TreeBUGS 0.6.2 (September 2016)
===========

* Bugfix: betweenSubjects with different number of chains
* Added data "arnold2013" by Arnold, Bayen, Kuhlmann, and Vaterrodt (2013)
* More examples in R help files
* Convergence plots for simpleMPT


TreeBUGS 0.6.1 (August 2016)
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* First CRAN release
* Fast C++ Gibbs sampler tailored standard (simple fixed-effects) MPT models (simpleMPT)
* Adjusted summary functions to account for standard MPT models


TreeBUGS 0.6.0 (August 2016)
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* Fast C++ Gibbs sampler tailored to beta-MPT models (betaMPTcpp)


TreeBUGS 0.5.3 (July 2016)
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* Better weakly-informative priors for continuous predictors on the standardized scale


TreeBUGS 0.5.2 (July 2016)
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* New function betweenSubjectMPT() that computes between-subject comparisons (e.g., differences) of parameters from two fitted hierarchical models
* Extended plotFit() to fit observed against posterior-predicted covariances
* Hyperpriors matched by vector names
* Split vignette into "Intro" and "Extended"


TreeBUGS 0.5.1 (June 2016)
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* Tests for participant/person heterogeneity implemented (Smith & Batchelder, 2008)


TreeBUGS 0.5.0 (June 2016)
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* function fitModel() that fits both trait and beta MPT (avoids duplicated code)
* correlations of parameters are computed in R, not in JAGS anymore (increase in speed)
* argument "covStructure" removed (all correlations computed by default)
* save posterior predictive samples in traitMPT/betaMPT object (i.e., expected/predicted/observed frequencies)
* to get posterior predictive p-values, use ppp=1000 (previously: M.T1=1000)
* getParam() and getGroupMean() allow to save results in .csv-file


TreeBUGS 0.4.9 (May 2016)
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* T2 statistic implemented (posterior predictive check of covariance structure)
* Posterior predictive checks with parallel computation using multiple cores
* Bug fix for posterior predictive with fixed effects


TreeBUGS 0.4.8 (May 2016)
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* New function posteriorPredictive() to draw samples of individual frequencies from posterior
* T1 statistic now computed outside of JAGS (more stable, smaller mcmc object, additional argument M.T1 to specifiy the number of posterior samples used)


TreeBUGS 0.4.7 (April 2016)
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* New function plotPriorPost() to compare prior vs. posterior densities
* Default prior for traitMPT changed to xi="dunif(0,10)" for stability


TreeBUGS 0.4.6 (April 2016)
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* Parameter-specific hyperpriors for betaMPT (alpha and beta) and traitMPT (mu and xi)


TreeBUGS 0.4.5 (March 2016)
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* Special case of a single hierarchical parameter in traitMPT()  [Wishart reduces to chi^2]
* Allow fixed effect MPT parameters (e.g., a single guessing parameter for all participants). Specified in restrictions = list("g=FE")
* Bayesian p-value in getGroupMeans() to test whether group mean differs from overall mean
* Estimation of correlations of theta parameters in betaMPT (based on the MCMC samples; no explicit prior)


TreeBUGS 0.4.4 (March 2016)
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* New function extendMPT() to get additional MCMC samples for fitted traitMPT and betaMPT
* Bug fixes if parameter appear twice in model equation (e.g., u*u)


TreeBUGS 0.4.3 (February 2016)
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* Use own summary function (functions in runjags are slow and unstable)
* Estimation of DIC requries argument "dic=TRUE" or can be estimated afterwards by: fit$dic <- extract(fit$runjags, "dic")


TreeBUGS 0.4.2 (February 2016)
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* Using the package runjags instead of R2jags (better functionality, e.g., provides progress bar during parallel sampling; max.time for autojags)
* Making the function summarizeMPT() visible to allow users to recompute nice MPT summaries after changing the mcmc object (e.g., after the exclusion of MCMC samples)


TreeBUGS 0.4.1 (February 2016)
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* new argument "T1group" to compute T1 statistic separately for a grouping factor (e.g., experimental condition; can be one of the predictors in traitMPT)
* changed name of parameter estimate plotting function to "plotParam()"
* new generic plotting function plot() for betaMPT and traitMPT (a convenient wrapper for the convergence plots in coda)


TreeBUGS 0.4.0 (February 2016)
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* Possible to sample correlations AND predictors in traitMPT (using covStructure vs. predStructure)
* Defaults for traitMPT: No predictors ; correlations for all covariates that are not included in predStructure
* Changed argument name "covType" to "predType" (since it is only relevant for predStructure in traitMPT)
* New argument corProbit to specify whether to compute correlations for probability- or probit-scaled MPT parameters
* Allow to round to specific number of digits, e.g.: summary(fittedModel, round=6)
* New function getParam() to conveniently extract posterior estimates (e.g., posterior mean, median, sd)
* New function getGroupMeans() to get group estimates in traitMPT with discrete predictors (for single factors or combinations)
* Updated vignette


TreeBUGS 0.3.5 (February 2016)
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* Back to comma-separated data format for 'data.csv' and 'covData.csv'
* Less informative Cauchy prior as default for continuous predictors in traitMPT
* Additional argument IVprec in traitMPT to specify hyperprior for precision of continuous slope paramters
* Data-generating function genMPT using general matrices of individual parameters
* Parameter labels for output in fittedModel$mcmc$BUGSoutput


TreeBUGS 0.3.4 (February 2016)
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* Support for WinBUGS and OpenBUGS removed
* New function plotFreq to plot individual and mean raw frequencies per tree


TreeBUGS 0.3.3 (February 2016)
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* autojags fixed
* BCI and R^hat included in individual statistics
* Better checks for input arguments for betaMPT, traitMPT


TreeBUGS 0.3.2 (January 2016)
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* csv-format for "data" and "covData": semicolon (;) instead of comma (,) to separate cells
* Printing of summary output to "parEstFile" improved


TreeBUGS 0.3.1 (January 2016)
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* New function plotDistribution() to plot histograms of individual mean estimates


TreeBUGS 0.3.0 (January 2016)
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* Discrete factors as covariates in traitMPT with fixed and random effects (see argument: covType)
* Improved covariate handling: irrelevant columns are neglected
* Goodness of fit plots for mean frequencies (plotFit)
* Removed default values for arguments that were NULL previously
* Updated vignette
* Various Bugfixes


TreeBUGS 0.2.3 (January 2016)
===========

* Predictors can be included in traitMPT (same arguments covData and covStructure as in betaMPT)
* Nice summary for covariates in betaMPT and predictors in traitMPT
* Checked and fixed data generation and fitting for latent trait and beta MPT model
* Remaining issue: SD of parameters in betaMPT not precisely estimated
* Informative error message if N=0 in a tree for a person
* Updated vignette


TreeBUGS 0.2.2 (December 2015)
===========

* Covariates can be included in betaMPT (see arguments covData and covStructure)
* Data generation for latent trait MPT model: genTraitMPT()
* Example model files (2HTM and 2HTSM) in library path: /TreeBUGS/MPTmodels/
* Examples for readEQN and data generation (genBetaMPT, genTraitMPT)



TreeBUGS 0.2.0 (December 2015)
===========

* Implementation of Beta-MPT and latent-trait MPT model: betaMPT() ; traitMPT()
* Sample and summarize transformed parameters (e.g., "deltaD=d1-d2")
* Posterior predictive checks (T1 statistic for group and individual data)
* Basic summary and plotting functionality
* Functions to generate data according to the Beta-MPT: genBetaMPT()
* Package vignette with examples: vignette("TreeBUGS")
* Checking EQN file for consistency (identifiability etc.): readEQN()
