stan v2.10.0

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

• 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)

• 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)

• 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)