openEBGM version history

v0.10.0

• Improved numerical stability of hyperparameter calculations.
• Now requires ‘numDeriv’ package for calculating Hessian matrices.
• Removed ‘param_lower’ and ‘param_upper’ arguments from hyperEM().
• Added ‘transformed’ argument to the likelihood functions to allow for optimization on the log & logit scales.
• Added ‘min_theta’ & ‘max_theta’ arguments to Qn(), ebgm(), quantBisect(), & ebScores(). Alpha values now must also be between one half & twice the value of the corresponding beta values. Values outside these ranges are replaced by the limits.
• Updates to vignettes, data, examples, etc.
• Fixed NOTES regarding documentation.

v0.9.1

• Ensured that no more than two threads are used for CRAN checks.
• Optimized examples for speed.
• Minor changes to vignettes.

v0.9.0

• Use the new special sentinel “_PACKAGE” for package documentation.
• Various minor updates (URLs, etc.).

v0.8.3

• Fixed unit testing problems caused by R’s future switch to stringsAsFactors = FALSE.

v0.8.2

• Adjusted calculation for expected counts using suggestion from Piotr Świnarski. Previously, calculation failed when marginal counts became too large for integer multiplication.

v0.8.1

• Corrected unit test failures for processRaw() resulting from base R changes to the sample() function.
• Added DEoptim::DEoptim() example to hyperparameter estimation vignette.

v0.8.0

• processRaw() now lists all strata when stratification is used.
• Added argument ‘list_ids’ to processRaw().

v0.7.0

• Added the autoSquash() function to automate data squashing.
• Changed exit condition for while loop in hyperEM(). hyperEM() now throws an error if the number of “stuck” or repeated estimates of theta exceeds 20 when using ‘method = “nlminb”’.
• Changed upper limit from 1 to 0.999 in hidden functions .updateThetaLL() and .updateThetaLLD(), which are called by hyperEM().

v0.6.0

• Changed ‘keep_bins’ formal argument in squashData() to ‘keep_pts’ for added flexibility.

v0.5.0

• Efficiency and code hygiene improvements to processRaw() and squashData().

v0.4.0

• Added the hyperEM() function to estimate hyperparameters using an implementation of the EM algorithm.

v0.3.0

• Added confidence intervals to autoHyper() and standard errors to autoHyper() and exploreHypers().
• processRaw() now returns Inf instead of 99999 when PRR results in division by zero.
• Fixed minor bug in exploreHypers().

v0.2.0

• Minor aesthetic changes to plot(), summary(), and print() methods.
• Relaxed convergence requirements for exploreHypers() and autoHyper().