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. Clarifies that mixture mean and SD are always computed in closed form; only the density (used for plotting) is approximated numerically. Updated @examples to include a Beta informative prior case with suppressWarnings().

  • elicit_mixture() — added @details section documenting the same numerical density approximation behaviour at the lower level where mixtures are first constructed. Notes that suppressWarnings() should only be used after verifying the mixture is appropriate, not as a blanket silence.

  • Robust Mixture density plot — warning redirected from console to UI. The “Components have different distribution families. Mixture densities computed numerically.” warning is now intercepted and surfaced as an amber showNotification() in the Shiny app rather than printed to the R console. The warning is informative — it signals numerical approximation rather than closed-form density computation — and should be visible to the analyst. Previously it was suppressed entirely, which was not ideal.

bayprior 0.2.3

New features

  • Poisson data type in Power Prior Calibration — the power prior module now supports Poisson/count endpoints alongside Binary and Continuous. Uses the Gamma-Poisson conjugate update (same closed-form formula as Gamma-continuous).

  • Prior-data compatibility warning in Power Prior — an amber alert now appears when the active prior family is incompatible with the selected data type (e.g. Normal prior with binary data, Beta prior with Poisson data), guiding users to re-elicit with an appropriate family before calibrating.

  • Mahalanobis module limitations documented — the Multivariate Conflict Setup panel now shows an inline note clarifying that the test assumes multivariate Normal summary statistics, that proportion/HR endpoints should be entered on the log-odds/log scale, and that k > 2 endpoints are a planned extension.

Architecture

  • base_prior reactive — introduced shared$base_prior (written only by elicitation and pooling) alongside active_prior() (written by all modules). Sensitivity analysis, Robust Mixture, and Power Prior reset observers now watch base_prior() instead of active_prior(), eliminating the self-invalidation loop that wiped results immediately after they were produced.

  • Robust mixture compounding SD bug fixed — the robust prior fit handler now always uses base_prior() as the informative component. Previously, repeated clicks used the previous robust mixture as the input, causing the vague SD to compound exponentially across clicks.

Tests

  • Added tests/testthat/test-robust.R — 33 tests covering robust_prior(), sceptical_prior() (all three families and strength levels), calibrate_power_prior() (all methods and data types), elicit_exponential(), elicit_weibull(), plot.bayprior_power_prior(), and print.bayprior_power_prior().

  • Added tests/testthat/test-validation.R — 10 tests covering all four functions in validation_utils.R.

  • Added skip_on_ci() to all shinytest2 Chromote tests to prevent 30-second timeout failures in non-interactive and CI environments.

Documentation

  • Added @details to conflict_mahalanobis() documenting the multivariate Normal assumption, required scale transformations for proportion and HR endpoints, and the bivariate (k = 2) limitation.

bayprior 0.2.2

UX improvements

  • Three-state auto theme — theme now cycles Auto → Dark → Light on toggle. In Auto mode the app follows the OS prefers-color-scheme setting, which most operating systems tie to time of day. The button label shows the active state and whether it is following the OS or set manually (e.g. Auto (dark), Dark (manual)). Switching back to Auto removes the stored preference and resumes OS tracking.

  • Disabled downstream buttons — analysis buttons (Run Diagnostics, Run Sensitivity Analysis, Build robust/sceptical/power prior, Compute consensus prior) are now greyed out with a not-allowed cursor when no prior has been fitted. Hovering shows the tooltip “Fit a prior in Prior Elicitation first”. Buttons re-enable immediately when a prior is fitted. The Mahalanobis Conflict Setup button is intentionally excluded as it does not require an elicited prior.

  • Prior summary card in sidebar — the active prior badge now shows a mini stats table with Mean, SD, and 95% CrI (where available) below the distribution family and label. Updates reactively on every prior change. Mixture priors show Mean and SD only (no closed-form CrI).

  • Diagnostic tooltips — each conflict value box (Box p-value, Surprise index, Overlap coefficient) now has an info icon that displays a plain- language explanation on hover, useful for non-statistician stakeholders.

Bug fixes

  • Accepted updated plot snapshots for plot_tornado() and plot_sensitivity() following the axis label formatting change in v0.2.1 (snake_case -> title case).

Documentation

  • Sensitivity plot labels updated in plot_tornado() and plot_sensitivity() package functions directly (not just the Shiny layer), so label formatting applies when functions are called from R as well as in the app.

bayprior 0.2.1

UX improvements

  • Welcome tab now shows an SVG workflow diagram of all six analytical steps with colour-coded boxes and arrows.
  • Sidebar menu items now show a green glowing dot when each step is complete (elicitation, pooling, conflict, sensitivity, robust priors).
  • Export Report compliance checklist is now fully reactive — items update live with colour-coded icons (green check, amber minus, red X) and a ready/not- ready summary alert.
  • Package version (bayprior vX.X.X) now displayed in the sidebar footer.

Deployment fixes

  • Removed pkgload::load_all() from app.R — it was a development-only line that caused startup failure on shinyapps.io.
  • Added renv::snapshot(type = "explicit") to deployment workflow to prevent dev tools (pkgload, pkgbuild, callr, desc) from entering renv.lock.

Documentation

  • Information boxes on Welcome tab updated: Distributions 4 → 6, Conflict diagnostics → Data types (Binary · Continuous · Poisson · Survival).

bayprior 0.2.0

New features

  • Added elicit_exponential() — elicits an Exponential(rate) prior for constant hazard rates and Poisson rate priors. Supports "moments" (mean to rate), "rate" (direct), and "quantile" (1D optimisation) methods. The Exponential distribution is conjugate for Poisson and survival data via Gamma-Poisson/Exponential updating.

  • Added elicit_weibull() — elicits a Weibull(shape, scale) prior for non-constant hazard survival times (OS, PFS). Supports "moments" (2D Nelder-Mead), "params" (direct shape and scale), and "quantile" (2D Nelder-Mead) methods. Posteriors are approximated via Normal matching.

  • Added "poisson" data type to prior_conflict(), sensitivity_grid(), and sensitivity_cri(). Supports count/adverse-event-rate endpoints: list(type = "poisson", x = 12, n = 100) (events / person-time). Conjugate update: Gamma(shape + x, rate + n).

  • Added "survival" data type to prior_conflict(), sensitivity_grid(), and sensitivity_cri(). Supports OS/PFS hazard rate endpoints: list(type = "survival", x = 20, n = 400) (events / total follow-up time). Conjugate update: Gamma(shape + x, rate + n) (Gamma-Exponential).

  • Added density and x-range support for Exponential and Weibull distributions in plot.bayprior(). Previously these distributions rendered blank density plots; they now display correctly.

  • Added comprehensive validation layer across all modules:

    • .check_prior_data_compat() — warns when a prior family is atypical for the chosen data type (e.g. Beta prior + Poisson data).
    • .check_pooling_compat() — blocks pooling of distributions with incompatible supports (e.g. Beta + Normal); warns for same-support cross-family pooling (e.g. Gamma + Exponential).
    • .check_sensitivity_compat() — warns for single-parameter families (Exponential) and cross-family mixtures; blocks incompatible-support mixture sensitivity.
    • .validation_alert() — renders Bootstrap alert boxes for inline UI feedback in the Shiny app.

  • Sensitivity analysis is now fully independent of conflict diagnostics. The Sensitivity Analysis module has its own data entry UI (data type selector, events/n for binary, mean/SD/n for continuous, events/exposure for Poisson, events/follow-up for survival) that auto-populates the correct type from the active prior family. Previously, running conflict diagnostics was required before sensitivity analysis could proceed.

  • All Shiny modules now reset outputs automatically on input change, preventing stale results from being displayed alongside new inputs. Each module uses observeEvent(list(...)) watching all its relevant inputs to reset result reactives immediately. The active prior sidebar indicator is preserved during elicitation input changes (only the density plot and parameter table reset; shared$current_prior is retained until a new prior is explicitly fitted).

Bug fixes

  • Fixed prior_report() producing blank figures in Word (.docx) reports. knitr was writing absolute figure paths to the markdown; pandoc could not resolve them. Fixed by using fig.path = "figures/" (relative) with base.dir = tmp_dir for docx/pdf, and knitr::image_uri for HTML.

  • Fixed prior_report() failing for PDF with “tikzfill.image.sty not found”. Added tinytex::tlmgr_install() recommendation in documentation. The default-image-extension: pdf Quarto default is now overridden to png via YAML injection in the pre-executed markdown.

  • Fixed mixture prior hyperparameters section in prior_report.qmd rendering as literal markdown (## Hyperparameters not available) rather than as formatted text. Added #| results: asis to the fitted-params chunk and updated to show a component summary table for mixture priors.

  • Fixed mod_conflict_mahal.R containing a stale duplicate definition of mod_conflict_ui that was overriding the correct 4-choice version in mod_conflict.R (files sourced alphabetically, mahal comes after conflict). Removed the duplicate; mod_conflict_mahal.R now only contains mod_mahal_ui and mod_mahal_server.

Documentation

  • Updated bayprior-package.R to document all six distribution families, all four data types for conflict diagnostics and sensitivity, and the new validation functions.
  • Updated all six vignettes to cover Exponential and Weibull elicitation, Poisson and survival conflict diagnostics, independent sensitivity data entry, and the output reset behaviour.
  • Updated README with new badges, six-family distribution table, four-data-type conflict table, and updated Quick Start examples.

bayprior 0.1.2

Bug fixes

  • Fixed prior_report() failing on remote platforms (shinyapps.io, Posit Connect) due to Quarto spawning a subprocess that could not find the bayprior package. The report now uses a two-step approach: knitr::knit() executes all R code in the current session, then quarto::quarto_render(execute = FALSE) handles formatting via pandoc only. No R subprocess is spawned in the second step (#1).

  • Fixed mod_sensitivity: sensitivity analysis no longer requires conflict diagnostics to have been run first. The module now has its own data entry UI (data type, events/n for binary; mean/SD/n for continuous) that auto-selects the correct type based on the prior family (Beta → binary, others → continuous). Previously the fallback always used type = "continuous", causing conjugate updating to fail for Beta priors and returning NA for all grid evaluations.

  • Fixed “Using data from Conflict Diagnostics” label appearing even when no conflict diagnostics had been run. The label is now generated inside renderUI conditionally on shared$conflict.

  • Fixed non-ASCII characters (─, —) in R/app_ui.R causing an R CMD check WARNING. All box-drawing and em-dash characters replaced with ASCII equivalents.

  • Fixed prior_report() missing @param documentation for prior_plot, overlay_plot, tornado_plot, and heatmap_plot, causing an R CMD check WARNING about undocumented arguments.

New features

  • Added robust_prior, sceptical_prior, power_prior, robust_plot, sceptical_plot, and power_plot arguments to prior_report(). When supplied, robust and sensitivity priors appear as a dedicated section in the report with parameter tables and density plots. The compliance checklist row “Robust / sceptical prior computed” is automatically marked Complete.

  • Added bayprior hex logo to the Shiny app header and browser favicon. Logo is served from inst/app/www/favicon.png.

bayprior 0.1.1

Initial release

Prior Elicitation

  • Quantile matching, moment matching, and SHELF roulette for Beta, Normal, Gamma, and Log-Normal families
  • elicit_beta(), elicit_normal(), elicit_gamma(), elicit_lognormal(), elicit_roulette(), elicit_mixture()

Expert Pooling

  • Linear and logarithmic pooling with Bhattacharyya agreement diagnostics
  • aggregate_experts()

Conflict Diagnostics

  • Box p-value, surprise index, KL divergence, Bhattacharyya overlap
  • Multivariate Mahalanobis distance for co-primary endpoints
  • prior_conflict(), conflict_mahalanobis()

Sensitivity Analysis

  • Posterior quantity grid and credible interval sensitivity with tornado plots and influence heatmaps
  • sensitivity_grid(), sensitivity_cri()

Robust Priors

  • Robust mixture prior (Schmidli et al., 2014): robust_prior()
  • Sceptical prior (Spiegelhalter & Freedman, 1994): sceptical_prior()
  • Calibrated power prior (Ibrahim & Chen, 2000): calibrate_power_prior()

Reporting

  • HTML, PDF, and Word prior justification reports via Quarto: prior_report()
  • FDA/EMA regulatory compliance checklist

Documentation

  • Added Quarto GitHub Pages documentation site at https://ndohpenngit.github.io/bayprior/ with six rendered vignettes, a Changelog page, and a Cheat Sheet. Site auto-rebuilds on every push to main via GitHub Actions.

  • Updated all six vignettes to document new prior_report() arguments, the sensitivity analysis CrI toggle, and the robust priors report integration.

  • Updated README.md with live app badge, and Documentation section linking to the GitHub Pages site.

App

  • Full interactive Shiny application: run_app()
  • Dark/light mode toggle with localStorage persistence
  • bayprior hex logo in header and browser tab