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NEWS

• added citation info for 2020 book chapter
• new function gibbsPotts for updating mu, sd and z for a fixed value of beta
• changed URLs from http:// to https://

• updated citation info for Bayesian Analysis (2020) paper
• added a hex logo to the README
• removed duplicate vignette entry

• modified vignette swNoData to only use PottsUtils conditionally
• deleted vignette PFAB due to problems with Stan and Boost on gannet/ripley/tests-ATLAS

• changed maintainer email address due to new academic affiliation
• reorganised package vignettes
• NAMESPACE is now generated by roxygen2
• added LICENSE file for GPL 2

• new vignette introducing the parametric functional approximate Bayesian (PFAB) algorithm
• removed all @seealso from Roxygen docs due to CRAN WARNings because PottsUtils has now been permanently removed from the CRAN repository

• improvements to Bayesian indirect likelihood (BIL) algorithm (mh$alg="aux"):
  • MH hyperparameter Ecrit for 2nd order phase transition when k > 4
  • MH hyperparameter factor to inflate the variance of the surrogate model
  • separate MH hyperparameters Vmax1,Vmax2 for \(\beta < \beta_{crit}\) and \(\beta > \beta_{crit}\), respectively
• option mh$sort to impose an ordering constraint on the component means

• removed OpenMP options from Makevars to fix problems with RcppArmadillo. Users should edit ~/.R/Makevars to enabel multithreading.

• no longer wait for mh$auxiliary iterations before beginning to update \(\beta\) using the exchange algorithm or ABC. For \(\beta > \beta_{crit}\), this increased the propensity of the Gibbs sampler to become stuck in a suboptimal local mode, far from the true parameter value.

• added jss.bst and jss.cls to .Rbuildignore

• removed the deprecated slices parameter from mcmcPotts()

• some minor edits to the Roxygen documentation

• added ORCID to DESCRIPTION

• removed the R package PottsUtils from Suggested packages; added mcmcse

• moved README-chunkname.png images from root directory to inst/images

• Functions getNeighbors(), getEdges(), getBlocks() contributed by Dai Feng. These are currently exact copies of the equivalent functions in the R package PottsUtils. The reason for duplicating this code is to avoid picking up dependencies on miscF, R2jags, BRugs, etc.

  • https://cran.r-project.org/package=PottsUtils

• Added new option to swNoData and mcmcPottsNoData to initialise the labels using either random or deterministic values. This can be useful when comparing the convergence of the Swendsen-Wang and Gibbs sampling algorithms to known distributions (e.g. when \(\beta\)=0 or \(\infty\))

• Additional documentation in README.md with an example of usage

• Fixed compile errors on SPARC Solaris

  • https://www.r-project.org/nosvn/R.check/r-patched-solaris-x86/bayesImageS-00check.html

• Fixed compile warnings from icpc (Intel Parallel Studio XE) on Linux

• Added bayesImageS_init.cpp to call R_registerRoutines and R_useDynamicSymbols

• First version released on CRAN

• First public release on RunMyCode.org:
  • http://www.runmycode.org/companion/view/546

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