fitPS development news

Purpose

This file records user-facing and developer-facing changes for fitPS. It is a release-note summary, not a commit-by-commit history.

fitPS 1.0.6.013

• Rationalise the Bayesian fitting API around method = “bayes” and bayesOptions$posteriorMethod.
• Add deprecated legacy aliases for numerical integration, MCMC, Laplace, and importance posterior methods.
• Preserve compatibility by translating legacy Bayesian method values into canonical bayesOptions.
• Add tests for Bayesian method alias translation and default option handling.
• Validated by the Stage 4.6.1.1 full package runner.

fitPS 1.0.6.011

• Added an internal importance-sampling helper for zero-inflated zeta Bayesian posteriors using the Laplace approximation as a proposal.
• Returned weighted samples, posterior means, covariance estimates, and diagnostics including effective sample size and maximum normalized weight.
• Added deterministic offline tests for weighted samples, seeded reproducibility, and fitZIDist dispatch through bayesOptions$posteriorMethod = “importance”.
• Added ignore/build-ignore coverage for generated built-package path files so package checks do not inspect runner artifacts.
• Ran the full package validation workflow for this package-impacting stage.

fitPS 1.0.6.010

• Repaired the Stage 4.4 numerical posterior grid file by restoring the missing bracket in the returned pi value.
• Kept the Stage 4.4 Laplace approximation work unchanged while making the installed R code parsable for roxygen documentation.
• Preserved ignore/build-ignore coverage for generated built-package path files so package checks do not inspect runner artifacts.
• Ran the full package validation workflow for this package-impacting repair stage.

fitPS 1.0.6.006

• Added Bayesian options plumbing so method = “bayes” can select posterior engines through bayesOptions$posteriorMethod.
• Stripped inherited names from scalar transform inputs and outputs before constructing working-scale vectors.
• Routed fitDist() numerical integration through method = “bayes” with posteriorMethod = “numerical” while retaining method = “integrate” as a legacy alias.
• Kept zero-inflated zeta MCMC available through posteriorMethod = “mcmc” until the numerical Stage 4 posterior is implemented.
• Kept deterministic offline test coverage unchanged while repairing the helper implementation.

fitPS 1.0.6.001

• Added the Stage 4.1 design audit for deterministic and semi-deterministic Bayesian posterior approximations for zero-inflated zeta fits.
• Recorded the recommended path for transformed posterior helpers, grid quadrature, Laplace diagnostics, importance sampling diagnostics, and plotting integration.
• Preserved existing Bayesian MCMC behavior and user-facing defaults; this lightweight documentation stage did not run package validation.

fitPS 1.0.5.008

• Stabilised the generated stage runner so controlled paths are staged one at a time.
• Prevented absent optional directories from masking git add failures and leaving new files untracked.
• Preserved the controlled commit scope while keeping the workflow compatible with package roots that do not contain every optional directory.
• Kept the no-ChatGPT-bundle workflow and completed-stage archive cleanup behaviour.
• Validated by the strict fitPS stage workflow.

fitPS 1.0.5.007

• Added plotPosterior() for posterior-density plots from Bayesian psFit objects.
• Supported zeta MCMC chains, zeta numerical posterior density functions, and zero-inflated MCMC chains for shape and pi.
• Kept existing plot.psFit() fitted-probability plots unchanged for backward compatibility.
• Added deterministic offline tests using small fake psFit objects rather than long MCMC runs.
• Validated by the strict fitPS stage workflow.

fitPS 1.0.5.003

• Added Stage 3.2 workflow documentation for the Windows Ghostscript R CMD check NOTE under dev/.
• Kept strict package validation while allowing only the known missing-Ghostscript PDF-size reduction NOTE in the stage runner.
• Documented why the Ghostscript NOTE is a local check-environment issue rather than a package failure.
• Preserved the Stage 3 1.0.5.xxx build convention, including one consumed build number per attempt.
• Validated by the strict fitPS stage workflow.

fitPS 1.0.5.002

• Added the Stage 3.1 Bayesian posterior plotting audit under dev/.
• Recommended a separate plotPosterior() API for posterior parameter-density plots while preserving plot.psFit() for fitted probabilities.
• Documented support requirements for MCMC-backed zeta and zero-inflated zeta fits, integrated zeta posterior densities, credible intervals, deterministic tests, and shape-parameterisation safeguards.
• Reset the Stage 3 development series to the 1.0.5.xxx build convention.
• Validated by the strict fitPS stage workflow.

fitPS 1.0.4.018

• Migrated the user-facing vignette sources from Sweave .Rnw files to R Markdown .Rmd files.
• Removed generated vignette build artifacts from the staged source tree so they can be regenerated by the package toolchain.
• Added rmarkdown to Suggests for the R Markdown vignette builder.
• Preserved the Stage 2 zeta shape wording while making the vignettes easier to maintain.

fitPS 1.0.4.017

• Removed user-facing discussion of VGAM’s shifted zeta parameterisation from help and vignette source text.
• Kept documentation focused on the fitPS shape parameter, where shape > 1.
• Corrected spelling, grammar, and punctuation issues in the vignette source using NZ English conventions.
• Regenerated help with devtools::document() during the strict stage workflow.

fitPS 1.0.4.016

• Cleaned roxygen comments and README wording for the Stage 2 zeta shape parameterisation documentation.
• Fixed spelling, punctuation, and grammar in the fitDist(), fitZIDist(), and predict.psFit() help source.
• Kept documentation on NZ English wording, including parameterisation and optimisation.
• Left generated help files to be refreshed by devtools::document() during the stage workflow.

fitPS 1.0.4.015

• Updated documentation so shape consistently refers to the standard zeta parameter alpha with shape > 1.

• Removed obsolete VGAM-shifted wording from fitDist() and fitZIDist() help text.

• Documented that the default Bayesian prior is placed on log(shape - 1), giving support only on valid standard-shape values.

• Added README guidance for users who compare fitPS results with VGAM zeta functions.

• Validated by the strict fitPS stage workflow. ## fitPS 1.0.4.014

• Refactored zeta and zero-inflated zeta workflows so fitPS shape means the standard zeta parameter alpha with shape > 1.

• Converted to VGAM’s shifted parameter only at VGAM boundaries using shape - 1.

• Added active regression tests for fitting, probability functions, prediction, fitted values, and random generation under the standard-shape convention.

• Validated by the strict fitPS stage workflow.

fitPS 1.0.4.012

• Added Stage 2.1.1 corrective notes for the zeta shape parameterisation workflow.
• Removed active target-behaviour tests from tests/testthat because they intentionally fail before the Stage 2.2 refactor.
• Preserved the standard-shape expectations in dev/ so Stage 2.2 can reinstate them with the implementation repair.
• Validated by the strict fitPS stage workflow.

fitPS 1.0.4.010

• Added README.md with installation, data-format, fitting, prediction, comparison, and development-check examples.
• Updated .gitignore to exclude the fitPS built-package path marker produced by stage runners.
• Kept the stage focused on documentation and local-build hygiene without changing package APIs.
• Validated by the strict stage 1.4 package workflow before commit.

fitPS 1.0.4.009

• Added NEWS.md as durable package release notes rather than a stage transcript.
• Recorded the stage 1 stabilization series, including baseline tests, build hygiene, start-value handling, and zero-inflated prediction fixes.
• Kept entries version-numbered and newest-first for future fitPS maintenance.
• Validated by the strict stage 1.3 package workflow before commit.

fitPS 1.0.4 development series

• Added baseline testthat infrastructure for core psData and psFit workflows.
• Added deterministic tests for data construction, CSV import, model fitting, prediction, and logLik.psFit().
• Repaired stage check issues by documenting the fitDist() prior argument and adding required stats imports.
• Cleaned package-build inputs by excluding local development files, generated archives, stage runners, scripts, and generated vignette artifacts from R package builds.
• Repaired start-value handling for fitDist() and fitZIDist() while preserving backward-compatible shape aliases.
• Repaired zero-inflated zeta prediction logic so fitted predictions use the model object’s pi component.
• Validated through the staged fitPS workflow before completed stage commits.