NEWS

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prLogistic 2.0.2 (2026-06-19)

• Added \value documentation to the print(), summary() and plot() methods.
• Replaced \dontrun{} with \donttest{} in examples, following CRAN feedback.

prLogistic 2.0.1

• 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

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 (2011-10-26)

• Added NAMESPACE and ChangeLog files.
• Replaced mean with colMeans() in pr.marginal().
• Modified vcov() structure for S4 compatibility.

prLogistic 1.0 (2011-07-23)

• Initial release.