runMCMCbtadjust 1.1.1

Major revisions: - Added 1000 to control\(time.max/Nchains in timeout argument to avoid "error reading from connection"; then replaced timeout = min(5184000,control\)time.max/Nchains+1000) by timeout = ifelse(is.finite(control\(time.max), 3*control\)time.max+3600,30243600) to have a maximum length of 30 days in case time.max is unspecified and allowing extra-time for WAIC & extra-calculations otherwise. - Modified multiplier of Nchains in set.seed in sections 2 and greater - using Ncycles to avoid repeated same values - Changed formula for niter related to duration/time to promote reproducibility in case of time.max not reached - Changed the way control\(check.thinmult behaves by adding a third level and changing the default - to conserve neffs.reached & convergence if they occurred prior to change - Changed the beginning of sections 2.3 & 2.5.3 - "Reshaping samplesList" sections - to better control samples and iterations being controlled from the end of the Markov chains - Added code for controlling sees in case of parallelization (control.MCMC\)parallelize), for reproducibility issues: seeds <- getseeds(Nchains, control\(seed); results.temp <- parallel::clusterApply(cl, seeds, worker.seed), with specifications of functions getseeds and worker.seed. - Added function window.seq to allow coherence with modifications in 2.3 and 2.5.3 and used it instead of window (in case thin was specified) - Added arguments decrease.thinmult.multiplier and decrease.thinmult.threshold to control and changed the formula for thinmult decrease when adapting it from thinmult<-thinmult-1 to thinmult<-ifelse(thinmult>control\)decrease.thinmult.threshold, max(floor(control\(decrease.thinmult.multiplier*thinmult), control\)decrease.thinmult.threshold),thinmult-1) - Added time.MCMC.Preparation.num and shifted time-dependent formulas for niter from (control\(time.max-duration)*0.95 to (control\)time.max-duration)*max(0.5,time.MCMC.num/(duration-time.MCMC.Preparation.num)), so that control$time.max is the targeted maximum time - Added two vignettes to give expanations on two specific points: changing samplers with Nimble and doing extra-calaulcations with Nimble

Minor revisions: - Put back the call to library instead of requireNamespace in parallelizeInitExpr to avoid some problems. - Added a stop of the program if parallelize and library parallel is not loaded. Updated help accordingly. - Changed error message if APT and Nimble and not parallelized, and nimbleAPT is not loaded - Revised burnin in the output - in case of non-convergence - and revised thinning of result in case of non-convergence - to ensure proper resizing - Revised 2.5 section and especially 2.5.2 to reduce number of samples in case of convergence - done also if not check.thinmult; associated changes in checking.neffs.conserved and in section 2.1 for thin in case niter<0 - Removed a print command in 2.5.2 that was there just for diagnosing - Corrected function to have a maximum value that thinmult cannot overcome so that there are at least 10 values left in each Markov Chain. - Shifted index.conv.local<-index.conv.temp to index.conv.local<-indices.samplesList[index.conv.temp] before conveff_final calls due to burnin problems with conveff_final - Slight changes in the first Vignette - Slight changes in the text of the help - Changed default and help for component check.convergence.firstrun of control - Changed the error message in case names of control or control.MCMC do not match those in the function, to be more informative - Changed final thin multiplier section to make check.thinmult more active: added if else in: stop_decrease<-convergedtemp&neffs.reachedtemp&ifelse(control\(check.thinmult==3,neffs.conserved,TRUE)&min.Nvalues.OK - Changed examples in functions runMCMC_btadjust and findMCMC_strong_corrs: not running them - due to duration constraints on CRAN - and removing condition - Replaced: nu.burn=nburnin.min+sum(numIter.samplesList[1:(index.conv.local-1)]) by: nu.burn= nburnin.min0+sum(numIter.samplesList[1:(index.conv.local-1)]) for nu.burn to be better estimated with Jags. - Added printing messages at the end of MCMC sampling and at the beginning of WAIC sampling; Added printing of extra-calculation phase - otherwise silent… - Added components Nvalues, neff.min & neff.median in final.params component of the attributes of the output - Introduced arguments monitorParentNodes and monitorAllStochNodes in control.MCMC and slight changes in params, params.conv & - Added argument to control with a default to TRUE and changed the conveff_final function and its calls accordingly. Behavior in previous versions corresponded to in case of MCMC convergence. - Added arguments force.niter.max and force.time.max (respectively to control with a default to FALSE to be able to force the MCMC to go to niter.max (for force.niter.max) and control\)time.max (for force.time.max) (provided control\(time.max constraints and niter.max contrainsts are met) (resp. to disable niter.max - except if in force.niter.max or force.time.max phase - if control\)time.max is specified). - In section 2 - for in thinmult adaptations - turned samplesList to samplesList.temp & adapted related indices for diagstemp and minNvalues.OK calculations.

runMCMCbtadjust 1.1.0

runMCMCbtadjust 1.0.5

runMCMCbtadjust 1.0.4

runMCMCbtadjust 1.0.3

runMCMCbtadjust 1.0.2

runMCMCbtadjust 1.0.1

runMCMCbtadjust 1.0.0