This version of the function is still being developed, and as such will almost certainly contain numerous bugs.  If you find one or more (gasp!), or if you have any comments/criticisms/questions about the function, then please feel free to email me at m.denwood@vet.gla.ac.uk.  Thanks!


OPEN ISSUES


BUGS

None known.


FEATURES TO BE IMPLEMENTED

None planned.




VERSION HISTORY


Version 0.9.2

NEW FEATURES

autorun.jags and run.jags now produce trace and density plots of all monitored variables (if plots==TRUE), which are returned as $trace[[variable]] and $density[[variable]]

Multiple model files or strings (or a mixture) can now be specified as a character vector to read.winbugs

User can now change options for the Raftery and Lewis diagnostic via 'raftery.options' for autorun.jags(file)

When a simulation is aborted due to crashes or unexpected results from autorun.jags(file), an error message is now printed as well as returned

combine.mcmc will now ignore a request to return more samples than provided rather than returning an error

combine.mcmc can now accept a single mcmc list or mcmc object to be thinned (or returned unchanged if thin=1)

autodata and autoinits can now be specified as a vector (or array) of missing data


BUG FIXES

Bug fixed that could result in chain values being returned as infinite causing an error with the gelman rubin statistic if normalise==TRUE

Bug fixed in combine.mcmc that resulted in mcmcchains with only 1 variable causing an error

Bug fixed that resulted in models being specified to (auto)run.jagsfile being ignored

Errors resulting from use of 'summary' in autorun.jags and run.jags now suppressed correctly

Efficiency of the normalise.mcmc function dramatically increased for chains with many variables

Time limit in autorun.jags now does not include time spent waiting for dialogs to be answered, and is only used for simulation extensions to improve convergence (simulation is always extended for sample size if necessary)

Bug fixed that could result in extended chains with non-stochastic monitored nodes causing an error in autorun.jags

Bug fixed that resulted in crashed datasets always causing autorun.jags to return an error

Bug fixed that prevented parameters specified as functions inside the datalist or initlist lists (or functions) being interpreted correctly


Version 0.9.1

NEW FEATURES

Number of failures to calculate the gelman-rubin statistic reduced by:
Checking for monitored variables that are not stochastic and remove from inclusion in gelman-rubin statistic
Option to improve normality of posterior distributions before estimating the gelman rubin statistic in run.jags and autorun.jags (normalise.mcmc option).
New function to catch instances where gelman.diag fails for multiple parameters and calcualte the psrf individually (without multivariate psrf)

autorun.jags and run.jags now returns 'psrf.target' as part of $psrf

psrf.target added as an option to run.jags the same as autorun.jags

NAMESPACE file used now

Output of read.winbugs is now consistent - if data or initial value blocks are not found their values are returned as NA

Warning that JAGS under Windows may be slower than Unix now removed


BUG FIXES

Bug fixed in combine.mcmc that could prevent thinning being performed as specified

Bug fixed in autorun.jags that resulted in the output chain being replicated and combined together

Bug fixed in run.jagsfile that caused problems when monitors weren't supplied in the model file

Typo fixed in run.jags that caused simulations with only 1 chain to print a converged message

Behaviour changed in run.jags so that a warning is printed if initial values are not the right length

Bug fixed in run.jagsfile (findparams) that caused data containing any missing data to not be found

autorun.jags now recalculates the gelman rubin statistic on the final chains and prints a warning if the chains have fallen out of convergence

Bug fixed in run.jags that caused issues with calculating the Gelman Rubin statistic when the number of expected monitored nodes was not equal to the number of actual monitored nodes

Bug fixed in autorun.jags and run.jags that caused the gelman rubin diagnostic to be calculated on the second half of the chain only

For run.jagsfile, when n.chains was not consistent with length of inits it was ignored.  Now the length of inits is altered to match n.chains, with a warning.

Bug fixed in new_unique that caused the counter to be added and not incremented if a file ending with '_1' existed already

Delay after reading coda files partially replaced with flush.console() for Windows/Aqua, and removed for other OS types

Bug fixed in autorun.jags that could produce a warning message if the chains were extended for convergence

Bug fixed in run.jags that resulted in an error if the convergence calculation failed

autorun.jags modified to attempt to reduce some of the strange errors and warnings sometimes encountered



Version 0.9.0

New to version 0.9; separated from bayescount to form 2 distinct packages.
For version history of the package before 0.9 see the version_history file for bayescount.