NEWS
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
- 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.