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.
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.
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).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.
.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.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.
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.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.
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.
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.
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.
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.
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/testthat/test-robust.R (33 tests).tests/testthat/test-validation.R (10 tests).skip_on_ci() to all shinytest2
Chromote tests.pkgload::load_all() from
app.R.renv::snapshot(type = "explicit") to deployment
workflow.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.
prior_report() blank figures in Word
reports.prior_report() PDF “tikzfill.image.sty not found”
error.mod_conflict_mahal.R stale duplicate definition
of mod_conflict_ui.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.
Added robust, sceptical, and power prior arguments to
prior_report().
Added bayprior hex logo to Shiny app header and browser favicon.
elicit_beta(),
elicit_normal(), elicit_gamma(),
elicit_lognormal(), elicit_roulette(),
elicit_mixture().aggregate_experts() with Bhattacharyya
diagnostics.prior_conflict(),
conflict_mahalanobis().sensitivity_grid(),
sensitivity_cri().robust_prior(),
sceptical_prior(),
calibrate_power_prior().prior_report() (HTML, PDF, Word).run_app().