Fix verbose parameter not being passed to insight::get_parameters() (#744)

* Initial plan

* Fix verbose parameter passing to insight::get_parameters in utils_hdi_ci.R and rope.R

Co-authored-by: IndrajeetPatil <[email protected]>

* Fix verbose parameter in bci.R, eti.R, hdi.R, spi.R, equivalence_test.R, and ci.R

Co-authored-by: IndrajeetPatil <[email protected]>

* Fix verbose parameter in p_rope.R and si.R

Co-authored-by: IndrajeetPatil <[email protected]>

---------

Co-authored-by: copilot-swe-agent[bot] <[email protected]>
Co-authored-by: IndrajeetPatil <[email protected]>

Author: Copilot

R/bci.R

@@ -102,7 +102,7 @@ bci.bamlss <- function(x,
                        component = "all",
                        verbose = TRUE,
                        ...) {
-  d <- insight::get_parameters(x, component = component)
+  d <- insight::get_parameters(x, component = component, verbose = verbose)
   dat <- .compute_interval_dataframe(x = d, ci = ci, verbose = verbose, fun = "bci")
   attr(dat, "data") <- insight::safe_deparse_symbol(substitute(x))
   dat
@@ -111,7 +111,7 @@ bci.bamlss <- function(x,
 
 #' @export
 bci.bcplm <- function(x, ci = 0.95, verbose = TRUE, ...) {
-  d <- insight::get_parameters(x)
+  d <- insight::get_parameters(x, verbose = verbose)
   dat <- .compute_interval_dataframe(x = d, ci = ci, verbose = verbose, fun = "bci")
   attr(dat, "data") <- insight::safe_deparse_symbol(substitute(x))
   dat
@@ -169,7 +169,7 @@ bci.sim <- function(x, ci = 0.95, parameters = NULL, verbose = TRUE, ...) {
 
 #' @export
 bci.emmGrid <- function(x, ci = 0.95, verbose = TRUE, ...) {
-  xdf <- insight::get_parameters(x)
+  xdf <- insight::get_parameters(x, verbose = verbose)
   dat <- bci(xdf, ci = ci, verbose = verbose, ...)
   dat <- .append_datagrid(dat, x, long = length(ci) > 1L)
   attr(dat, "object_name") <- insight::safe_deparse_symbol(substitute(x))
@@ -208,7 +208,8 @@ bci.stanreg <- function(x,
         x,
         effects = effects,
         component = component,
-        parameters = parameters
+        parameters = parameters,
+        verbose = verbose
       ),
       ci = ci,
       verbose = verbose,
@@ -246,7 +247,8 @@ bci.brmsfit <- function(x,
         x,
         effects = effects,
         component = component,
-        parameters = parameters
+        parameters = parameters,
+        verbose = verbose
       ),
       ci = ci,
       verbose = verbose,

R/ci.R

@@ -361,7 +361,7 @@ ci.bamlss <- function(x,
                       verbose = TRUE,
                       ...) {
   ci(
-    insight::get_parameters(x, component = component),
+    insight::get_parameters(x, component = component, verbose = verbose),
     ci = ci,
     method = method,
     verbose = verbose,

R/equivalence_test.R

@@ -222,7 +222,7 @@ equivalence_test.rvar <- equivalence_test.draws
 
 #' @export
 equivalence_test.emmGrid <- function(x, range = "default", ci = 0.95, verbose = TRUE, ...) {
-  xdf <- insight::get_parameters(x)
+  xdf <- insight::get_parameters(x, verbose = verbose)
   out <- equivalence_test(xdf, range = range, ci = ci, verbose = verbose, ...)
   out <- .append_datagrid(out, x)
   attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))

R/eti.R

@@ -124,7 +124,7 @@ eti.mcmc <- function(x, ci = 0.95, verbose = TRUE, ...) {
 
 #' @export
 eti.bamlss <- function(x, ci = 0.95, component = "all", verbose = TRUE, ...) {
-  d <- insight::get_parameters(x, component = component)
+  d <- insight::get_parameters(x, component = component, verbose = verbose)
   dat <- .compute_interval_dataframe(x = d, ci = ci, verbose = verbose, fun = "eti")
   attr(dat, "data") <- insight::safe_deparse_symbol(substitute(x))
   dat
@@ -133,7 +133,7 @@ eti.bamlss <- function(x, ci = 0.95, component = "all", verbose = TRUE, ...) {
 
 #' @export
 eti.bcplm <- function(x, ci = 0.95, verbose = TRUE, ...) {
-  d <- insight::get_parameters(x)
+  d <- insight::get_parameters(x, verbose = verbose)
   dat <- .compute_interval_dataframe(x = d, ci = ci, verbose = verbose, fun = "eti")
   attr(dat, "data") <- insight::safe_deparse_symbol(substitute(x))
   dat
@@ -191,7 +191,7 @@ eti.sim <- function(x, ci = 0.95, parameters = NULL, verbose = TRUE, ...) {
 
 #' @export
 eti.emmGrid <- function(x, ci = 0.95, verbose = TRUE, ...) {
-  xdf <- insight::get_parameters(x)
+  xdf <- insight::get_parameters(x, verbose = verbose)
   dat <- eti(xdf, ci = ci, verbose = verbose, ...)
   dat <- .append_datagrid(dat, x, long = length(ci) > 1L)
   attr(dat, "object_name") <- insight::safe_deparse_symbol(substitute(x))
@@ -232,7 +232,8 @@ eti.stanreg <- function(x,
         x,
         effects = effects,
         component = component,
-        parameters = parameters
+        parameters = parameters,
+        verbose = verbose
       ),
       ci = ci,
       verbose = verbose,
@@ -269,7 +270,8 @@ eti.brmsfit <- function(x,
         x,
         effects = effects,
         component = component,
-        parameters = parameters
+        parameters = parameters,
+        verbose = verbose
       ),
       ci = ci,
       verbose = verbose,

R/hdi.R

@@ -240,7 +240,7 @@ hdi.bamlss <- function(x,
                        verbose = TRUE,
                        ...) {
   ci_fun <- .check_ci_fun(list(...))
-  d <- insight::get_parameters(x, component = component)
+  d <- insight::get_parameters(x, component = component, verbose = verbose)
   dat <- .compute_interval_dataframe(x = d, ci = ci, verbose = verbose, fun = ci_fun)
   dat <- .add_clean_parameters_attribute(dat, x)
   attr(dat, "data") <- insight::safe_deparse_symbol(substitute(x))
@@ -261,7 +261,7 @@ hdi.mcmc <- function(x, ci = 0.95, verbose = TRUE, ...) {
 #' @export
 hdi.bcplm <- function(x, ci = 0.95, verbose = TRUE, ...) {
   ci_fun <- .check_ci_fun(list(...))
-  d <- insight::get_parameters(x)
+  d <- insight::get_parameters(x, verbose = verbose)
   dat <- .compute_interval_dataframe(x = d, ci = ci, verbose = verbose, fun = ci_fun)
   attr(dat, "data") <- insight::safe_deparse_symbol(substitute(x))
   dat
@@ -321,7 +321,7 @@ hdi.sim <- function(x, ci = 0.95, parameters = NULL, verbose = TRUE, ...) {
 
 #' @export
 hdi.emmGrid <- function(x, ci = 0.95, verbose = TRUE, ...) {
-  xdf <- insight::get_parameters(x)
+  xdf <- insight::get_parameters(x, verbose = verbose)
   out <- hdi(xdf, ci = ci, verbose = verbose, ...)
   out <- .append_datagrid(out, x, long = length(ci) > 1L)
   attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
@@ -363,7 +363,8 @@ hdi.stanreg <- function(x,
         x,
         effects = effects,
         component = component,
-        parameters = parameters
+        parameters = parameters,
+        verbose = verbose
       ),
       ci = ci,
       verbose = verbose,
@@ -403,7 +404,8 @@ hdi.brmsfit <- function(x,
         x,
         effects = effects,
         component = component,
-        parameters = parameters
+        parameters = parameters,
+        verbose = verbose
       ),
       ci = ci,
       verbose = verbose,

R/p_rope.R

@@ -75,7 +75,7 @@ p_rope.rvar <- p_rope.draws
 
 #' @export
 p_rope.emmGrid <- function(x, range = "default", verbose = TRUE, ...) {
-  xdf <- insight::get_parameters(x)
+  xdf <- insight::get_parameters(x, verbose = verbose)
   out <- p_rope(xdf, range = range, verbose = verbose)
   out <- .append_datagrid(out, x)
   attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))

R/rope.R

@@ -344,7 +344,7 @@ rope.emmGrid <- function(x,
                          complement = FALSE,
                          verbose = TRUE,
                          ...) {
-  xdf <- insight::get_parameters(x)
+  xdf <- insight::get_parameters(x, verbose = verbose)
   dat <- rope(
     xdf,
     range = range,
@@ -405,7 +405,7 @@ rope.BFBayesFactor <- function(x,
     range <- rope_range(x, verbose = verbose)
   }
   out <- rope(
-    insight::get_parameters(x),
+    insight::get_parameters(x, verbose = verbose),
     range = range,
     ci = ci,
     ci_method = ci_method,
@@ -476,7 +476,7 @@ rope.bcplm <- function(x,
                        verbose = TRUE,
                        ...) {
   out <- rope(
-    insight::get_parameters(x),
+    insight::get_parameters(x, verbose = verbose),
     range = range,
     ci = ci,
     ci_method = ci_method,
@@ -528,7 +528,8 @@ rope.stanreg <- function(x,
       x,
       effects = effects,
       component = component,
-      parameters = parameters
+      parameters = parameters,
+      verbose = verbose
     ),
     range = range,
     ci = ci,
@@ -609,6 +610,7 @@ rope.brmsfit <- function(x,
             effects = effects,
             component = component,
             parameters = parameters,
+            verbose = verbose,
             ...
           ),
           range = range[[dv_item]],
@@ -636,7 +638,7 @@ rope.brmsfit <- function(x,
     )
   } else {
     rope_data <- rope(
-      insight::get_parameters(x, effects = effects, component = component, parameters = parameters),
+      insight::get_parameters(x, effects = effects, component = component, parameters = parameters, verbose = verbose),
       range = range,
       ci = ci,
       ci_method = ci_method,
@@ -673,7 +675,7 @@ rope.sim.merMod <- function(x,
   }
 
   rope_list <- lapply(c("fixed", "random"), function(.x) {
-    parms <- insight::get_parameters(x, effects = .x, parameters = parameters)
+    parms <- insight::get_parameters(x, effects = .x, parameters = parameters, verbose = verbose)
 
     getropedata <- .prepare_rope_df(parms, range, ci, ci_method, complement, verbose)
     tmp <- getropedata$tmp
@@ -742,7 +744,7 @@ rope.sim <- function(x,
     insight::format_error("`range` should be 'default' or a vector of 2 numeric values (e.g., c(-0.1, 0.1)).")
   }
 
-  parms <- insight::get_parameters(x, parameters = parameters)
+  parms <- insight::get_parameters(x, parameters = parameters, verbose = verbose)
   getropedata <- .prepare_rope_df(parms, range, ci, ci_method, complement, verbose)
 
   dat <- getropedata$tmp

R/si.R

@@ -184,7 +184,7 @@ si.predictions <- si.emmGrid
 
 #' @export
 si.stanfit <- function(posterior, prior = NULL, BF = 1, verbose = TRUE, effects = "fixed", ...) {
-  out <- si(insight::get_parameters(posterior, effects = effects),
+  out <- si(insight::get_parameters(posterior, effects = effects, verbose = verbose),
     prior = prior, BF = BF, verbose = verbose
   )
   attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(posterior))

R/spi.R

@@ -161,7 +161,7 @@ spi.sim <- function(x, ci = 0.95, parameters = NULL, verbose = TRUE, ...) {
 
 #' @export
 spi.emmGrid <- function(x, ci = 0.95, verbose = TRUE, ...) {
-  xdf <- insight::get_parameters(x)
+  xdf <- insight::get_parameters(x, verbose = verbose)
   out <- spi(xdf, ci = ci, verbose = verbose, ...)
   out <- .append_datagrid(out, x, long = length(ci) > 1L)
   attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(x))
@@ -203,7 +203,8 @@ spi.stanreg <- function(x,
         x,
         effects = effects,
         component = component,
-        parameters = parameters
+        parameters = parameters,
+        verbose = verbose
       ),
       ci = ci,
       verbose = verbose,

R/utils_hdi_ci.R

@@ -80,13 +80,13 @@
   random <- random.data <- NULL
 
   if (effects %in% c("fixed", "all")) {
-    fixed.data <- insight::get_parameters(x, effects = "fixed", parameters = parameters)
+    fixed.data <- insight::get_parameters(x, effects = "fixed", parameters = parameters, verbose = verbose)
     fixed <- .compute_interval_dataframe(fixed.data, ci, verbose, fun)
     fixed$Group <- "fixed"
   }
 
   if (effects %in% c("random", "all")) {
-    random.data <- insight::get_parameters(x, effects = "random", parameters = parameters)
+    random.data <- insight::get_parameters(x, effects = "random", parameters = parameters, verbose = verbose)
     random <- .compute_interval_dataframe(random.data, ci, verbose, fun)
     random$Group <- "random"
   }
@@ -103,7 +103,7 @@
 
 #' @keywords internal
 .compute_interval_sim <- function(x, ci, parameters, verbose, fun) {
-  fixed.data <- insight::get_parameters(x, parameters = parameters)
+  fixed.data <- insight::get_parameters(x, parameters = parameters, verbose = verbose)
   d <- .compute_interval_dataframe(fixed.data, ci, verbose, fun)
   list(result = d, data = fixed.data)
 }