NEWS
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
ppwdeming 0.99.0
- Minor updates to documentation.
ppwdeming 0.0.0.9012
- Most recently updated simplified examples