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@syclik syclik released this 20 Jun 22:18
· 3568 commits to develop since this release
v2.3.0
cedef70

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)
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