output file without using any Sweave or LaTeX?
Try using command knit2pdf if you haven't already.
Related
I am using RMarkdown to write a journal article. For various reasons I'd prefer to have the R analysis script in a separate Jupyter notebook. Is there a nice way to call R code from MyAnalysis.ipynb in MyArticle.Rmd?
I know I can use knitr syntax to have the .Rmd file read and execute chunks of R code from a .R file like so. And that you can use knitr::purl to call code chunks from one rmarkdown doc in another like so.
But I would like to be able to "purl" the code from the .ipynb file. Is there any way to do this?
I´m trying to insert a number directly from R into a LaTeX file. I have only been able to do it as a table and that doesn´t allow me to put it in the middle of a sentence.
I would like the output to look like this:
"The final number is [number directly from R]"
What should I do?
If you use the Sweave or knitr (assuming .Rnw file), use \Sexpr{foo}. Then run the file through R + Sweave or R + knitr and you'll have a LaTeX source with the value of foo inserted in place of \Sexpr{foo}.
Basically you need to markup your LaTeX source appropriately, run it through a system using R to identify the things you want to replace and insert the actual data into the source file, and output a LaTeX source which you can then compile.
There are other systems besides Sweave and Knitr so find a system you like that suits your workflows. For example, there is brew.
Why is it important? My collaborators would like to be able to modify my .pdf reports and they are not able to modify the actual .tex code. They are sooo used to word !
How I write my reports? I use knitr. What a great and useful tool; thanks Yihui :)
What I'm looking for? convert the generated pdf report into .doc (my collaborators favorite !)
a solution might help: Pandoc (http://johnmacfarlane.net/pandoc/). As it's explained in the introduction of page of Pandoc, it can be used to convert LaTex to .docx and to markup. I then thought converting the .tex file of each of my reports (a .tex file is generated when I run my knitr .Rnw file) and convert it to .docx using pandoc:
pandoc -s myTexRepot.tex -o aDocReport.docx
issue: 1) Figures are missing in my .docx file. 2) I generate all my tables in my reports using xtable(), none of them can be converted! 3) Also, I lose all table of contents, section numbering.
Markup to Word: Issue (1) above is still an issue in converting Markup code to .doc
Is there any better idea to approach the issue of converting latex to doc. If Pandoc is the best, would you know how I can solve the issues above?
I really appreciate your help.
since you are already using knitr, you can call the rmarkdown:render() function to knit the document.
there is a parameter in render() called output_format[1]. the parameter along with the YAML header in your knitr document will allow you do generate the pdf and word document simultaneously
[1] output_format
R Markdown output format to convert to. Pass "all" to render all formats defined within the file. Pass the name of a format (e.g. "html_document") to render a single format or pass a vector of format names to render multiple formats. Alternatively you can pass an output format object; e.g. html_document(). If NULL is passed then the output format is the first one defined in the YAML metadata of the input file (defaulting to HTML if none is specified).
Is there a simple way to create R documentation file for simple R functions?
I know I can edit a .Rd file in R-studio and preview it in HTML file. But how to put it into latex to edit and preview? Is there some latex package producing R documentation format?
There is the Rd2latex function in the tools package that will convert from the .Rd format to LaTeX format. This will let you preview the documentation in LaTeX. However this does not allow converting edits to the LaTeX document back to the .Rd document.
Look at Sweave, maybe it helpful for you.
Sweave is a tool that allows to embed the R code for complete data analyses in latex documents.
The purpose is to create dynamic reports, which can be updated automatically if data or analysis change. Instead of inserting a prefabricated graph or table into the report, the master document contains the R code necessary to obtain it. When run through R, all data analysis output (tables, graphs, etc.) is created on the fly and inserted into a final latex document.
The report can be automatically updated if data or analysis change, which allows for truly reproducible research.
Check out printr http://yihui.name/printr/ . It should do what you need if you are using knitr.
The problem with Rd2latex is that i haven't figured out which style file I need to use, otherwise it works fine.
When you generate the latex code with the Rd2latex function, make sure that you copy the Rd.sty file from the R directory, paste it and somewhere that latex can see it and use \usepackage{Rd}.
Try the knitr package, an easy way to generate flexible and fast dynamic reports with R for LaTex.
my question(s) might be less general than the title suggests. I am running R on Mac OS X with a MySQL database to store the data. I have been working with the Komodo / Sciviews-R for some time. Recently I had the need for auto-generated reports and looked into Sweave. I guess StatET / Eclipse appears to be the "standard" solution for Sweavers.
1) Is it reasonable to switch from Komodo to StatET Eclipse? I tried StatET before but chose Komodo over StatET because I liked the calltip / autosuggest and the more convenient config from Komodo so much.
2) What´s a reasonable workflow to generate Sweave files? Usually I develop my R code first and then care about the report later. I just learned today that there is one file in Sweave that contains R code and Latex code at once and that from this file the .tex document is created. While the example files look handily and can't really imagine how to enter my 250 + lines of R code to a file and mixed it up with Latex.
Is it possible to just enter the qplot() and ggplot() statements to a such a document and source the functionality like database connection and intermediate results somehow?
Or is it just a matter of being used to the mix of Latex and R code?
Thx for any suggestions, hints, links and back-to-the-roots-shout-outs…
You've asked several questions, so here's several answers;
Is StatEt/Eclipse the right way to do Sweave ?
Not nessarily (note: I'm an avid StatEt/Eclipse user, and use it for both pure R and Sweave/R and love it, I haven't used Komodo / sciviews-R). You should be able to run the sweave command from any R command line which will generate a .tex file. You can then turn the .tex file into something readable (like pdf) from any tex environment.
What's a good Sweave workflow ?
When I have wanted to turn an r script into a sweave report I generaly start with an empty sweave template and copy/paste my entire R script into a sweave R block just after the title, i.e;
<<label=myEntireRScript, echo=false, include=false>>
#Insert code here
myTable<-dataframe(...)
myPlot<-qplot(....)
#
Then I go through and find the parts I want to report. For instance, if i want to put a table into the report, I'll cut the R block and put an xtable block in, and the same for variables and plots.
<<label=myEntireRScript, echo=false, include=false>>=
#Insert code here
#
Put any text I want before my table here, maybe with a \Sexpr{print(variable)} named variable
<<label=myTable, result=Tex>>=
myTable<-dataframe(...)
print(xtable(mytable,...),...)
#
Any text I want before my figure
<label=myplot, result=figure>>=
myPlot<-qplot(....)
print(qplot)
#
You may want to look at these related SO posts. The rest of my post relates to your question 2.
When creating reports with Sweave, I usually keep most of the R code and the report text separate. If the R code is fast to run, then I prefer I will include something like the following at the start of the .Rnw file:
<<>>
source('/path/to/script.r')
#
On the other hand, if the R code takes a long time, I will often include something like the following at the end of the R script:
Sweave('/path/to/report.Rnw'); system('pdflatex report.tex')
That way, I can re-generate the report quickly, without needing to run all the R code again. Then, the only work R has to do in the Sweave file is print tables, make graphs and maybe extract a few figures.
Like nullglob, I prefer to keep the R and Sweave files separate, but I prefer to save the workspace with save.image() rather than to source() the file. This avoids running the R calculations with each .Rnw file compiling (and I always end up tinkering with the typesetting more than I'd like).
My general work flow is to do each paper/project in it's own folder with it's own R file(s). When the calculation side is "done", I save.image() to store all the workspace variables as-is.
Then, in the .Rnw file in the same directory I set the working directory with setwd() and load all variables with load(".Rdata"). Of course, you can change the name you use for your workspace, but I do one workspace per folder and keep the default name. Oh, and if you tinker with the R file, be sure save the workspace image and watch out for variables that linger in the workspace and .Rnw file, but are no longer part of the R file... this is where the save.image() approach can cause some headaches.
I am on a Mac and I suggest TextMate if you're mildly geeky and emacs/ess if you're really geeky. I use vim and command line R, but emacs/ess works best for most. If you're in this for the long haul, I doubt you'll regret learning emacs/ess for R, Sweave, and LaTeX.