Updated CITATION file using bibentry() as per CRAN request.
Version 2.3-1, June 27, 2023
The strict uniqueness of n.clones in dc.fit can be relaxed by the
new check.nclones argument.
The update argument of dc.fit can be of length 1 or more, updatefun
must return a list when length(update) > 1.
Bugfix: stan.fit and stan.parfit were not able to read in model file
because model_chr was undefined (#15).
R2WinBUGS is now in Imports (#14).
Version 2.3-0, Mar 21, 2019
Support for Stan incorporated.
New functions: stan.fit, stan.parfit, stan.model.
dc.fit and dc.parfit accepts flavour=“stan”.
Version 2.2-0, Feb 26, 2018
Removed dependence on superseded package snow, now imports from
parallel.
Functions related to parallel load balancing (e.g. parLapplySB) have
been rewritten.
Version 2.1-3, Feb 2, 2018
dc.fit: n.clones=1 is acceptable and will not throw error.
dc.fit and dc.parfit gained return.all argument so that not only the
mcmc.list corresponding to highest number of clones is returned.
write.jags.model does not write into the user’s working directory
but uses tempdir() as per CRAN requirements. The function returns the
full path for cleanup. Tested to work with sequential and parallel
functions.
Version 2.1-2, Jan 14, 2016
snowWrapper deprecated.
codaSamples and parCodaSamples gained na.rm argument following
rjags::coda.samples (starting with rjags 4-4, thus the version
dependency in DESCRIPTION).
Version 2.1-1, Jan 11, 2016
Extensive NAMESPACE changes to import from other packages.
Import: rjags and snow, so that functions can be imported by
NAMESPACE.
Version 2.1-0, Nov 22, 2015
Matrix as dependency: finding nearestPD in chisq.diag.
Version 2.0-0, Sept 27, 2013
Parallel functions (parJagsModel, parUpdate, parCodaSamples)
triggered a Note by R CMD check for modifying the global environment.
This is now resolved as described below.
New function: parDosa (meaning: wolf spider). This replaces the
snowWrapper. It comes with 2 hidden environments (.DcloneEnvModel,
.DcloneEnvResults) defined as global variables. The .DcloneEnvModel is
meant to store temporary objects for model fitting, and swiped clean
after use. The .DcloneEnvResults is meant to store result objects on the
workers.
These environments come with functions for manipulating them:
pullDcloneEnv, pushDcloneEnv, clearDcloneEnv, listDcloneEnv,
existsDcloneEnv.
snowWraper is now deprecated with a warning.
R2OpenBUGS added to DESCRIPTION as suggested package.
R2WinBUGS::* notation explicitly added to avoid clashes with
R2OpenBUGS.
The program=“openbugs” in bugs.fit now calls R2OpenBUGS::bugs
instead of R2WinBUGS::openbugs. The latter can be achieved by
program=“brugs” and gives a warning the “openbugs” via R2WinBUGS is the
preferred interface. The reason is that as.mcmc.list.bug coercion
produces slightly different ts attributes under BRugs. WinBUGS (via
R2WinBUGS) and R2OpenBUGS implementations give consistent ts attributes
and can be seamlessly coerced into mcmc.list object, which is the
preferred format for dclone.
bugs.parfit: new-old function from extras directory. This is for
parallel computations. See help file for details on suggested best
practices.
dc.parfit: now allows flavour=“bugs” for all partypes options.
Removed reference to parallel:::.reg default cluster.
SystemRequirements in DESCRIPTION changed to ‘one or more of
…’.
rjags related functions call requireNamespace(“rjags”) instead of
require(rjags).
Depends on R 2.15.1 because of the declaration of global variables
.DcloneEnvModel and .DcloneEnvResults.
Version 1.8-2, March 4, 2013
custommodel: splits length 1 character model by ‘’. This is the type
of model specification that is used in STAN related examples.
New cloning option added: dctr, allows cloning column-wise. This
change was motivated by some STAN related data specification
difficulties.
dctable: failed when mcmc.list had 1 parameter. This is now fixed by
using varnames(x, allow.null=FALSE).
Version 1.8-1, September 3,
2012
clusterSplit now checks inheritance of its cl argument in R-devel
(2.16.0 to be), as a result plotClusterSize threw an error when
supplying a simple vector to clusterSplit (reported by B Ripley), this
is now fixed.
Version 1.8-0, July 6, 2012
dciid: new function added, it is similar to dcdim. dciid attaches an
attribute to data frames or matrices about columns to be treated as
i.i.d. observations by dclone(). This aims to facilitates working with
the INLA package to generate approximate marginals based on DC.
dclone.dciid: proper cloning of objects with “dciid” tag. It
respects possible groupings of observations.
Version 1.7-2, March 21, 2012
custommodel and write.jags.model fixed and modified. These now
accept connection as filename argument.
lambdamax.diag and chisq.diag are now generics. Methods for
mcmc.list is defined.
inst/COPYING file removed (standard license).
Version 1.7-1, January 31,
2012
Now that rjags is only suggested rjags is loaded by snowWrapper if
JAGS is used (dc.parfit, jags.parfit, parJagsModel).
n.chains argument was not passed by dc.parfit with partype %in%
c(“parchains”, “balancing”). Bug is now fixed, thanks to K. Nadeem
(UofA).
length(cl) >= n.chains is required in parJagsModel, parUpdate and
parCodaSamples recognizes empty workers accordingly.
lecuyer module is checked only for clusters and not for
forking.
Rd files cleaned up, documentation is up-to-date.
Version 1.7-0, January 25,
2012
Preparing for major CRAN release.
Version 1.6-0, December 19,
2011
Depends on parallel and R >= 2.14.0 for multicore type forking on
Linux/Unix machines. Heavy lifting is still done by showWrapper for easy
transitioning.
parallel is now a dependency, snow is suggested only.
list type declaration of params argument not working with
partype=“both” in dc.parfit. This option is defunct at the moment.
Windows specific suggested packages removed from dependency list due
to seamless Linux based testing of forking type parallel features
(rsprng, BRugs).
cl argument in parallelized functions that use snowWrapper can be
NULL in which case it takes the value from the mc.cores global option
getOption(“mc.cores”). If mc.cores is not set (NULL) of 1, an error is
produced.
mclapplySB added to mimic size balancing with forking.
parJagsModel, parUpdate and parCodaSamples works only with snow
clusters.
evalParallelArgument added for consistent handling of parallel
arguments.
jags.parfit and dc.parfit falls back to sequential evaluation if cl
is NULL (and default options for parallel processing are unset) or
1.
stack method for mcmc.list objects to facilitate creating graphics
with lattice and ggplot2. Experimental ggplot2 based plotting functions
are in dcextras package on R-Forge.
The package was extensively tested on Windows XP and 7 (32 and 64
bit) and Ubuntu Linux 11.10 using JAGS, OpenBUGS and WinBUGS (latter
only on Windows). For testing suite see /devel on R-Forge.
Version 1.5-1, October 18,
2011
“[.mcmc.list.dc” added to extract parts of a fitted object and
retain its n.clones attribute (no other attributes though, e.g. dcdiag,
dctable, updated.model).
params argument in dc.*fit can take a 2 element list. Union of the 2
vectors will be used as parameters to monitor (as in jags.fit), while
the 2nd element of the list is used to calculate statistics in dcdiag().
This way transformations of nodes or the deviance monitor won’t be used
in diagnostic tests.
Version 1.5-0, October 17,
2011
Major CRAN release with improved parallel features (double
initialization overhead is removed); with bugfixes from devel
versions.
The package also has bee extensively tested using Classic BUGS
examples (see ChangeLog for dcmle package).
Version 1.4-2, October 16,
2011
New function: parallel.inits make use of rjags:::parallelseeds to
control RNG settings for initial values in parallel computations.
parJagsModel: adapted to initial RNG setup by parallel.inits.
jags.parfit: adapted to initial RNG setup by parallel.inits.
dc.parfit: adapted to initial RNG setup by parallel.inits
(partype=both, also partype=parchains via jags.parfit, partype=balancing
depends on underlying JAGS settings as in jags.fit).
Version 1.4-1, September 28,
2011
plot.dcdiag: dcdiag colnames from .dcFit were non standard, so plot
failed to select columns. Now fixed.
dc.fit and dc.parfit: got n.chains argument for clean handling in
parallel work. (dc.parfit failed with partype=“both” when n.chains was
other than 3.)
plotClusterSize: can plot if length(size) < n without
error/warnings.
parLoadModule, parUnloadModule, parListModules, parSetFactory,
parListFactories: workers returned values as expected, but did not
actually made changes, bugs fixed, allowing full control of JAGS
settings on workers.
dcdiag and dctable: return NA when subroutines fail (gelman.diag,
lambdamax.diag, chisq.diag). dc.fit and dc.parfit neglects these NA
values when issuing warning based on Rhat.
dcoptions()$overwrite changed to TRUE by default, this might spare
some headaches when going parallel.
lambdamax.diag returned sd instead of variance for one parameter
case, bug fixed (reported by S Lele).
Version 1.4-0, September 28,
2011
Major CRAN release with new parallel features.
Version 1.3-6, September 7,
2011
jags.fit return jags model with n.clones attribute when
n.iter=0.
parJagsModel and parCodaSamples: passes the n.clones info from data
argument.
jagsModel and codaSamples added as wrapper around jags.model and
coda.samples functions of rjags package to track dclone information
passed through data argument and allow custommodel specification of
model argument (similarly to par* versions of similar functions).
.onLoad added to zzz.R
Version 1.3-5, August 23,
2011
n.update=1000 is now the default instead of 0 to ensure independence
after adaptation. Warning is issued if n.adapt>0 and n.update=0.
New argument partype added to dc.parfit, possible options
(balancing, parchains, both) are described on the help page.
dc.parfit gained args (update, updatefun, initsfun) which are
ignored if type is not “parchains”.
dc.fit and dc.parfit (with “parchains” type) now call new internal
function .dcFit (former dc.fit reworked to allow parallel chains via
jags.parfit). This function is not exported by namespace, thus not user
visible and undocumented.
dclone is loaded to workers by snowWrapper only if .packages() does
not contain it yet.
dclone method for environment added: it returns a cloned list.
data argument can be environment, it is coerced to a list for
handling n.clones attribute.
jags.fit: quiet argument of jags.model used along with verbose
dcoption to possibly suppress printout during compilation.
Parallel functionality added replicating main rjags functions to
allow easy updating of jags model objects. Functions added:
parListModules, parLoadModule, parUnloadModule, parListFactories,
parSetFactory, parJagsModel, parUpdate, parCodaSamples, parUpdate; with
help pages taken and edited from rjags package of M Plummer.
.DcloneEnv is created at startup, and removed on unloading dclone.
This is intended to store temporary stuff passed to workers by
snowWrapper.
snowWrapper got new argument: unload=FALSE to unload packaged from
pkg argument.
snowWrapper: if name=NULL, .DcloneEnv is used to store temporary
data.
Data cloning compatible jagsModel and codaSamples function added for
sequential computations. Both functions copied after rjags equivalents,
jags.model and coda.samples.
New method: pairs for mcmc.list objects. It plots bivariate kernel
density estimates and scatterplots in a matrix with univariate densities
as diagonal.
dctable add object name even if length(n.clones)==1.
initsfun handling in dc.parfit partly allowed, this new feature is
now documented, testing, Example added.
All documented S3 methods are now exported by NAMESPACE (dependent
packages could not import them).
Version 1.3-4, July 9, 2011
dc.fit: updating fixed (only updated after 2nd iteration).
dc.fit: updatefun and initsfun now accepts 2 arguments, 1st is
model, 2nd is n.clones to allow for cloning latent variable vectors on
the go. Example reworked accordingly.
snowWrapper: cleanup=TRUE cleans up after lib and dir args,
too.
New option ‘overwrite’ in dcoptions (used by write.jags.model).
packageStartupMessage used in zzz.R .onAttach
… is now passed to snowWrapper in *.parfit (thanks to Emmanuel
Charpentier for reporting the bug).
Version 1.3-3, May 13, 2011
*.parfit: write model to hard drive only if cluster type is SOCK
(shared memory)
snowWrapper: dir=NULL is set as the default.
mcmcapply functions simplified, FUN can be missing.
jags.parfit help notes that there is no update method for parallel
mcmc.list objects.
snowWrapper got cleanup=TRUE argument to remove data after
evaluating main function.
Version 1.3-2, March 2, 2011
Partial argument match fixed (NOTE from R CMD CHECK).
write.jags.model got new argument overwrite=FALSE.
Typo in rng.type argument of snowWrapper fixed.
plotClusterSize: col arg is reordered according to balancing
type.
Version 1.3-1, January 4,
2011
JASA paper (Lele et al. 2010) citation added to Rd.
loading rjags changed: it is now only suggested. Reason: some dclone
functionality might be useful without JAGS/rjags present, and now
loading rjags won’t cause error if JAGS shared library not found.
glm module not loading at startup because it cannot be nicely
unloaded in parallel versions.
dcoptions RNG got “none” value as default, *.parfit functions use
dcoptions for snowWrapper. As a result, dependencies changed a bit.