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Changes in JAGS 3.1.1 User-visible changes ==================== * New observable function "dround" may be used to represent data that have been rounded to a given number of decimal places. Bug fixes ========= * BaseRNGFactory did not recycle RNGs correctly. * DMState now declares itself to be a discrete-valued distribution. * Likelihood calculations were incorrect for the binomial distribution with unobserved size parameter. * The Holmes-Held sampler for logistic regression models with binary outcomes is now more numerically stable. Internal changes in modules =========================== * New ShiftedCount sampler samples nodes with a Poisson, binomial or negative binomial prior distribution that are used as the size parameter of a binomial distribution. * New ShiftedMultinomial sampler is a multivariate version of shiftedCount. It samples nodes with a multinomial prior distribution, elements of which are used as the size parameters of distinct binomial children. * Headers in the GLM module are properly documented. --------------------------------------------------------------------- Changes in JAGS 3.1.0 User-visible changes ==================== * Allow progress bar in batch mode if user gives "by" option to update or adapt. Bug fixes ========= * If a monitor is requested while the model is in adaptive mode, then adaptive mode is turned off, with a NOTE to the user, instead of throwing an exception. Library changes =============== * BUGSModel::setMonitor will return after the first error message is reported from a MonitorFactory. Internal changes in modules =========================== * dic - Improved error messages from PDTraceFactory in case a pD monitor cannot be generated. ----------------------------------------------------------------------- Changes in JAGS 3.0.0 User-visible changes ==================== * Functions and distributions may now have an alias, so that they can be referred to by more than one name. This allows compatibility with the naming conventions of OpenBUGS (e.g. ddirch vs ddirich) and of R (e.g. dbin vs dbinom). * Progress bar - The width of the progress bar is extended from 40 to 50 characters - In batch mode, the progress bar is not printed - Adaptive mode is always indicated by symbol "+" * In batch mode JAGS halts on the first error * New distributions in the bugs module - Non-central chi-square (dnchisqr) - Beta binomial (dbetabin) - Generalized gamma (dgen.gamma) * Separate messages are printed during compilation and initialization of the model. * The multinomial distribution (dmulti) can take a scalar probability parameter (like dcat) * A warning is printed if a user tries to initialize a model before it is compiled. This was previously silently ignored. * The user has more control over the adaptive phase. The adapt command does not automatically turn off the adaptive phase and so may be run sequentially until adaptation is complete. * When a monitor cannot be defined an attempt is made to return an informative error message. * A single installer for Windows contains both 32-bit and 64-bit versions of JAGS. Library changes =============== * logLikelihood function renamed to logDensity. This function now takes an argument allowing fast calculation of likelihoods and priors. * New error functions declared in the header module/ModuleError.h can be called from a module instead of throwing an exception. This allows safe handling when the library is statitically linked to the C++ runtime, as exceptions cannot be thrown across DLL boundaries in this case. * New subclasses of runtime_error for functions (FuncError), distributions (DistError) * Mixture nodes may share a common MixMap, with substantial memory savings. * Models with large multivariate nodes have been optimized for speed. Configuration changes ===================== * Use up-to-date m4 macros for blas and lapack from gnu autoconf archive * For modules, drop the -no-undefined linker flag except on Windows, where it is necessary. * On Solaris, the macro for detecting blas automatically has been updated to use new syntax -library=sunperf. Internal changes in modules =========================== * bugs - The base RNG factory only uses the time stamp once, during construction, to fix the random number seed. Use the bugs namespace consistently in the bugs module - Changed all instances of lgamma (C library) to lgamma_fn (R math) - The DSum sampler may be multi-level (i.e. it may sample two nodes, one of which is the descendant of the other) * glm - The HolmesHeld sampler has been (temporarily) suppressed as its numerical instability problems have not been solved. - The glm module now contains a copy of CHOLMOD, AMD, COLMOD * mix - The DNormMix sampler may be multi-level Bug fixes ========= * Fixed segfault in BUGSModel when requesting monitor for node with wrong dimensions * Fixed segfault in ConjugateMNormal * Fixed glm module in case of GLMs with mis-measured covariates - Holmes-Held method cannot work with such models - With Albert-Chib method we need to update all auxiliary data at the start of each iteration * The lexer now accepts floating point expressions when the exponent has no sign (e.g. 6.022E23 now accepted as well as 6.022E+23) * Corrected random number generation for - Pareto distribution - Multivariate T distribution - Hypergeometric distribution (seg fault) * The constructors for Vector- and ArrayStochasticNodes now check the number of parameters. * Fixed serious bug in NodeArray::find (It always returned 0 and led to the creation of spurious aggregate nodes). * More informative error messages in case of module loading failure * Random walk Metropolis sampler now copes with non-finite log-densities * CalKLExact was only returning half the correct value, with consequences for the pD and popt monitors. * The binomial distribution now allows a zero size parameter * Fixed bug in PDMonitorFactory that stopped Monitor objects being created when any node in the model is bounded. * The scanner throws an exception if it encounters the Unicode replacement charcter U+FFFD