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()). Root cause: cli output
functions detect the rendering environment via the RSTUDIO
/ POSITRON environment variables, which are absent in
callr subprocesses spawned by
rmarkdown::render(). All four print methods now route
output through internal .bp_* helpers that fall back to
plain cat() when no IDE or real terminal is detected, while
preserving full cli styled output in interactive sessions
(#40).Added tests/testthat/test-print-methods.R – 28 tests
covering all four print.bayprior* methods and all six
.bp_* internal helpers in non-interactive
(callr-like) contexts, and the as_prior()
constructor.
Expanded test-aggregation.R – added logarithmic
pooling tests for Beta, Gamma, and Log-Normal families; added
Bhattacharyya agreement tests for close vs distant expert pairs; added
three-expert logarithmic pooling.
Expanded test-conflict.R – added
conflict_mahalanobis() edge cases (no-conflict, severe
conflict, custom alpha, default labels); added
print.bayprior_conflict_mv() non-interactive context
test.
Expanded test-elicitation.R – added
elicit_exponential() rate method; added
elicit_weibull() params method; added
elicit_mixture() normal component and three-component
tests; added .validate_quantiles() error path
coverage.
Expanded test-robust.R – added
.power_prior_update() tests for Normal, Gamma-Poisson,
Gamma-continuous, and Log-Normal data types; added mixture prior power
update tests; added delta=1 full borrowing boundary test.
Expanded test-sensitivity.R – added Normal-Normal,
Gamma-Poisson, Poisson, and survival data type tests for
sensitivity_grid() and sensitivity_cri();
added plot_sensitivity() with posterior_sd and
prob_efficacy targets; added 80% vs 95% CrI width
comparison.
Expanded test-plots-snapshots.R – added functional
tests for plot.bayprior_conflict() and
plot_sensitivity() with cri_width and
prob_efficacy targets.
Overall non-Shiny test coverage increased from ~74% to 81.7%
(excluding Shiny modules, which require shinytest2 and are
covered separately).
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().
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