NEWS

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ppwdeming 2.1.0 (2026-03-15)

• Correction to the storage in PWD_outlier function, leading to slightly different z-scores in the output.
• Output to PWD_outlier function was adjusted to include a dataframe element with more easily-readable output.
• The option to print (via the printem argument) during the function application was thus removed for simplicity.
• Updated the primary reference to the now-known publication date.

ppwdeming 2.0.0 (2026-01-09)

• Sizable update, refining functions to operate more efficiently.
• PWD_RL is no longer called by other functions, but it is retained for individual application.
• PWD_get_gh is the major update, in which the original search algorithm is replaced by an improved algorithm, which we refer to as the unified approach, focusing on the ratio rho=sigma/kappa. This results in a many-fold decrease in computing speed.
• The interconnected functions now also incorporate an optional starting point for all the parameters in the search algorithm: PWD_get_gh, PWD_inference, and PWD_outlier include options to initialize any of rho, alpha, beta, or the vector mu.
• PWD_known is also updated to reflect the full likelihood, leading to an improved algorithm using the optim function.
• Various housekeeping and grammatical edits were also integrated:
• Adjusted various functions to better handle missing values.
• Expand the reference to our paper by adding its title wherever we just have the DOI.
• Under PWD_get_gh Details, removed "reduces the number of optimized parameters..."
• Under PWD_inference Description, deleted "Currently".
• Under WD_Linnet Details, added "since the underlying precision profile models are not the same."
• Removed double-spacing in message-outputs (artifact of retaining "\n" from cat, no longer needed)
• Inside PWD_outlier function, removed extraneous text output and double-spacing.
• Under PWD_outlier values, edited the description of scalr.
• Clarification in details for PW_outlier.
• Clarification in the description of PWD_resi.
• Streamlined the package Description.
• Standardized the argument definitions using the parameter notation (versus words) and ended each with a period (as is standard) instead of a comma.
• Revised the Details section for PWD_get_gh to reflect the fewer number of parameters.
• Updated the Reference for the primary reference paper with the new doi and accepted status.
• The main change was updates to the PWD_resi function: removed Pvals, and edited documentation to match, reflecting removal from the submitted paper.
• Minor documentation edits, standardizing the annotation.
• Adjusted output name to be L instead of like for -2 log Likelihood.
• Added details for default initial values of parameters.
• Set printem defaults to reduce automatic output for PWD_outlier.
• Minor adjustments to documentation language.
• Added Argument notes and Details for PWD_get_gh documentation, defining rho as the ratio sigma/kappa.
• Fixed output formatting for PWD_outlier.

ppwdeming 1.0.6 (2025-09-09)

• revised individual function documentation to reference arXiv document by arXiv DOI in format doi:10.48550/arXiv.YYMM.NNNNN.
• adjusted one other doi reference correspondingly.

ppwdeming 1.0.5

• updated algorithm in function PWD_RL to better handle rare non-convergence.

ppwdeming 1.0.4

• revised primary reference in DESCRIPTION file to include author names and to have consistent format.
• For runnable (but >10s running) code in examples, replaced \dontrun with \donttest. This was applied to functions: PWD_inference, PWD_outlier.
• Removed the default console output by: (1) setting the printem to default to FALSE; and (2) replacing any print()/cat() with message(). This was applied for: PWD_get_gh, PWD_inference, PWD_known, PWD_outlier, PWD_resi, and WD_Linnet. Relevant items are elements on the list-value of the function.
• Replaced print() with message() and stop() for possible error in WD_General.

ppwdeming 1.0.3

• placed examples directly into function-building files;
• used \dontrun{} to keep runtime under 10s.

ppwdeming 1.0.2

• Corrected Github address.

ppwdeming 1.0.1

• Updated arXiv URL and Description to more closely meet auto-check.

ppwdeming 1.0.0

• Initial CRAN submission.

ppwdeming 0.99.0

• Minor updates to documentation.

ppwdeming 0.0.0.9012

• Most recently updated simplified examples