Issues with parameters() on marginaleffects objects (#901)

* Issues with `parameters()` on `marginaleffects` objects Fixes #887 * update RD * update * update * fix
easystats · Sep 11, 2023 · ad4e985 · ad4e985
1 parent 66e93af
commit ad4e985
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: parameters
 Title: Processing of Model Parameters
-Version: 0.21.1.5
+Version: 0.21.1.6
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",

diff --git a/NEWS.md b/NEWS.md
@@ -1,5 +1,13 @@
 # parameters 0.21.2
 
+## Changes
+
+* The `ci_digits` argument of the `print()` method for `model_parameters()` now
+  defaults to the same value of `digits`.
+
+* `model_parameters()` for objects from package *marginaleffects*  now also
+  accepts the `exponentiate` argument.
+
 ## Bug fixes
 
 * Fixed issue with wrong calculation of test-statistic and p-values in

diff --git a/R/display.R b/R/display.R
@@ -81,7 +81,7 @@ display.parameters_model <- function(object,
                                      footer = NULL,
                                      align = NULL,
                                      digits = 2,
-                                     ci_digits = 2,
+                                     ci_digits = digits,
                                      p_digits = 3,
                                      footer_digits = 3,
                                      ci_brackets = c("(", ")"),
@@ -132,7 +132,7 @@ display.parameters_brms_meta <- display.parameters_model
 display.compare_parameters <- function(object,
                                        format = "markdown",
                                        digits = 2,
-                                       ci_digits = 2,
+                                       ci_digits = digits,
                                        p_digits = 3,
                                        select = NULL,
                                        column_labels = NULL,
@@ -165,7 +165,7 @@ display.compare_parameters <- function(object,
 display.parameters_sem <- function(object,
                                    format = "markdown",
                                    digits = 2,
-                                   ci_digits = 2,
+                                   ci_digits = digits,
                                    p_digits = 3,
                                    ci_brackets = c("(", ")"),
                                    ...) {

diff --git a/R/equivalence_test.R b/R/equivalence_test.R
@@ -693,7 +693,7 @@ equivalence_test.ggeffects <- function(x,
 #' @export
 format.equivalence_test_lm <- function(x,
                                        digits = 2,
-                                       ci_digits = 2,
+                                       ci_digits = digits,
                                        p_digits = 3,
                                        ci_width = NULL,
                                        ci_brackets = NULL,
@@ -736,7 +736,7 @@ format.equivalence_test_lm <- function(x,
 #' @export
 print.equivalence_test_lm <- function(x,
                                       digits = 2,
-                                      ci_digits = 2,
+                                      ci_digits = digits,
                                       p_digits = 3,
                                       ci_brackets = NULL,
                                       zap_small = FALSE,
@@ -794,7 +794,7 @@ plot.equivalence_test_lm <- function(x, ...) {
 #' #' @export
 #' print_md.equivalence_test_lm <- function(x,
 #'                                          digits = 2,
-#'                                          ci_digits = 2,
+#'                                          ci_digits = digits,
 #'                                          p_digits = 3,
 #'                                          ci_brackets = NULL,
 #'                                          zap_small = FALSE,

diff --git a/R/format.R b/R/format.R
@@ -8,7 +8,7 @@ format.parameters_model <- function(x,
                                     split_components = TRUE,
                                     select = NULL,
                                     digits = 2,
-                                    ci_digits = 2,
+                                    ci_digits = digits,
                                     p_digits = 3,
                                     ci_width = NULL,
                                     ci_brackets = NULL,
@@ -259,7 +259,7 @@ format.compare_parameters <- function(x,
                                       split_components = TRUE,
                                       select = NULL,
                                       digits = 2,
-                                      ci_digits = 2,
+                                      ci_digits = digits,
                                       p_digits = 3,
                                       ci_width = NULL,
                                       ci_brackets = NULL,
@@ -468,16 +468,23 @@ format.compare_parameters <- function(x,
 #' @export
 format.parameters_sem <- function(x,
                                   digits = 2,
-                                  ci_digits = 2,
+                                  ci_digits = digits,
                                   p_digits = 3,
                                   format = NULL,
                                   ci_width = NULL,
                                   ci_brackets = TRUE,
                                   pretty_names = TRUE,
                                   ...) {
-  if (missing(digits)) digits <- .additional_arguments(x, "digits", 2)
-  if (missing(ci_digits)) ci_digits <- .additional_arguments(x, "ci_digits", 2)
-  if (missing(p_digits)) p_digits <- .additional_arguments(x, "p_digits", 3)
+  if (missing(digits)) {
+    digits <- .additional_arguments(x, "digits", 2)
+  }
+  if (missing(ci_digits)) {
+    ci_digits <- .additional_arguments(x, "ci_digits", digits)
+  }
+  if (missing(p_digits)) {
+    p_digits <- .additional_arguments(x, "p_digits", 3)
+  }
+
   .format_columns_multiple_components(
     x,
     pretty_names = TRUE,

diff --git a/R/methods_htest.R b/R/methods_htest.R
@@ -695,7 +695,7 @@ model_parameters.svytable <- function(model, verbose = TRUE, ...) {
   if ("ci_digits" %in% names(dot.arguments)) {
     attr(params, "ci_digits") <- eval(dot.arguments[["ci_digits"]])
   } else {
-    attr(params, "ci_digits") <- 2
+    attr(params, "ci_digits") <- NULL
   }
 
   if ("p_digits" %in% names(dot.arguments)) {
@@ -747,7 +747,7 @@ model_parameters.svytable <- function(model, verbose = TRUE, ...) {
   if ("ci_digits" %in% names(dot.arguments)) {
     attr(params, "ci_digits") <- eval(dot.arguments[["ci_digits"]])
   } else {
-    attr(params, "ci_digits") <- 2
+    attr(params, "ci_digits") <- NULL
   }
 
   if ("p_digits" %in% names(dot.arguments)) {

diff --git a/R/methods_lavaan.R b/R/methods_lavaan.R
@@ -152,11 +152,17 @@ p_value.blavaan <- p_value.BFBayesFactor
 # print ---------------------------
 
 #' @export
-print.parameters_sem <- function(x, digits = 2, ci_digits = 2, p_digits = 3, ...) {
+print.parameters_sem <- function(x, digits = 2, ci_digits = digits, p_digits = 3, ...) {
   # check if user supplied digits attributes
-  if (missing(digits)) digits <- .additional_arguments(x, "digits", 2)
-  if (missing(ci_digits)) ci_digits <- .additional_arguments(x, "ci_digits", 2)
-  if (missing(p_digits)) p_digits <- .additional_arguments(x, "p_digits", 3)
+  if (missing(digits)) {
+    digits <- .additional_arguments(x, "digits", 2)
+  }
+  if (missing(ci_digits)) {
+    ci_digits <- .additional_arguments(x, "ci_digits", digits)
+  }
+  if (missing(p_digits)) {
+    p_digits <- .additional_arguments(x, "p_digits", 3)
+  }
 
   verbose <- .additional_arguments(x, "verbose", TRUE)
 

diff --git a/R/methods_marginaleffects.R b/R/methods_marginaleffects.R
@@ -7,6 +7,7 @@
 #' @export
 model_parameters.marginaleffects <- function(model,
                                              ci = 0.95,
+                                             exponentiate = FALSE,
                                              ...) {
   insight::check_if_installed("marginaleffects")
   out <- insight::standardize_names(
@@ -18,10 +19,7 @@ model_parameters.marginaleffects <- function(model,
   colnames(out)[colnames(out) == "contrast"] <- "Comparison"
   colnames(out) <- gsub("^contrast_", "Comparison: ", colnames(out))
 
-  out <- tryCatch(
-    .add_model_parameters_attributes(out, model, ci, ...),
-    error = function(e) out
-  )
+  out <- .safe(.add_model_parameters_attributes(out, model, ci, exponentiate = exponentiate, ...), out)
 
   attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(model))
 
@@ -41,6 +39,8 @@ model_parameters.marginaleffects <- function(model,
     attr(out, "coefficient_name") <- "Estimate"
   }
 
+  # exponentiate coefficients and SE/CI, if requested
+  out <- .exponentiate_parameters(out, model = NULL, exponentiate)
 
   class(out) <- c("parameters_model", "see_parameters_model", class(out))
   out
@@ -70,6 +70,7 @@ model_parameters.slopes <- model_parameters.marginaleffects
 #' @export
 model_parameters.predictions <- function(model,
                                          ci = 0.95,
+                                         exponentiate = TRUE,
                                          ...) {
   insight::check_if_installed("marginaleffects")
 
@@ -89,12 +90,15 @@ model_parameters.predictions <- function(model,
     out[[resp]] <- NULL
   }
 
-  out <- .safe(.add_model_parameters_attributes(out, model, ci, ...), out)
+  out <- .safe(.add_model_parameters_attributes(out, model, ci, exponentiate = exponentiate, ...), out)
 
   attr(out, "object_name") <- insight::safe_deparse_symbol(substitute(model))
   attr(out, "coefficient_name") <- "Predicted"
   attr(out, "no_caption") <- TRUE
 
+  # exponentiate coefficients and SE/CI, if requested
+  out <- .exponentiate_parameters(out, model = NULL, exponentiate)
+
   class(out) <- c("parameters_model", "see_parameters_model", class(out))
   out
 }
diff --git a/R/print.compare_parameters.R b/R/print.compare_parameters.R
@@ -5,7 +5,7 @@ print.compare_parameters <- function(x,
                                      subtitle = NULL,
                                      footer = NULL,
                                      digits = 2,
-                                     ci_digits = 2,
+                                     ci_digits = digits,
                                      p_digits = 3,
                                      zap_small = FALSE,
                                      groups = NULL,
@@ -21,7 +21,7 @@ print.compare_parameters <- function(x,
     digits <- .additional_arguments(x, "digits", digits)
   }
   if (missing(ci_digits)) {
-    ci_digits <- .additional_arguments(x, "ci_digits", ci_digits)
+    ci_digits <- .additional_arguments(x, "ci_digits", digits)
   }
   if (missing(p_digits)) {
     p_digits <- .additional_arguments(x, "p_digits", p_digits)

diff --git a/R/print.parameters_model.R b/R/print.parameters_model.R
@@ -224,7 +224,7 @@ print.parameters_model <- function(x,
                                    caption = NULL,
                                    footer = NULL,
                                    digits = 2,
-                                   ci_digits = 2,
+                                   ci_digits = digits,
                                    p_digits = 3,
                                    footer_digits = 3,
                                    show_sigma = FALSE,
@@ -256,7 +256,7 @@ print.parameters_model <- function(x,
     digits <- .additional_arguments(x, "digits", digits)
   }
   if (missing(ci_digits)) {
-    ci_digits <- .additional_arguments(x, "ci_digits", ci_digits)
+    ci_digits <- .additional_arguments(x, "ci_digits", digits)
   }
   if (missing(p_digits)) {
     p_digits <- .additional_arguments(x, "p_digits", p_digits)
@@ -371,7 +371,7 @@ print.parameters_random <- function(x, digits = 2, ...) {
                         split_components = TRUE,
                         select = NULL,
                         digits = 2,
-                        ci_digits = 2,
+                        ci_digits = digits,
                         p_digits = 3,
                         zap_small = FALSE,
                         ci_width = "auto",

diff --git a/R/print_html.R b/R/print_html.R
@@ -11,7 +11,7 @@ print_html.parameters_model <- function(x,
                                         footer = NULL,
                                         align = NULL,
                                         digits = 2,
-                                        ci_digits = 2,
+                                        ci_digits = digits,
                                         p_digits = 3,
                                         footer_digits = 3,
                                         ci_brackets = c("(", ")"),
@@ -30,7 +30,7 @@ print_html.parameters_model <- function(x,
   }
 
   if (missing(ci_digits)) {
-    ci_digits <- .additional_arguments(x, "ci_digits", ci_digits)
+    ci_digits <- .additional_arguments(x, "ci_digits", digits)
   }
 
   if (missing(p_digits)) {
@@ -139,7 +139,7 @@ print_html.compare_parameters <- function(x,
                                           subtitle = NULL,
                                           footer = NULL,
                                           digits = 2,
-                                          ci_digits = 2,
+                                          ci_digits = digits,
                                           p_digits = 3,
                                           zap_small = FALSE,
                                           groups = NULL,
@@ -155,7 +155,7 @@ print_html.compare_parameters <- function(x,
   }
 
   if (missing(ci_digits)) {
-    ci_digits <- .additional_arguments(x, "ci_digits", ci_digits)
+    ci_digits <- .additional_arguments(x, "ci_digits", digits)
   }
 
   if (missing(p_digits)) {

diff --git a/R/print_md.R b/R/print_md.R
@@ -11,7 +11,7 @@ print_md.parameters_model <- function(x,
                                       footer = NULL,
                                       align = NULL,
                                       digits = 2,
-                                      ci_digits = 2,
+                                      ci_digits = digits,
                                       p_digits = 3,
                                       footer_digits = 3,
                                       ci_brackets = c("(", ")"),
@@ -26,7 +26,7 @@ print_md.parameters_model <- function(x,
     digits <- .additional_arguments(x, "digits", digits)
   }
   if (missing(ci_digits)) {
-    ci_digits <- .additional_arguments(x, "ci_digits", ci_digits)
+    ci_digits <- .additional_arguments(x, "ci_digits", digits)
   }
   if (missing(p_digits)) {
     p_digits <- .additional_arguments(x, "p_digits", p_digits)
@@ -124,7 +124,7 @@ print_md.parameters_simulate <- print_md.parameters_model
 #' @export
 print_md.compare_parameters <- function(x,
                                         digits = 2,
-                                        ci_digits = 2,
+                                        ci_digits = digits,
                                         p_digits = 3,
                                         caption = NULL,
                                         subtitle = NULL,
@@ -137,7 +137,7 @@ print_md.compare_parameters <- function(x,
     digits <- .additional_arguments(x, "digits", digits)
   }
   if (missing(ci_digits)) {
-    ci_digits <- .additional_arguments(x, "ci_digits", ci_digits)
+    ci_digits <- .additional_arguments(x, "ci_digits", digits)
   }
   if (missing(p_digits)) {
     p_digits <- .additional_arguments(x, "p_digits", p_digits)
@@ -178,7 +178,7 @@ print_md.compare_parameters <- function(x,
 #' @export
 print_md.parameters_sem <- function(x,
                                     digits = 2,
-                                    ci_digits = 2,
+                                    ci_digits = digits,
                                     p_digits = 3,
                                     ci_brackets = c("(", ")"),
                                     ...) {
@@ -188,7 +188,7 @@ print_md.parameters_sem <- function(x,
     digits <- .additional_arguments(x, "digits", digits)
   }
   if (missing(ci_digits)) {
-    ci_digits <- .additional_arguments(x, "ci_digits", ci_digits)
+    ci_digits <- .additional_arguments(x, "ci_digits", digits)
   }
   if (missing(p_digits)) {
     p_digits <- .additional_arguments(x, "p_digits", p_digits)

diff --git a/R/utils_format.R b/R/utils_format.R
@@ -273,7 +273,7 @@
 .format_columns_single_component <- function(x,
                                              pretty_names,
                                              digits = 2,
-                                             ci_digits = 2,
+                                             ci_digits = digits,
                                              p_digits = 3,
                                              ci_width = "auto",
                                              ci_brackets = TRUE,
@@ -758,7 +758,7 @@
                                                 pretty_names,
                                                 split_column = "Component",
                                                 digits = 2,
-                                                ci_digits = 2,
+                                                ci_digits = digits,
                                                 p_digits = 3,
                                                 coef_column = NULL,
                                                 format = NULL,