[Tex/LaTex] What do Sweave/knitr offer that make doesn’t

knitrmakefilesweave

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 updated automatically if data or analysis change.

But it seems to me that I already have this in my current workflow, with a makefile that runs my R scripts and then compiles my LaTeX with the figures and tables generated by the scripts.

The make approach is also really good with caching, e.g., it checks the timestamps of my data files as well as source files to know when to recompile individual components.

And it seems like with Sweave/knitr, I lose ability to run just my R or my LaTeX, separately.

Am I missing something? What do solutions like Sweave and knitr offer that make doesn't?

Best Answer

I'm still new to LaTeX (about 2 years of use) but have found knitr very helpful for:

inline code
code chunks - incredibly helpful for execution and then interspersing your document with it
dead simple graph integration into document
caching (I'm sure you could do this with make by watching file changes)
an amazingly responsive support community (at least on #r on freenode)

From the knitr website:

knitr ≈ Sweave + cacheSweave + pgfSweave + weaver + animation::saveLatex + R2HTML::RweaveHTML + highlight::HighlightWeaveLatex + 0.2 * brew + 0.1 * SweaveListingUtils + more

I do however use the now considered outdated rubber for compilation, so I'm sure others can provide more context with regards to make specifically.

Related Solutions

[Tex/LaTex] How to sweave Matlab or Mathematica code into LaTeX.

There are three ways of doing this:

Do the weaving at the application (Matlab, Mathematica, R) end. That is, the application should be aware of the TeX format and ignore everything other than \begin{code} ... \end{code} snippets. This is how Sweave and literate haskell work.
Do the weaving at the TeX end, that is, let TeX call the external application (with appropriate switches) and then display the result. This the approach that the R and gnuplot modules in ConTeXt follow.
Use a general purpose literate programming tool, like noweb (or those targeted to a specific language like Ocamweb).

For the second approach, I have written a ConTeXt module, filter, that allows you to pass the content of a program to an external program and read back the results. For example, you can replicate the functionality of sweave using:

\usemodule[filter]

\defineexternalfilter
  [R]
  [filtercommand={R CMD BATCH -q --save --restore \externalfilterinputfile\space \externalfilteroutputfile},
   output=\externalfilterbasefile.out,
   readcommand=\typefile,
   continue=yes]

Then, using

\startR
  ...
\stopR

will execute the resultant code using R and show the output generated by R. Using

\startR[read=no]
  ....
\stopR

will execute the code using R but not show the output. The same approach will work for Matlab or Mathematica by replacing the filtercommand by the appropriate call to Matlab/Mathematica. This approach can be used for other purposes as well

[Tex/LaTex] insert figure in sweave using knitr fig.path

Use \includegraphics{\Sexpr{f}}. LaTeX does not know the variables in R.

Best Answer

Related Solutions

[Tex/LaTex] How to sweave Matlab or Mathematica code into LaTeX.

[Tex/LaTex] insert figure in sweave using knitr fig.path

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