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 0.9.1

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.