v2.10.0

@syclik syclik released this Jun 17, 2016 · 712 commits to develop since this release

v2.10.0 (17 June 2016)

New Team Members

  • Aki Vehtari (Aalto Uni) --- GPs, LOO, statistical modeling,
    MATLAB
  • Rayleigh Lei (U. Michigan) --- vectorizing functions
  • Sebastian Weber (Novartis) --- diff eq models

New User-Facing Features

  • introduction of = for assignment; deprecating <- (#1819)
  • _lpdf, _lpmf, _lcdf, _lccdf and vertical bar notation
    for probability mass, density, and cumulative distribution
    functions; update user-defined function syntax;
    deprecate older forms (#1811)
  • target += lp to replace increment_log_prob(lp); target() to rpelace
    log_prob() function; remove lp__ variable access (#1800)
  • conditional (ternary) operator (#1125)
  • stiff diff eq solver CVODES from Sundials
  • add control parameters (tolerance, max iteraitons) to ODE solvers
  • rename ODE solvers based on algorithm, integrate_ode_rk45
    for existing non-stiff Runge-Kutta solver and integrate_ode_bdf
    for the stiff backward differentiation form; deprecate
    the unmarked integrate_ode function (#1886)
  • limiting diff eq iterations in solvers (Boost/CVODES)
  • unit_vector as parameter (#1713) [it never worked in the past]
  • rename multiply_log and log_binomial_coefficient
    to lmultiply and lchoose (also part of #1811)
  • incomplete beta function as inc_beta (#1540)

New Internal Features

  • exhaustive HMC (XHMC)
  • multinomial variant of NUTS (#1846)
  • simplified NUTS criterion (#1852)
  • uniform static HMC (#1849)
  • Riemannian HMC with SoftAbs (#304)
  • refactor semantic actions to header/implementation (#1795)
  • writer callback interface for algorithms (#1739)
  • error writer callbacks (#1836)
  • cleaner HMC diagnostic ouptut (#1790)
  • pull-request template on GitHub (#1794)
  • remove unused filename argument in parser (#1752)
  • remove unused lp_no_jacobian function (now controlled with
    template params)
  • writer callback interface for HMC (#1680)

Bug Fixes

  • index slicing not compiling for matrices (#1754, #1810)
  • parsing too eager for reserved words (#1077)
  • CSV reader whitespace sensitivity (#1907)
  • delayed reject multinomial NUTS (#1906)
  • PYTHON2 variable for cpplint (#1912)
  • size zero vectors, row vectors, matrices (#1909)
  • overflowing transition probs in multinomial NUTS (#1904)
  • all the manual bug fixes (#1431, #1709, #1734, #1753,
    #1826, #1874, #1879, #1890)
  • compiler fix for vector /. real to compile (#1883)
  • terminate infinite loops in optimization (#1896)
  • ADVI argument config failure (#1731)
  • double struct creation removed for forward-declaration
    of user-defined functions bug (#1079)
  • clarify deprecation of <- is only in Stan, not R (#1819)
  • memory leaking with command getting in way of debug (#1293)
  • makefile dependencies for stanc (#1682)
  • remove NaN init for integers in place of min (negative)
    value (#1766)
  • namespace pollution from log_mix removed (#1707)
  • message buffering reduced in ADVI
  • add pstream to user-defined CDFs supporting truncation (#1628)
  • initialization failure message clarification (#1736)

Downloads