README

Web versions of these reproducible papers (mostly based on the Madagascar platform: www.ahay.org) are at 

http://www.ahay.org/wiki/Reproducible_Documents.

One can access the contents of the papers quickly by searching for the title and author names of each paper in this website.

If you are interested in a particular paper, for example, reproducible_research/drr3d, you can use the following command (first install subversion in a Linux computer) to download it:

svn co https://github.com/chenyk1990/reproducible_research/trunk/drr3d ./drr3d

All sub-directories except for "nonMada" correspond to the reproducible packages (for each paper) based on Madagascar, which means that you can use one command "sftour scons lock && scons paper.pdf" in these sub-directories to reproducible the whole paper in the PDF format.

The "nonMada" sub-directory contains reproducible packages that are not based on Madagascar, e.g., based on Matlab, python, etc. 


NOTES
* sub-directories containing "matfun" require the Matlab-Madagascar interface (to do that, try ./configure API=c++,matlab --prefix=~/RSFROOT; scons install -k; add "~/RSFROOT/lib" into the Matlab path directories by "addpath(genpath('~/RSFROOT/lib')); savepath;". The "matfun" directory contains all the Matlab scripts/subroutines to output the data for plotting in SConstruct. 

* Other sub-directories not containing "matfun" are all based on Madagascar commands and are reproducible after Madagascar is installed successfully.

* These compact reproducible packages only include the python (named as "SConstruct") scripts that wrap up all the Linux/Madagascar commands, and necessary datasets. Most synthetic data are generated automatically from either "python or matlab scripts". Small field datasets are also attached with these packages.

* All C programs that are used to compile the Madagascar commands can be found at "~/RSFSRC/user/chenyk" (https://github.com/ahay/src/tree/master/user/chenyk), "~/RSFSRC/user" (https://github.com/ahay/src/tree/master/user), "~/RSFSRC/system" (https://github.com/ahay/src/tree/master/system). All Madagascar Application programming interface (API) (written in C programs) can be found at "~/RSFSRC/api/c".