From 8d44cd8e804bb27b704d4eb91cb70be5bad24372 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Wed, 21 Aug 2024 20:17:07 +0200
Subject: [PATCH] model_paramaters with exponentiate = TRUE not working with
 bootstrapped object from bootstrap_model Fixes #1004

---
 R/methods_base.R                |  8 ++++++--
 R/methods_posterior.R           |  4 ++++
 man/model_parameters.stanreg.Rd | 35 ++++++++++++++++++++-------------
 3 files changed, 31 insertions(+), 16 deletions(-)

diff --git a/R/methods_base.R b/R/methods_base.R
index 955660264..40afadda8 100644
--- a/R/methods_base.R
+++ b/R/methods_base.R
@@ -1,9 +1,13 @@
 #' @rdname model_parameters.stanreg
 #' @export
-model_parameters.data.frame <- function(model, as_draws = FALSE, verbose = TRUE, ...) {
+model_parameters.data.frame <- function(model,
+                                        as_draws = FALSE,
+                                        exponentiate = FALSE,
+                                        verbose = TRUE,
+                                        ...) {
   # treat data frame as bootstraps/posteriors?
   if (isTRUE(as_draws)) {
-    return(model_parameters.draws(model, verbose = verbose, ...))
+    return(model_parameters.draws(model, exponentiate = exponentiate, verbose = verbose, ...))
   }
   if (isTRUE(verbose)) {
     insight::format_warning(
diff --git a/R/methods_posterior.R b/R/methods_posterior.R
index 3b58b59bf..24e096659 100644
--- a/R/methods_posterior.R
+++ b/R/methods_posterior.R
@@ -8,6 +8,7 @@ model_parameters.draws <- function(model,
                                    test = "pd",
                                    rope_range = "default",
                                    rope_ci = 0.95,
+                                   exponentiate = FALSE,
                                    keep = NULL,
                                    drop = NULL,
                                    verbose = TRUE,
@@ -33,6 +34,9 @@ model_parameters.draws <- function(model,
     ...
   )
 
+  # exponentiate coefficients and SE/CI, if requested
+  params <- .exponentiate_parameters(params)
+
   attr(params, "ci") <- ci
   attr(params, "object_name") <- insight::safe_deparse_symbol(substitute(model))
   class(params) <- c("parameters_model", "see_parameters_model", class(params))
diff --git a/man/model_parameters.stanreg.Rd b/man/model_parameters.stanreg.Rd
index 3980d2292..ef2f3f623 100644
--- a/man/model_parameters.stanreg.Rd
+++ b/man/model_parameters.stanreg.Rd
@@ -27,7 +27,13 @@
   ...
 )
 
-\method{model_parameters}{data.frame}(model, as_draws = FALSE, verbose = TRUE, ...)
+\method{model_parameters}{data.frame}(
+  model,
+  as_draws = FALSE,
+  exponentiate = FALSE,
+  verbose = TRUE,
+  ...
+)
 
 \method{model_parameters}{brmsfit}(
   model,
@@ -61,6 +67,7 @@
   test = "pd",
   rope_range = "default",
   rope_ci = 0.95,
+  exponentiate = FALSE,
   keep = NULL,
   drop = NULL,
   verbose = TRUE,
@@ -171,6 +178,19 @@ the data frame is treated as posterior samples and handled similar to
 Bayesian models. All arguments in \code{...} are passed to
 \code{model_parameters.draws()}.}
 
+\item{exponentiate}{Logical, indicating whether or not to exponentiate the
+coefficients (and related confidence intervals). This is typical for
+logistic regression, or more generally speaking, for models with log or
+logit links. It is also recommended to use \code{exponentiate = TRUE} for models
+with log-transformed response values. \strong{Note:} Delta-method standard
+errors are also computed (by multiplying the standard errors by the
+transformed coefficients). This is to mimic behaviour of other software
+packages, such as Stata, but these standard errors poorly estimate
+uncertainty for the transformed coefficient. The transformed confidence
+interval more clearly captures this uncertainty. For \code{compare_parameters()},
+\code{exponentiate = "nongaussian"} will only exponentiate coefficients from
+non-Gaussian families.}
+
 \item{effects}{Should results for fixed effects, random effects or both be
 returned? Only applies to mixed models. May be abbreviated.}
 
@@ -188,19 +208,6 @@ argument - but no auxiliary parameters). For \code{component = "distributional"}
 (or \code{"auxiliary"}), components like \code{sigma}, \code{dispersion}, or \code{beta}
 (and other auxiliary parameters) are returned.}
 
-\item{exponentiate}{Logical, indicating whether or not to exponentiate the
-coefficients (and related confidence intervals). This is typical for
-logistic regression, or more generally speaking, for models with log or
-logit links. It is also recommended to use \code{exponentiate = TRUE} for models
-with log-transformed response values. \strong{Note:} Delta-method standard
-errors are also computed (by multiplying the standard errors by the
-transformed coefficients). This is to mimic behaviour of other software
-packages, such as Stata, but these standard errors poorly estimate
-uncertainty for the transformed coefficient. The transformed confidence
-interval more clearly captures this uncertainty. For \code{compare_parameters()},
-\code{exponentiate = "nongaussian"} will only exponentiate coefficients from
-non-Gaussian families.}
-
 \item{standardize}{The method used for standardizing the parameters. Can be
 \code{NULL} (default; no standardization), \code{"refit"} (for re-fitting the model
 on standardized data) or one of \code{"basic"}, \code{"posthoc"}, \code{"smart"},