18 add a broom augment like function

.Rbuildignore

@@ -13,3 +13,12 @@ manifest.json
 ^\.github$
 ^cran-comments\.md$
 ^CRAN-SUBMISSION$
+^\.claude$
+^CLAUDE\.MD$
+^ENHANCEMENTS\.md$
+^IMPLEMENTATION_PLAN\.md$
+^\.planning$
+^doc$
+^Meta$
+^README\.Rmd$
+^README\.html$

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: beeca
 Title: Binary Endpoint Estimation with Covariate Adjustment
-Version: 0.2.0
+Version: 0.3.0
 Authors@R: 
   c(person(given = "Alex", 
            family = "Przybylski", 
@@ -24,31 +24,36 @@ Authors@R:
            email = "dominic.magirr@novartis.com", 
            role = c("aut")
            ))
-Description: Performs estimation of marginal treatment effects for binary 
-  outcomes when using logistic regression working models with covariate 
-  adjustment (see discussions in Magirr et al (2024) <https://osf.io/9mp58/>). 
-  Implements the variance estimators of Ge et al (2011) <doi:10.1177/009286151104500409> 
+Description: Performs estimation of marginal treatment effects for binary
+  outcomes when using logistic regression working models with covariate
+  adjustment (see Magirr et al (2025) <doi:10.1002/pst.70021>).
+  Implements the variance estimators of Ge et al (2011) <doi:10.1177/009286151104500409>
   and Ye et al (2023) <doi:10.1080/24754269.2023.2205802>. 
 Maintainer: Alex Przybylski <alexander.przybylski@novartis.com>
 License: LGPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-Suggests: 
+Suggests:
+    cards,
+    ggplot2,
+    gt,
     knitr,
-    rmarkdown,
-    testthat (>= 3.0.0),
-    tidyr,
     marginaleffects,
     margins,
-    RobinCar (>= 0.3.0)
+    RobinCar (>= 0.3.0),
+    rmarkdown,
+    testthat (>= 3.0.0),
+    tidyr
 Config/testthat/edition: 3
 Depends: 
     R (>= 2.10)
 LazyData: true
-Imports: 
+Imports:
     dplyr,
+    generics,
     lifecycle,
+    rlang,
     sandwich,
     stats
 VignetteBuilder: knitr

NAMESPACE

@@ -1,15 +1,34 @@
 # Generated by roxygen2: do not edit by hand
 
+S3method(as_gt,beeca)
+S3method(as_gt,default)
+S3method(augment,beeca)
+S3method(plot,beeca)
+S3method(print,beeca)
 S3method(sanitize_model,default)
 S3method(sanitize_model,glm)
+S3method(summary,beeca)
+S3method(tidy,beeca)
 export(apply_contrast)
+export(as_gt)
+export(augment)
 export(average_predictions)
+export(beeca_fit)
+export(beeca_summary_table)
+export(beeca_to_cards_ard)
 export(estimate_varcov)
+export(format_pvalue)
 export(get_marginal_effect)
+export(plot_forest)
 export(predict_counterfactuals)
 export(sanitize_model)
+export(tidy)
 importFrom(dplyr,as_tibble)
+importFrom(generics,augment)
+importFrom(generics,tidy)
 importFrom(lifecycle,deprecated)
+importFrom(rlang,.data)
+importFrom(stats,binomial)
 importFrom(stats,cov)
 importFrom(stats,model.frame)
 importFrom(stats,model.matrix)

NEWS.md

@@ -1,3 +1,31 @@
+# beeca 0.3.0
+
+## New Features
+
+* `beeca_fit()`: Convenience function combining model fitting and marginal effect estimation in a single call.
+* `plot_forest()`: Forest plots for visualizing treatment effects with customizable confidence levels and styling.
+* `plot.beeca()`: S3 plot method for beeca objects.
+* `beeca_summary_table()`: Generate summary tables from beeca objects returning a data frame with arm statistics and treatment effects.
+* `beeca_to_cards_ard()`: Convert beeca results to Analysis Results Data format via cards.
+* `tidy.beeca()`: Tidy method returning treatment effect estimates as a tibble.
+* `augment.beeca()`: Augment method returning original data with fitted values and predictions.
+* `print.beeca()`: Concise print output showing treatment effect, standard error, Z-value, and p-value.
+* `summary.beeca()`: Comprehensive summary including marginal risks and treatment effects with confidence intervals.
+* `as_gt.beeca()`: Create publication-ready gt tables from beeca objects with customizable titles and footnotes.
+* `trial02_cdisc`: CDISC-compliant example dataset for clinical trial workflows.
+
+## Improvements
+
+* Updated Magirr et al. reference from OSF preprint to published version in Pharmaceutical Statistics (2025).
+* Added `rlang` and `generics` to package Imports for robust non-standard evaluation and S3 method support.
+* Added Suggests dependencies for enhanced visualization (`ggplot2`) and table formatting (`gt`, `cards`).
+* Enhanced vignettes with improved narrative flow, cross-referencing, and method guidance.
+
+## Bug Fixes
+
+* Fixed function name conflict in `plot_forest()` where base R's `diff()` was called incorrectly.
+* Replaced deprecated `geom_errorbarh()` with `geom_errorbar(orientation = "y")` in `plot_forest()` for ggplot2 4.0.0 compatibility.
+
 # beeca 0.2.0
 
 - Extensions to allow for more than two treatment arms in the model fit.

R/apply_contrast.R

@@ -41,8 +41,12 @@
 #' These appended component provide crucial information for interpreting
 #' the treatment effect using the specified contrast method.
 #'
+#' @seealso [predict_counterfactuals()] for generating counterfactual predictions
+#' @seealso [average_predictions()] for averaging counterfactual predictions
+#' @seealso [estimate_varcov()] for robust variance estimation
 #' @seealso [get_marginal_effect()] for estimating marginal effects directly
 #' from an original \code{\link[stats]{glm}} object
+#' @seealso [beeca_fit()] for streamlined analysis pipeline
 #'
 #' @examples
 #' trial01$trtp <- factor(trial01$trtp)