Apophenia co-evolved with Modeling with Data: Tools and Techniques for Statistical Computing. You can read about the book, or download a free PDF copy of the full text, at modelingwithdata.org.
As with many computer programs, the preferred manner of citing Apophenia is to cite its related book. Here is a BibTeX-formatted entry giving the relevant information:
The rationale for the apop_model struct, based on an algebraic system of models, is detailed in a U.S. Census Bureau research report:
The system is written to not require a registration or initialization step to add a new model or other such parts. Just write your code and include
it like any other C code. A new apop_model has to conform to some rules if it is to play well with apop_estimate, apop_draw, and so forth. See the notes at Writing new models. Once your new model or function is working, please post the code or a link to the code on the Apophenia wiki.
For your convenience, here are links to some other libraries you are probably using.