support rvar columns in data.frames

R/bayesfactor_parameters.R

@@ -89,15 +89,15 @@
 #' to match the `posterior`-type input:
 #'
 #' - **A numeric vector** - `prior` should also be a _numeric vector_, representing the prior-estimate.
 #' - **A data frame** - `prior` should also be a _data frame_, representing the prior-estimates, in matching column order.
 #'   - If `rvar_col` is specified, `prior` should be _the name of an `rvar` column_ that represents the prior-estimates.
 #' - **Supported Bayesian model (`stanreg`, `brmsfit`, etc.)**
 #'   - `prior` should be _a model an equivalent model with MCMC samples from the priors *only*_. See [unupdate()].
 #'   - If `prior` is set to `NULL`, [unupdate()] is called internally (not supported for `brmsfit_multiple` model).
 #' - **Output from a `{marginaleffects}` function** - `prior` should also be _an equivalent output_ from a `{marginaleffects}` function based on a prior-model
 #'  (See [unupdate()]).
 #' - **Output from an `{emmeans}` function**
 #'   - `prior` should also be _an equivalent output_ from an `{emmeans}` function based on a prior-model (See [unupdate()]).
 #'   - `prior` can also be _the original (posterior) model_, in which case the function
 #'      will try to "unupdate" the estimates (not supported if the estimates have undergone
 #'      any transformations -- `"log"`, `"response"`, etc. -- or any `regrid`ing).
@@ -185,7 +185,12 @@
 #' @author Mattan S. Ben-Shachar
 #'
 #' @export
-bayesfactor_parameters <- function(posterior, ...) {
+bayesfactor_parameters <- function(posterior,
+                                   prior = NULL,
+                                   direction = "two-sided",
+                                   null = 0,
+                                   ...,
+                                   verbose = TRUE) {
   UseMethod("bayesfactor_parameters")
 }
 
@@ -195,8 +200,8 @@
                                   prior = NULL,
                                   direction = "two-sided",
                                   null = 0,
-                                  verbose = TRUE,
-                                  ...) {
+                                  ...,
+                                  verbose = TRUE) {
   if (length(null) > 1L && verbose) {
     insight::format_alert("`null` is a range - computing a ROPE based Bayes factor.")
   }
@@ -217,8 +222,8 @@
                              prior = NULL,
                              direction = "two-sided",
                              null = rope_range(posterior, verbose = FALSE),
-                             verbose = TRUE,
-                             ...) {
+                             ...,
+                             verbose = TRUE) {
   if (length(null) < 2 && verbose) {
     insight::format_alert("'null' is a point - computing a Savage-Dickey (point null) Bayes factor.")
   }
@@ -251,15 +256,15 @@
                                            prior = NULL,
                                            direction = "two-sided",
                                            null = 0,
-                                           verbose = TRUE,
-                                           ...) {
+                                           ...,
+                                           verbose = TRUE) {
   # nm <- insight::safe_deparse(substitute(posterior)
 
   if (is.null(prior)) {
     prior <- posterior
     if (verbose) {
       insight::format_warning(
         "Prior not specified! Please specify a prior (in the form 'prior = distribution_normal(1000, 0, 1)') to get meaningful results."
       )
     }
   }
@@ -284,11 +289,11 @@
                                            prior = NULL,
                                            direction = "two-sided",
                                            null = 0,
-                                           verbose = TRUE,
                                            effects = c("fixed", "random", "all"),
                                            component = c("conditional", "location", "smooth_terms", "sigma", "zi", "zero_inflated", "all"),
                                            parameters = NULL,
-                                           ...) {
+                                           ...,
+                                           verbose = TRUE) {
   cleaned_parameters <- insight::clean_parameters(posterior)
   effects <- match.arg(effects)
   component <- match.arg(component)
@@ -330,8 +335,8 @@
                                            prior = NULL,
                                            direction = "two-sided",
                                            null = 0,
-                                           verbose = TRUE,
-                                           ...) {
+                                           ...,
+                                           verbose = TRUE) {
   cleaned_parameters <- insight::clean_parameters(posterior)
 
   samps <- .clean_priors_and_posteriors(posterior, prior,
@@ -363,8 +368,8 @@
                                            prior = NULL,
                                            direction = "two-sided",
                                            null = 0,
-                                           verbose = TRUE,
-                                           ...) {
+                                           ...,
+                                           verbose = TRUE) {
   samps <- .clean_priors_and_posteriors(
     posterior,
     prior,
@@ -404,8 +409,8 @@
                                               direction = "two-sided",
                                               null = 0,
                                               rvar_col = NULL,
-                                              verbose = TRUE,
-                                              ...) {
+                                              ...,
+                                              verbose = TRUE) {
   x_rvar <- .possibly_extract_rvar_col(posterior, rvar_col)
   if (length(x_rvar) > 0L) {
     cl <- match.call()
@@ -467,7 +472,7 @@
     class(bf_val)
   ))
 
   attr(bf_val, "hypothesis") <- null # don't change the name of this attribute - it is used only internally for "see" and printing
   attr(bf_val, "direction") <- direction
   attr(bf_val, "plot_data") <- .make_BF_plot_data(posterior, prior, direction, null, ...)
 
@@ -480,8 +485,8 @@
                                          prior = NULL,
                                          direction = "two-sided",
                                          null = 0,
-                                         verbose = TRUE,
-                                         ...) {
+                                         ...,
+                                         verbose = TRUE) {
   bayesfactor_parameters(
     .posterior_draws_to_df(posterior),
     prior = if (!is.null(prior)) .posterior_draws_to_df(prior),