v2.3.0

This is the first separate release of CmdStan!

To use CmdStan, download the cmdstan-2.3.0.tar.gz using the green button below, untar, then type make on the command line from within the cmdstan directory.

[If you wish to clone the repository directly, you'll need to update the Stan submodule.]

From the Stan v2.3.0 release notes:

We had a record number of user-submitted patches this go around.
Thanks to everyone!

New Features

• user-defined function definitions added to Stan language
• cholesky_corr data type for Cholesky factors of correlation matrices
• a^b syntax for pow(a,b) (thanks to Mitzi Morris)
• reshaping functions: to_matrix(), to_vector(), to_row_vector(),
  to_array_1d(), to_array_2d()
• matrix operations: quad_form_sym() (x' *Sigma * x), QR decompositions
  qr_Q(), qr_R()
• densities: Gaussian processes multi_gp_log(), multi_gp(),
  and alternative negative binomial parameterization neg_binomial_2()
• random number generator: multi_normal_cholesky_rng()
• sorting: sort_indices_*() for returning indexes in sorted order by
  value
• added JSON parser to C++ (not exposed through interfaces yet; thanks
  to Mitzi Morris)
• many fixes to I/O for data and inits to check consistency and
  report errors
• removed some uses of std::cout where they don't belong
• updated parser for C++11 compatibility (thanks to Rob Goedman)

New Developer

• added Marco Inacio as core developer

Optimizations

• turned off Eigen asserts
• efficiency improvements to posterior analysis print

Documentation

• Clarified licensing policy for individual code contributions
• Huge numbers of fixes to the documentation, including many
  user-contributed patches (thanks!), fixes to parallelization in
  CmdStan, Windows install instructions, boundaries for Dirichlet and
  Beta, removed suggestion to use floor and ceiling as indices,
  vectorized many models, clarified that && doesn't short circuit,
  clarified von Mises normalization, updated censoring doc (thanks
  to Alexey Stukalov), negative binomial doc enhanced, new references,
  new discussion of hierarchical models referencing Betancourt and
  Girolami paper,
• Avraham Adler was particularly useful in pointing out and fixing
  documentation errors

Bug Fixes

• fixed bug in lkj density
• fixed bug in Jacobian for corr_matrix data type
• fix cholesky_cov_matrix test code to allow use as parameter
• fixed poisson_rng, neg_binomial_rng
• allow binary operations (e.g., < and >) within range constraints
• support MS Visual Studio 2008
• fixed memory leaks in categorical sampling statement, categorical_log
  function, and softmax functions
• removed many compiler warnings
• numerous bug fixes to arithmetic test code conditions and messages,
  including calls from
• fixed model crashes when no parameter specified
• fixed template name conflicts for some compiler bugs (thanks Kevin
  S. Van Horn)

Code Reorganizations & Updates

• CmdStan is now in its own repository on GitHub: stan-dev/cmdstan
• consolidate and simplify error handling across modules
• pulled functionality from CmdStan command class and PyStan and RStan
  into Stan C++
• generalized some interfaces to allow std::vector as well as Eigen
  for compatibility
• generalize some I/O CSV writer capabilities
• optimization output text cleaned up
• integer overflow during I/O now raises informative error messages
• const correctness for chains (thanks Kevin S. Van Horn)