prLogistic 2.0.2 (2026-06-12)
- Added documentation to the print(), summary() and plot()
methods.
- Replaced with in examples, following CRAN feedback.
prLogistic 2.0.1 (2026-06-06)
- CRAN resubmission. Single-quoted software names and added
parentheses to function names in the DESCRIPTION, and removed a broken
LICENSE link from the README, following CRAN feedback. No changes to
functionality.
prLogistic 2.0.0 (2025-06-05)
Breaking changes
- Minimum R version raised to 4.1.0.
prLogisticDelta() now takes a fitted model
object as its first argument (instead of a formula + dataset).
This aligns with standard R modelling conventions and allows the same
function to handle all supported model types.
- The
cluster and pattern arguments of the
old prLogisticDelta() are replaced by
standardisation. Use
standardisation = "conditional" (default) or
standardisation = "marginal".
- The
Hmisc dependency has been removed (it was
unused).
- Return value is now a
prLogistic S3 object rather than
a plain matrix, with print, summary,
coef, confint, and plot
methods.
New features
- Continuous covariates: reference value defaults to
the sample median (configurable via
ref_continuous = "mean"). The old implementation only
supported binary (0/1) predictors.
- Flexible baseline: use
ref_values = list(var = value) to set the reference value
of any predictor. This overrides both automatic defaults and the model’s
contrast coding.
- GEE support (
prLogisticGEE()):
prevalence ratios for longitudinal / repeated-measures data fitted with
geepack::geeglm(). Robust (sandwich) variance is used
automatically.
- Complex survey support
(
prLogisticSurvey()): prevalence ratios for data from
complex survey designs fitted with survey::svyglm().
Design-consistent variance is used automatically.
plot.prLogistic(): base-R forest plot for quick
visualisation of PR estimates and confidence intervals.
- Improved delta-method gradient for marginal standardisation: uses
the full sample-averaged counterfactual gradient (not a single fixed
row), giving more accurate variance estimates.
Bug fixes
- Fixed incorrect variance calculation in
pr_marginal()
for models with more than one continuous covariate.
- Negative confidence interval bounds are no longer silently truncated
at 0 without a warning; a diagnostic warning is now issued.
pr.conditional() no longer crashes on
glmerMod objects that use lme4::fixef()
instead of @beta (the slot accessor was fragile across lme4
versions).
Internal changes
- Complete rewrite using roxygen2 documentation.
- All internal functions prefixed with
. to avoid
namespace pollution.
- Comprehensive
testthat (edition 3) test suite covering
utilities, delta method, bootstrap, GEE, and survey model types.
- pkgdown website with
_pkgdown.yml configuration.
- GitHub Actions CI/CD workflow for multi-platform
R CMD check and automatic pkgdown deployment.
prLogistic 1.2 (2013-09-19)
- Replaced
lmer class with glmerMod for
compatibility with lme4 ≥ 1.0-4.
prLogistic 1.1 (2011-10-25)
- Added
NAMESPACE and ChangeLog files.
- Replaced
mean with colMeans() in
pr.marginal().
- Modified
vcov() structure for S4 compatibility.
prLogistic 1.0 (2010-03-29)