Getting latexmk working within LyX

If you would like to add latexmk as an export option in Lyx, here are the two basic steps to do in Tools -> Options.

1) In File Handling -> File Format, hit "New" and then put in these options, then "Apply".

2) Then in File Handling -> Converter, click on any existing converter, change the options to the below, and then click "Add", then "Save".

Now you should be able to File->Export->PDF (Latexmk). Hope that works for you.

If you are on Windows, then you might have problems with Perl versions (Lyx has one, MiKTeK another). Initially, I was getting that perl couldn't find File::Glob in @INC when latexmk was run. Turns out that Lyx was running it's own version of perl 5.18.2 and had @INC set to just the Lyx/lib (which oddly did have File/Glob.pm). I installed Strawberry Perl same version (needed that!) then set the PERL5LIB to the Strawberry perl folder.  Then it works fine.

This was on LyX 2.1.2, updated MiKTeX, and Windows 8.

Easy LyX Beamer products

When making presentations in LyX with the Beamer template, one often wants to make three PDFs every time: slides, handouts, and handouts+notes. Here are some scripts to do this. You will need Cygwin installed if you are on Windows.

Command-line version:
In Windows I've added this functionality to the right-click menu for LyX files. It requires the slightly modified script below. To edit the right-click menu I use the FileMenu Tools utility. In a new entry, set the program as a shell (I've tested git -- "C:\Program Files (x86)\Git\bin\sh.exe" and cygwin -- "C:\cygwin64\bin\mintty.exe"). For arguments put "absolute/path/to/beamer_outputs.sh %FILENAME1%".

Bigfoot module for LyX

For the lazy, here is a module for support for the bigfoot package for LyX (outlined here). Find your User directory from Help > About LyX and then put the file in "<User directory>/layouts/". Then do Tools > Reconfigure.

StatWeave in LyX

While it's pretty easy to integrate R into LyX documents (using Sweave or knitr) I hadn't found any native way of integrating Stata code. I've hacked StatWeave (which allows Stata, R, and a bunch of other stat languages) to work in my LyX (in Windows 7 with LyX 2.0.4) and thought that others might like this as well. Here's the steps:

1. Copy statweave.module to the "Resources/layouts" of your user directory (See Help→About LyX).
2. Open LyX and go to  Tools→Reconfigure. 
3. Restart LyX and go to  Tools→Preferences. 
4. On the left choose File Handling→File Formats.
5. Click the New... button and then fill in  Format: StatWeave, check Document format, Short Name: statweave, Extension: swv. Then Apply.
6. On the left choose File Handling→Converters. 
7. Using the drop-down menus, create a new one from "StatWeave" to "LaTeX (pdflatex)" with the command "statweave --target tex $$i" (make the changes and then click "Add" in the upper right). Then Save.

Once you get that setup you should be able to compile: stata-test-bq.lyx. Notes:

• LyX disables the enter key from inserting a line-break in insets (anyone who knows about this please let me know why or a work around). You can paste them, though, so copying several lines of code into a Stata Code Chunk insert works fine (if you are writing it in LyX then just copy a line break from somewhere and paste as needed). 
• If you don't want to use the custom insets you can always just use plain TeX code (e.g. You can always just use TeX code inserts \begin{Statacode} ... \end{Statacode} or \Stataexpr{...})
• The StatWeave manual is helpful for the non LyX part.
• When configuring your Stata executable do not include "do " before "%codefile%".
• You may need to edit the MiKTex path given the default ones are for version 2.6.
• If you want to use relative paths for input files then you can pass the directory of the LyX file to Stata as an environment variable. In the converter replace the statweave command with "set orig_PWD=$$r && statweave --target tex $$i" (then Modify, Save). Then in Stata you can change do that directory with -global orig_PWD =trim("`:environment orig_PWD'")"- (it will have the final slash). Don't cd around in the program or StatWeave wont' know where it's graphics files are for conversion.

Suggestions very appreciated.

Update: I've made a newer version the just focuses on Stata and allows for code block options. You can easily show figures now right-clicking in the block, choosing opts, and then putting in a string like fig, height=4.5in, width=9in, dispw=4in.