NEWS

BSL 2021-04

Added a new method ("BSLmisspec") in the main function "bsl", which considers model misspecification when running BSL.
Added an option "whitening" in the main function "bsl", which allows greater shrinkage when using the Warton's shrinkage estimator.
Re-designed S4 classes "BSL", "MODEL", and "PENALTY". More methods are supported in the classes.
The package now uses a progress bar to track running progress in the "bsl" function (verbose = 1L).
Other minor changes and bug fixes.

Added a new method ("uBSL") in the main function "bsl".
Two shrinkage methods ("glasso" and "Warton") are available now for methods "BSL" and "semiBSL".
A new S4 object class "BSLMODEL" is introduced to encapsulate the simulation function, summary statistic function, a point estimate of the parameter value and other arguments that are related to the model of interest.
"BSLMODEL" now uses log of the prior function for numerical stability.
"BSLMODEL" supports vectorised simulation function ("fnSimVec") that produces n model simulations simultaneously.
A number of arguments ("fnSim", "fnSum", "theta0", "fnPrior", "simArgs", "sumArgs" and "thetaNAmes") are replaced by "model" and will be deprecated in a future release.
Added a function "gaussianRankCorr" that computes the Gaussian rank correlation matrix.
It is now possible to use Gaussian rank correlation (GRC = TRUE) in the "BSL" method for more robustness.
Other minor changes.

Second major release. Please note some arguments have been renamed.
Added a new method ("semiBSL") in the main function "bsl".
Now bsl returns an S4 class object instead of S3. The plot method gives an option for whether ggplot2 or R graphics (the default) will be used.
The simulation function and summary statistics function do not need to have a list as the second argument now.
The new bsl function uses "parallelArgs" instead of "parallel_packages", where users can specify all arguments supported by "foreach".
Code update for three examples: MA(2), multivariate G & K, and cell biology.