News

NOTE: for more news about the package, see https://github.com/florianhartig/BayesianTools/releases

BayesianTools 0.1.6

New features

• calibrationTest + helper functions to test for https://github.com/florianhartig/BayesianTools/pull/172

Major changes

• None

Minor changes

• Help improvements and clarifications

Bugfixes

• Bugfix AR1 likelihood https://github.com/florianhartig/BayesianTools/issues/169
• Bugfix restart MCMC https://github.com/florianhartig/BayesianTools/issues/158

BayesianTools 0.1.5

Changes / improvements

• marginalPlot changed / updated

Minor changes

• getSample behavior https://github.com/florianhartig/BayesianTools/issues/133
• Create a check of start values / check matrix at the runMCMC level https://github.com/florianhartig/BayesianTools/issues/114

Bugfixes:

• Removed package dependency in unit tests https://github.com/florianhartig/BayesianTools/issues/136
• Bugfix in bridge sampling https://github.com/florianhartig/BayesianTools/issues/121
• Missing -Inf -> - Inf check in DEzs and DREAMzs with parallel = T https://github.com/florianhartig/BayesianTools/issues/113

BayesianTools 0.1.4

Compatibility

• added NIMBLE support to getSample and plotting functions
• added coda support to plotTimeSeriesResults and plotMarginals

Changes

• IMPORTANT: added a warning when calling runMCMC with the "twalk" sampler. At the moment, using this sampler is discouraged
• marginalPlot can now plot prior and/or posterior, either as histogram or as violin plots
• added bridge sampling to marginalLikelihood
• added shortcuts for AM, DR and DRAM samplers

Bugfixes:

• when calling getSample on mcmcSamplerList, the chains are now merged instead of concatenated
• formulas in the vignette are now rendered correctly
• fixed a bug in VSEM help

Minor Changes:

• changed the ordering of the summary metrics of summary.mcmcSampler, and summary.mcmcSamplerList
• renamed marginalLikelihood output to "ln.ML"
• added tests for plotTimeSeriesResults, marginalPlot and marginalLikelihood
• added an example with restart to DEzs

BayesianTools 0.1.3

Compatibility

• created compatibility to new Rcpp standard

Changes

• getSample extended to coda objects, so that all plot functions can also be used on coda objects
• plotTimeSeriesResults now includes the option to create residual plots from posterior predictive simulations, calling the DHARMa package
• added new utitility functions sampleEquallySpaced and correctThin

Bugfixes

• IMPORTANT: fixed a bug in createPriorDensity - results with createPriorDensity prior to this bugfix may be unrealiable
• getSample now corrects wrong inputs for thin and numSamples instead of throwing an error
• smaller bugfixes in plot functions

BayesianTools 0.1.2

Bugfixes

• various smaller improvement / bugfixes in getSample, plot functions / Help (0.1.2)
• warnings / bugfixes associated to burnin arguments (0.1.1.2)
• bugfix in marginal plots (0.1.1.1)

BayesianTools 0.1.1

Mostly a bugfix release

Minor changes

• implemented method for estimating posterior volume (0.1.0.1)
• implemented GOF (0.1.0.2)

Bugfixes

• removed erroneously created help files (0.1.0.1)
• dynload change to conform to R 3.4.x requirements (0.1.1)
• smaller bugxfixes and help updates (0.1.1)

BayesianTools 0.1.0

• initial release

Reference manual