Changes in JAGS 3.4.0
=====================
New features
====================
* You can now set a monitor of type "mean" for any node, which records
the running mean.
* The order function in the bugs module returns a permutation that sorts
its argument in ascending order (the inverse of the permutation
provided by the rank function).
* The Windows installer now offers a choice of personal or global
installation for users with Admin access.
* The negative binomial distribution is extended to allow parameters
size=0 and probability=1.
Bug fixes
=========
* LogicalNode::isClosed could throw a logic_error due to a bug in
the checkLinear function (Linear.cc)
* Setting a monitor with thinning interval 0 prints an error message
but no longer throws a logic_error exception.
* The command line interface could print a spurious warning that
".RNG.seed" or ".RNG.state" was unused.
* A function or distribution with zero arguments caused a segmentation
fault. This now gives a compilation error.
* The "dround" function (bugs module) was incorrectly calling fprec
(round to n significant figures) when it should have been calling
fround (round to n decimal places).
* The sd() function divided by n (sample size) instead of (n-1).
* The Windows uninstaller did not correctly uninstall personal
installations for users with administrative access.
Internal changes in modules
===========================
* base module
- The Pow function has alias "pow" so it can be invoked either as "a^b"
or as "pow(a,b)"
* bugs module
- The Pow function has been removed: it was a duplicate of base::pow
- The DSum distribution no longer throws an exception if the parameters
are inconsistent with the value. This gives a more informative error
message.
Changes in JAGS 3.3.0
=====================
User-visible changes
====================
* JAGS now prints a warning about unused initial values
* Failure to set a "pD" monitor from the "dic" module should produce a
more informative error messages
* The Windows installer no longer creates a shortcut in the start menu
to the uninstaller. Use the Control Panel to uninstall JAGS on Windows.
Bug fixes
=========
* The inverse and logdet functions now work on scalars
* NodeArray::setValue could overwrite values of observed nodes.
At the user-interface level, one could change the value of a constant
node by providing an initial value.
* Underflow errors in the Weibull distribution are now caught.
* The auxiliary mixture sampling method now works with binomial data
that have a zero denominator.
* The multinomial distribution now allows a zero size parameter.
* The log-density of the uniform distribution was incorrect when
doing likelihood calculations.
* The ConjugateWishart distribution did not work correctly in mixture
models.
* The choose and lchoose functions in the JRmath library could go into
an infinite recursion, overflowing the C stack and crashing JAGS.
* The Poisson log-likelihood function did not return zero for non-integer
values. This could lead to a crash in the glm module.
* Multiple bug fixes in the IWLS sampler in the glm module.
Internal changes in modules
===========================
bugs module
* The InProd and MatMult functions now use BLAS calls.
glm module:
* Cutoff for left and right expansions in Holmes-Held sampler is now optimal.
* IWLS sampler only works with certain link functions.
dic module
* Faster Kullback-Leibler calculations for the Bernoulli distribution.
--------------------------------------------------------------------------
Changes in JAGS 3.2.0
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