gtregression 1.1.0

Added

• Added an internal Data Prep workflow to the gtregression app, with explicit original/prepared analysis-data selection, quick starts, undo/redo, confirmed reset, prepared-data download, and reproducible preparation code. This code is included directly in gtregression and does not add gtstats as a dependency.
• Added observed-level reference category controls for categorical regression predictors in the app. Selected baselines are applied with reproducible factor releveling and included in generated and exported R scripts.
• Added publication-ready flextable output as the default table format across package table functions, while retaining gt and tibble-style outputs where appropriate.
• Added support for unquoted option values in common arguments, including model approaches and output formats, so users can write calls such as approach = logit and format = flextable.
• Added adjust_for support for adjusted multivariable workflows, including downstream regression plots and combined regression plots.
• Added adjusted-variable notes to regression plots and combined regression plots.
• Added optional model-fit statistics for uni_reg() and multi_reg() via model_stats = TRUE, with AIC, BIC, log-likelihood, deviance, pseudo R-squared, linear-model R-squared, and model N stored in $model_stats.
• Added approach = "firth" / approach = firth for Firth penalized logistic regression in uni_reg(), multi_reg(), stratified_uni_reg(), and stratified_multi_reg(), with OR tables and compatibility with regression plots and forest plot helpers.
• Added data_endometrial, a classic endometrial cancer dataset with a separation pattern, for teaching and testing Firth logistic regression.
• Added cox_reg() for Cox proportional hazards regression using time, event, exposures, and optional adjust_for, returning HR and adjusted HR tables.
• Added surv_reg() for parametric survival regression using time, event, exposures, optional adjust_for, and a selectable survival distribution, returning time-ratio tables.
• Added stratified Cox and parametric survival workflows through the stratifier argument in cox_reg() and surv_reg(), with stratum-specific N, event counts, and formatted regression tables.
• Added km_plot() for Kaplan-Meier survival curves with optional confidence intervals, censoring marks, log-rank p-values, and number-at-risk tables.
• Added more publication controls to km_plot(), including y-axis limits, percentage-scale display, optional grid removal, theme selection, confidence interval styling, and title/subtitle sizing for patchwork-style figure panels.
• Added km_risk_table() for standalone Kaplan-Meier risk tables at requested follow-up times, with at-risk, event, and censored counts.
• Added rmst_table() for restricted mean survival time summaries up to a chosen follow-up time, with optional two-group RMST difference.
• Added surv_model_compare() for comparing candidate parametric survival distributions by AIC, BIC, log-likelihood, scale, events, and N.
• Added plot_surv_fit() for visually comparing observed Kaplan-Meier curves with fitted parametric survival curves.
• Added surv_predict() for model-based survival probability predictions from fitted parametric survival regression models.
• Added survival_summary() for Kaplan-Meier median survival summaries with total N, events, censored counts, and publication-style table outputs.
• Added survival_quantiles() for Kaplan-Meier survival time quantiles, including event percentiles, corresponding survival probabilities, and confidence intervals.
• Added survival_prob() for Kaplan-Meier survival probabilities at fixed follow-up times, with at-risk, event, censored, and confidence interval columns.
• Added logrank_test() for formal comparison of Kaplan-Meier survival curves, with observed and expected events plus formatted p-value output.
• Added check_ph() for proportional hazards screening of Cox models using Schoenfeld residual tests, with flextable, gt, and tibble outputs.
• Added plot_model_fit() for visual model diagnostics from fitted lm/glm models and from models stored in uni_reg() and multi_reg() outputs.
• Added mediation_analysis() for regression-based mediation analysis with formatted direct, indirect, total, and proportion mediated tables.
• Added plot_mediation() for drawing a mediation path diagram from mediation_analysis() outputs.
• Added data_diabetes_mediation, a health-related diabetes teaching dataset for practicing obesity, glucose, and diabetes mediation workflows.
• Added compare_models() for publication-ready comparison of fitted gtregression model outputs, including AIC, BIC, log-likelihood, likelihood ratio statistics, primary exposure estimates, percent change, analysis-sample checks, and highlighted best-fit summaries.
• Added a guided candidate-model builder to the app’s Compare Models workflow. Users can name and fit two to six logistic, linear, count, Cox, or parametric survival candidates with model-specific exposures, adjustment variables, and optional interactions before producing a reproducible comparison table and complete copyable R code.
• Added save_forest() for exporting forest_reg() outputs with reproducible sizing across graphics devices and operating systems.
• Added automatic support for variable label attributes, including labels set with labelled::var_label(), across descriptive, regression, stratified, merged, plotted, and forest-style outputs.
• Added formatted display outputs for diagnostic and review functions including dissect(), select_models(), interaction_models(), and identify_confounder().
• Added Mantel-Haenszel comparison support to identify_confounder() to support confounding assessment alongside crude and adjusted model comparisons.
• Added manual case-study scripts under dev/manual-tests/ for real-time testing of logistic, linear, log-binomial, robust Poisson, Poisson, negative binomial, Cox, parametric survival, Firth, and mediation workflows.

Changed

• Improved descriptive_table(), uni_reg(), multi_reg(), stratified_uni_reg(), and stratified_multi_reg() documentation with clearer examples using package datasets.
• Improved pkgdown organization, homepage content, reference grouping, and rendered examples to better show publication-ready tables and plots.
• Improved README and pkgdown documentation with an explicit dependency overview showing the trusted R packages used for modelling, tidying, tables, Word export, figures, diagnostics, and forest plots.
• Improved merge_tables() so descriptive, crude, and adjusted tables can be combined more reliably, including when visible variable labels differ between input tables.
• Improved modify_table() so merged tables retain clean headers, spanners, and footnotes after relabelling.
• Improved forest_df() and forest_reg() support for descriptive summaries combined with univariable and multivariable regression outputs.
• Improved forest_df() and forest_reg() support for stratified regression outputs, including one-object stratified forest plots with highlighted stratum headers and preserved row order.
• Improved downstream survival support so cox_reg() and surv_reg() outputs work with plot_reg(), plot_reg_combine(), forest_df(), forest_reg(), merge_tables(), modify_table(), and select_models().
• Improved cox_reg() and surv_reg() consistency with the rest of the package: both now support single multivariable models, adjusted exposure workflows, interaction terms, stratified workflows, and coherent table labels.
• Improved compare_models() output so user-supplied or object-derived model names are displayed instead of generic model labels, and context-aware warnings distinguish same-sample comparisons from different-sample comparisons.
• Improved save_table() handling for wide Word tables by preferring landscape orientation before reducing font size, respecting minimum font sizes, and allowing users to turn width fitting off.
• Improved table footer and source-note spacing across formatted tables so abbreviations, adjustment notes, and caveats render more compactly in flextable, gt, Word, and pkgdown outputs.
• Improved Word export so flextable outputs are fitted to a standard Word page width by default, with save_docx(table_width = ...) available for custom document layouts.
• Improved select_models() output so formatted tables clearly report the model selection direction used.
• Improved repository organization for CRAN readiness, including excluding development-only manual scripts from package builds.

Fixed

• Fixed merge_tables() flextable headers so internal merge suffixes such as _p1, _p2, and _p3 are not shown in rendered tables.
• Fixed merge_tables() row alignment when descriptive and regression tables contain the same variables but different visible labels.
• Fixed modify_table() handling of merged flextable outputs so clean subheaders and group spanners are preserved.
• Fixed check_convergence() so failed multivariable model fits return a clear non-converged table rather than failing during table formatting.
• Fixed pkgdown reference metadata for internal print methods.
• Fixed save functions so files are written to a temporary directory when users do not provide an explicit destination, supporting CRAN-safe examples and tests.
• Fixed univariable Cox regression preprocessing so each exposure is fitted on complete cases for time, event, and the current exposure rather than using a single complete-case dataset across all exposures.
• Fixed Cox and parametric survival validation so zero follow-up times are allowed when accepted by the underlying survival model functions, while negative follow-up times remain invalid.
• Fixed regression and publication-ready outputs so user-supplied variable order is preserved rather than alphabetically reordered.
• Fixed forest plot merging so adjusted reference rows are left blank for variables that were not included in the adjusted model.
• Fixed forest_df() row-order handling after joins and merges so forest plots follow the same display order as the source regression table.
• Replaced CRAN-incompatible diabetes demo data that depended on removed mlbench Pima data with data_SynthDiabetes, a synthetic replacement based on mlbench::SynthDiabetes2 (mlbench >= 2.1-11), and regenerated all mediation teaching fixtures that depended on the prior dataset.

gtregression 1.0.0

• Initial release of gtregression.
• Added support for logit, log-binomial, linear, Poisson, robust Poisson, and negative binomial models.
• Added functions for confounder identification, model selection, diagnostics, plotting, and saving output.
• Added forest plot functions (plot_reg(), plot_reg_combine()).
• Added initial documentation and pkgdown homepage.

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