NEWS.md

In bayprior: Bayesian Prior Elicitation and Diagnostics for Clinical Trials

bayprior 0.3.2

Bug fixes

• sensitivity_grid() and sensitivity_cri() now moment-match a mixture prior's actual pooled mean and SD to a working prior, instead of silently analyzing only the dominant component by weight. Under equal or near-equal expert weights, this previously meant the sensitivity grid could reflect a single expert's prior without any indication that other experts' input had been dropped. A message now reports the working prior used; a warning is issued if the mixture's family cannot be moment-matched from mean/SD (Exponential, Weibull), in which case the dominant-component fallback is used and clearly identified.

• Fixed the pairwise Bhattacharyya agreement coefficient (aggregate_experts()) silently reporting near-total disagreement for any pair of experts using Lognormal, Exponential, or Weibull priors (or Gamma, via a related integration-range issue), regardless of how similar their actual priors were. This always triggered the "substantial expert disagreement" warning for these families.

• Fixed plot() on a bayprior_conflict object and plot_prior_likelihood() silently clipping the likelihood curve when it falls substantially outside the prior's own range. Both functions previously built their plotting grid from the prior's range alone; since these plots exist specifically to visualise prior-vs-data agreement or conflict, a genuinely severe conflict (the case the plot is meant to surface) could mean the likelihood curve was dropped from the visible range entirely. The grid now spans both the prior's and the likelihood's range.

• Fixed plot() on a bayprior_conflict object erroring for any prior other than Beta (Normal, Gamma, Lognormal, Exponential, Weibull), and the plotted x-axis range being incorrectly clamped to [0, 1] regardless of the prior's actual support.

• Fixed plot_prior_likelihood()'s likelihood curve for Poisson/count and survival data types being centred at the raw event count rather than the event rate, and referencing an SD field that is never collected for these data types (only continuous data has one). This affected the "Prior-Likelihood-Posterior overlay" panel in the Shiny app's Conflict Diagnostics tab for any Poisson or survival analysis.

• Fixed .conjugate_update() aborting for any prior/data-type pairing with no exact conjugate formula (e.g. a Beta prior with continuous data), which contradicted the compatibility warning shown elsewhere in the package promising the analysis would proceed via a Normal approximation. Now falls back to a Normal-approximation posterior instead, consistent with that promise. This also fixes the Shiny app's "Prior-Likelihood-Posterior overlay" panel erroring ("Could not update any mixture component with the supplied data") for a pooled mixture prior with any component/data-type pairing lacking an exact conjugate update.

• Removed a duplicate, dead definition of sensitivity_cri() that had fallen out of sync with the version actually in use; the live version had the same mixture-handling issue described above, now fixed.

• Fixed a crash (argument is of length zero) in mixture-handling logic when called on a logarithmically-pooled prior, whose fit_summary$sd is NULL by design.

• sensitivity_grid()'s Shiny UI parameter-range defaults now use the same working-prior logic as the underlying function, so the interface's suggested ranges no longer risk diverging from what is actually analyzed.

bayprior 0.3.1

Documentation improvements

• Corrected the title of the FDA's 2026 draft guidance as cited throughout the package documentation, vignettes, Shiny app, and regulatory report template. The guidance is titled "Use of Bayesian Methodology in Clinical Trials of Drug and Biological Products."

• Updated the EMA reference in the regulatory report, Shiny app, and vignettes to reflect the agency's current published position: a 2026 concept paper proposing the development of guidance on Bayesian methods (EMA/CHMP/1813/2026), with the full reflection paper expected in 2027-2028.

• Corrected the FDA guidance section references in the regulatory-reporting vignette's compliance-checklist table to match the guidance document's structure (Sections V.A, V.C, V.D, V.F, and VIII.B).

• Clarified attribution of the sceptical prior and the enthusiastic/ sceptical sensitivity pairing to Spiegelhalter & Freedman (1994).

• Removed an inaccurate cross-reference to ICH E9(R1) in the sensitivity-analysis vignette; ICH E9(R1) addresses estimands and intercurrent events rather than prior specification.

• Aligned the package website overview (index.qmd) with the README's description of related packages.

bayprior 0.3.0

Bug fixes

• Fixed print.bayprior(), print.bayprior_conflict(), print.bayprior_conflict_mv(), and print.bayprior_power_prior() producing no output when called inside rmarkdown::render(), knitr vignettes, or any non-interactive R subprocess (e.g. callr::r()). Output now renders correctly in both interactive and non-interactive sessions (#40).

bayprior 0.2.12

CRAN reviewer fixes (v0.2.11 review)

• Wrapped software name in single quotes in DESCRIPTION: 'Shiny', per CRAN policy on package and software name formatting.

• Added six methodology references to DESCRIPTION in CRAN-required format (authors, year, doi/ISBN): O'Hagan et al. (2006), Box (1980), Oakley and O'Hagan (2010), Schmidli et al. (2014), Ibrahim and Chen (2000), Spiegelhalter et al. (1994).

• Added \value documentation tag to four exported print methods: print.bayprior(), print.bayprior_conflict(), print.bayprior_conflict_mv(), and print.bayprior_power_prior(). Each documents that the function returns the input object invisibly, called for its side effect of printing a formatted summary.

• Restored par() settings after use in the robust-priors vignette. The par(oldpar) call was incorrectly placed before the for loop and legend(). Moved to after all plotting operations, per CRAN policy.

• Removed LICENSE file and | file LICENSE from DESCRIPTION. The GPL-3 licence does not require an additional file.

• Updated inst/WORDLIST: added biom, doi, and ss -- fragments extracted by the spell checker from DOI strings in the DESCRIPTION references field.

bayprior 0.2.11

CRAN resubmission fix

• Corrected malformed .Rbuildignore pattern for cran-comments.md. The pattern ^^cran-comments\\.md$$ (double caret, double dollar) never matched the file, so it was included in every previous tarball. Fixed to the correct regex ^cran-comments\.md$ and verified absent from the v0.2.11 tarball.

bayprior 0.2.10

CRAN resubmission fixes

• Switched Language from en-US to en-GB in DESCRIPTION to correctly reflect the British English used throughout the package (sceptical, colour, behaviour, normalised etc.). British spellings are now handled by the en-GB dictionary and no longer need to be in inst/WORDLIST.

• Replaced "Kullback-Leibler divergence" in DESCRIPTION with "information divergence". Kullback and Leibler are proper nouns not in any standard dictionary and cannot be resolved via inst/WORDLIST for CRAN's DESCRIPTION spell check.

• Updated inst/WORDLIST: added HR, Inf, Var, heatmaps, prior's, R's, VignetteBuilder, Poisson, etc. Removed British spellings now covered by en-GB dictionary.

bayprior 0.2.9

CRAN resubmission fix

• Added 'Kullback' and 'Leibler' to inst/WORDLIST. These are proper nouns (the Kullback-Leibler divergence is named after statisticians Solomon Kullback and Richard Leibler) and are standard terminology in Bayesian statistics. Flagged as possibly misspelled by CRAN's automated pre-check in v0.2.8.

bayprior 0.2.8

CRAN resubmission fixes

• Resolved the persistent "Package has a VignetteBuilder field but no prebuilt vignette index" NOTE that appeared across v0.2.4--v0.2.7. Root cause: ^build$ was incorrectly added to .Rbuildignore, which excluded build/vignette.rds from the tarball. This file is generated by R CMD build during vignette processing and is the exact file R CMD check looks for (tools/R/QC.R). Removing ^build$ from .Rbuildignore resolves the note permanently.

• Revised Description field in DESCRIPTION to remove all regulatory body references and abbreviations. The description now describes what the software does. Regulatory context is retained in vignettes and README.

bayprior 0.2.7

CRAN resubmission fixes

• Resolve EMA in DESCRIPTION. The EMA acronym (European Medicines Agency) was flagged as a possible misspelling in the DESCRIPTION file, causing a CRAN resubmission WARNING.

• Updated inst/WORDLIST.

bayprior 0.2.6

CRAN resubmission fixes

• Updated inst/WORDLIST to include all package-specific terms flagged by the spelling checker, and package infrastructure terms (golem, shinydashboard, knitr, pandoc). Resolved spelling.Rout vs spelling.Rout.save mismatch in tests.

• Changed Language field in DESCRIPTION from en-US to en-GB to reflect the package's consistent use of British English spelling throughout documentation and vignettes (sceptical, colour, behaviour, centred).

• Added prebuilt vignette index (inst/doc/index.html) to resolve the "no prebuilt vignette index" NOTE reported by CRAN's automated pre-check on Windows and Debian.

bayprior 0.2.5

CRAN resubmission fixes

• Removed all Unicode characters from R source files that caused LaTeX PDF generation errors on CRAN's Windows and Debian build servers. Affected characters: U+2014 em dash (replaced with --), U+2212 Unicode minus (replaced with -), U+221E infinity (replaced with Inf), U+2019/U+2018 curly quotes (replaced with '), and others. All replacements made in comments and roxygen documentation only -- no functional code changed.

• Added inst/WORDLIST declaring package-specific acronyms (EMA, FDA, CrI, MAP, Mahalanobis, Bhattacharyya, SHELF, PFS, PK) that were flagged as possibly misspelled in the DESCRIPTION file.

• Rebuilt prebuilt vignette index via devtools::build_vignettes() to resolve the "no prebuilt vignette index" NOTE.

bayprior 0.2.4

Documentation & UX

• robust_prior() -- added @details section explaining that the vague component is always Normal, making cross-family mixtures (e.g. Beta + Normal) structurally inevitable for non-Normal informative priors.

• elicit_mixture() -- added @details section documenting the numerical density approximation behaviour at the lower level where mixtures are first constructed.

• Robust Mixture density plot warning redirected from console to UI. The "Components have different distribution families. Mixture densities computed numerically." warning is now surfaced as an amber showNotification() in the Shiny app.

bayprior 0.2.3

New features

• Poisson data type in Power Prior Calibration.
• Prior-data compatibility warning in Power Prior module.
• Mahalanobis module limitations documented inline.

Architecture

• Introduced shared$base_prior reactive to eliminate the self-invalidation loop that wiped sensitivity/robust/power prior results immediately after they were produced.

• Fixed robust mixture compounding SD bug -- repeated clicks no longer compound the vague SD exponentially.

Tests

• Added tests/testthat/test-robust.R (33 tests).
• Added tests/testthat/test-validation.R (10 tests).
• Added skip_on_ci() to all shinytest2 Chromote tests.

bayprior 0.2.2

UX improvements

• Three-state auto theme (Auto / Dark / Light) following OS preference.
• Disabled downstream buttons when no prior has been fitted.
• Prior summary card in sidebar showing Mean, SD, and 95% CrI.
• Diagnostic tooltips on conflict value boxes.

bayprior 0.2.1

UX improvements

• Welcome tab SVG workflow diagram.
• Sidebar completion indicators (green glowing dot per completed step).
• Export Report compliance checklist is fully reactive.
• Package version displayed in sidebar footer.

Deployment fixes

• Removed pkgload::load_all() from app.R.
• Added renv::snapshot(type = "explicit") to deployment workflow.

bayprior 0.2.0

New features

• elicit_exponential() -- Exponential(rate) prior for hazard rates and Poisson rate priors. Supports moments, rate, and quantile methods.

• elicit_weibull() -- Weibull(shape, scale) prior for survival times. Supports moments, params, and quantile methods.

• "poisson" and "survival" data types in prior_conflict(), sensitivity_grid(), and sensitivity_cri().

• Density and x-range support for Exponential and Weibull in plot.bayprior().

• Comprehensive validation layer: .check_prior_data_compat(), .check_pooling_compat(), .check_sensitivity_compat(), .validation_alert().

• Sensitivity analysis fully independent of conflict diagnostics.

• All Shiny modules reset outputs automatically on input change.

Bug fixes

• Fixed prior_report() blank figures in Word reports.
• Fixed prior_report() PDF "tikzfill.image.sty not found" error.
• Fixed mixture prior hyperparameters section rendering as literal markdown.
• Fixed mod_conflict_mahal.R stale duplicate definition of mod_conflict_ui.

bayprior 0.1.2

Bug fixes

• Fixed prior_report() failing on remote platforms due to Quarto spawning a subprocess that could not find the bayprior package.

• Fixed mod_sensitivity always using type = "continuous" regardless of prior family.

• Fixed non-ASCII characters in R/app_ui.R causing R CMD check WARNING.

• Fixed prior_report() missing @param documentation for plot arguments.

New features

• Added robust, sceptical, and power prior arguments to prior_report().

• Added bayprior hex logo to Shiny app header and browser favicon.

bayprior 0.1.1

Initial release

• Prior elicitation: elicit_beta(), elicit_normal(), elicit_gamma(), elicit_lognormal(), elicit_roulette(), elicit_mixture().
• Expert pooling: aggregate_experts() with Bhattacharyya diagnostics.
• Conflict diagnostics: prior_conflict(), conflict_mahalanobis().
• Sensitivity analysis: sensitivity_grid(), sensitivity_cri().
• Robust priors: robust_prior(), sceptical_prior(), calibrate_power_prior().
• Reporting: prior_report() (HTML, PDF, Word).
• Shiny application: run_app().
• GitHub Pages documentation site.

bayprior documentation built on Aug. 27, 2026, 1:09 a.m.