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CHANGELOG.md

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Changes

Version 22.8.1.0.4

The following fixes are in version 1.0.4

- Fixed valgrind initialization issue with polyK test. 
- There is no added functionality in this release.  Keeping the 22.8 moniker.

Version 22.8.1.0.3

The following fixes are in version 1.0.3

- Fixed an NLOPT warning with CLANG 15 to keep on CRAN. 
- There is no added functionality in this release.  Keeping the 22.8 moniker.

Version 22.8.1.0.2

The following fixes are in version 1.0.2:

- Function 'single_continuous_fit' and 'ma_continuous_fit' changed error when defining default priors
	 for 'distribution=normal-ncv' when data are negative. Originally the variance was described as mean(Y)/var(Y); 
	however, for negative means, this causes NA error. It is now defined as abs(mean(Y))/var(Y). 
- Log-normal distribution fits were incorrect when summarized data was used. The correct transformation of
	summarized data is now performed. The formula for standard deviation was typed in as sqrt(log((sd)^2/mu + 1)) it is now sqrt(log((sd/mu)^2+1)). 
- Changed default priors for dichotomous fits to be consistant with Wheeler et al. (2020).

The following changes to fitting were made:

- Changed MLE Polynomial fit behavior.  Now the terms up to the quadratic are constrained to be in the direction 
  of the response.  After this, i.e., degree >= 3, the parameters are unconstrained. 
- Added summary and print methods for mcmc model averaging.

Known Problems not yet fixed

- GoF for MA individual models not given. 
- GoF for dichotomous models with (0/1) data fails.

Version 22.5.1.0.1

The following fixes are in version 22.5.1.0.1:

- Function `single_continuous_fit' fixed prior issue with Log-Normal data, when sufficient statistics are given.
- Log-Normal deviance for Exponential 3/5 was producing incorrect values. Now reporting correct values. 
- Function `single_dichotomous_fit' did not return bmd_dist as an element of the return object when fit_type = 'mcmc'.
- Dichotomous MA individual models were mislabled.  They now are consistant with Continuous model averaging using the 
  `Individual_model' naming. 
- Inf, NA, NaN rows are now removed before fitting.

The following changes to fitting were made:

- Changed the profile likelihood stopping criteria for profile likelihood equality constrained optimization for continuous models to be 5e-5 for the absolute change in the parameter value, i.e., |\beta_n - \beta_{n+1}| < 5e-5  is the stopping criteria. 
- When OpenMP is enabled, the fitting of single continuous models and deviance models is done with multiple threads. 
- MCMC Metropolis-Hastings algorithm proposal changed.  Proposals are now 125% MAP variance. This change improves mixing and increases effective
sample size by around 10 to 20%.

The following additional functionality was added:

- Added summary/print functions for Single Continuous and Single Dichotomous Models.
- Added summary/print function for Model Averaging.
- ntp tests (Williams/Shirley/PolyK/Dunn/Dunnett) e.g. ?ntp_williams
- Data set from Wheeler, Bailer, Piegorsh (2019) added.