Add call as attribute (#572)

* Add call as attribute

* fix test

* fix

* fix test

Author: strengejacke

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: modelbased
 Title: Estimation of Model-Based Predictions, Contrasts and Means
-Version: 0.13.0.8
+Version: 0.13.0.9
 Authors@R:
     c(person(given = "Dominique",
              family = "Makowski",

R/estimate_contrasts.R

@@ -413,6 +413,11 @@ estimate_contrasts.default <- function(
   attr(out, "p_adjust") <- p_adjust
   attr(out, "backend") <- backend
 
+  # we want to store the generic, not the ".default" method, in the call
+  cl <- match.call()
+  cl[[1L]] <- quote(estimate_contrasts)
+  attr(out, "call") <- cl
+
   # add attributes from workhorse function
   attributes(out) <- utils::modifyList(attributes(out), info[.info_elements()])
 

R/estimate_means.R

@@ -470,6 +470,7 @@ estimate_means <- function(model,
   attr(means, "ci") <- ci
   attr(means, "backend") <- backend
   attr(means, "coef_name") <- intersect(.valid_coefficient_names(model), colnames(means))
+  attr(means, "call") <- match.call()
 
   # add attributes from workhorse function
   attributes(means) <- utils::modifyList(attributes(means), info[.info_elements()])

R/estimate_slopes.R

@@ -186,6 +186,7 @@ estimate_slopes <- function(model,
   attr(trends, "model") <- model
   attr(trends, "response") <- insight::find_response(model)
   attr(trends, "ci") <- ci
+  attr(trends, "call") <- match.call()
 
   # add attributes from workhorse function
   attributes(trends) <- utils::modifyList(attributes(trends), info[.info_elements()])

tests/testthat/test-attributes_estimatefun.R

@@ -6,22 +6,24 @@ test_that("attributes_means", {
   model <- lm(Sepal.Length ~ Species + Sepal.Width, data = iris)
 
   estim <- suppressMessages(estimate_means(model, "Species", backend = "emmeans"))
+  # fmt: skip
   expect_named(
     attributes(estim),
     c(
       "names", "row.names", "class", "at", "by", "table_title", "table_footer",
-      "model", "response", "ci", "backend", "coef_name", "focal_terms",
+      "model", "response", "ci", "backend", "coef_name", "call", "focal_terms",
       "predict", "transform", "keep_iterations"
     )
   )
   estim <- suppressMessages(estimate_means(model, "Species", backend = "marginaleffects"))
+  # fmt: skip
   expect_named(
     attributes(estim),
     c(
       "names", "class", "row.names", "at", "by", "focal_terms", "adjusted_for",
       "predict", "estimate", "transform", "datagrid", "preserve_range",
       "model_info", "keep_iterations", "joint_test", "vcov", "table_title",
-      "table_footer", "model", "response", "ci", "backend", "coef_name"
+      "table_footer", "model", "response", "ci", "backend", "coef_name", "call"
     )
   )
 })
@@ -32,42 +34,55 @@ test_that("attributes_means, contrasts", {
   model <- lm(Sepal.Length ~ Species + Sepal.Width, data = iris)
 
   estim <- suppressMessages(estimate_contrasts(model, "Species", backend = "emmeans"))
+  # fmt: skip
   expect_named(
     attributes(estim),
     c(
       "names", "class", "row.names", "table_title", "table_footer",
-      "model", "response", "ci", "p_adjust", "backend", "predict",
+      "model", "response", "ci", "p_adjust", "backend", "call", "predict",
       "comparison", "contrast", "transform", "keep_iterations", "joint_test"
     )
   )
   estim <- suppressMessages(estimate_contrasts(model, "Species", backend = "marginaleffects"))
+  # fmt: skip
   expect_named(
     attributes(estim),
     c(
       "names", "row.names", "class", "table_title", "table_footer",
-      "model", "response", "ci", "p_adjust", "backend", "focal_terms",
+      "model", "response", "ci", "p_adjust", "backend", "call", "focal_terms",
       "adjusted_for", "predict", "comparison", "contrast", "estimate",
       "transform", "datagrid", "preserve_range", "coef_name", "model_info",
       "keep_iterations", "joint_test", "vcov"
     )
   )
-  estim <- suppressMessages(estimate_contrasts(model, "Species=c('setosa','virginica')", backend = "marginaleffects"))
+  estim <- suppressMessages(estimate_contrasts(
+    model,
+    "Species=c('setosa','virginica')",
+    backend = "marginaleffects"
+  ))
+  # fmt: skip
   expect_named(
     attributes(estim),
     c(
       "names", "row.names", "class", "table_title", "table_footer",
-      "model", "response", "ci", "p_adjust", "backend", "focal_terms",
+      "model", "response", "ci", "p_adjust", "backend", "call", "focal_terms",
       "adjusted_for", "predict", "comparison", "contrast", "estimate",
       "transform", "datagrid", "preserve_range", "coef_name", "model_info",
       "keep_iterations", "joint_test", "vcov"
     )
   )
-  estim <- suppressMessages(estimate_contrasts(model, "Species=c('setosa','virginica')", backend = "marginaleffects", estimate = "average"))
+  estim <- suppressMessages(estimate_contrasts(
+    model,
+    "Species=c('setosa','virginica')",
+    backend = "marginaleffects",
+    estimate = "average"
+  ))
+  # fmt: skip
   expect_named(
     attributes(estim),
     c(
       "names", "row.names", "class", "table_title", "table_footer",
-      "model", "response", "ci", "p_adjust", "backend", "focal_terms",
+      "model", "response", "ci", "p_adjust", "backend", "call", "focal_terms",
       "adjusted_for", "predict", "comparison", "contrast", "estimate",
       "transform", "datagrid", "preserve_range", "coef_name", "model_info",
       "contrast_filter", "keep_iterations", "joint_test","vcov"
@@ -81,21 +96,23 @@ test_that("attributes_means, slopes", {
   model <- lm(Sepal.Length ~ Species + Sepal.Width, data = iris)
 
   estim <- suppressMessages(estimate_slopes(model, "Sepal.Width", backend = "emmeans"))
+  # fmt: skip
   expect_named(
     attributes(estim),
     c(
       "names", "row.names", "class", "table_title", "table_footer",
-      "model", "response", "ci", "trend", "transform", "coef_name",
+      "model", "response", "ci", "call", "trend", "transform", "coef_name",
       "keep_iterations"
     )
   )
   estim <- suppressMessages(estimate_slopes(model, "Sepal.Width", backend = "marginaleffects"))
+  # fmt: skip
   expect_named(
     attributes(estim),
     c(
       "names", "class", "row.names", "trend", "p_adjust", "transform",
       "coef_name", "slope", "ci", "model_info", "keep_iterations",
-      "vcov", "table_title", "table_footer", "model", "response"
+      "vcov", "table_title", "table_footer", "model", "response", "call"
     )
   )
 })
@@ -109,6 +126,7 @@ test_that("attributes_means", {
     by = c("Species", "Petal.Width = [fivenum]"),
     preserve_range = FALSE
   )
+  # fmt: skip
   expect_named(
     attributes(estim),
     c(

tests/testthat/test-keep_iterations.R

@@ -10,15 +10,17 @@ test_that("estimate_means() - posterior draws", {
   m <- insight::download_model("brms_1")
   skip_if(is.null(m))
   out <- estimate_means(m, by = "wt", keep_iterations = 5)
+  # fmt: skip
   expect_named(
     attributes(out),
     c(
       "names", "class", "row.names", "at", "by", "focal_terms", "adjusted_for",
       "predict", "estimate", "transform", "datagrid", "preserve_range",
       "model_info", "keep_iterations", "joint_test", "table_title",
-      "table_footer", "model", "response", "ci", "backend", "coef_name"
+      "table_footer", "model", "response", "ci", "backend", "coef_name", "call"
     )
   )
+  # fmt: skip
   expect_named(
     out,
     c(
@@ -33,15 +35,17 @@ test_that("estimate_means() - posterior draws", {
   expect_identical(dim(out), c(10L, 4009L))
 
   out <- estimate_means(m, by = "wt")
+  # fmt: skip
   expect_named(
     attributes(out),
     c(
       "names", "class", "row.names", "at", "by", "focal_terms", "adjusted_for",
       "predict", "estimate", "transform", "datagrid", "preserve_range",
       "model_info", "keep_iterations", "joint_test", "table_title",
-      "table_footer", "model", "response", "ci", "backend", "coef_name"
+      "table_footer", "model", "response", "ci", "backend", "coef_name", "call"
     )
   )
+  # fmt: skip
   expect_named(
     out,
     c(
@@ -57,16 +61,18 @@ test_that("estimate_contrasts() - posterior draws", {
   m <- insight::download_model("brms_1")
   skip_if(is.null(m))
   out <- estimate_contrasts(m, "wt=c(3,4,5)", keep_iterations = 5)
+  # fmt: skip
   expect_named(
     attributes(out),
     c(
       "names", "row.names", "class", "table_title", "table_footer",
-      "model", "response", "ci", "p_adjust", "backend", "focal_terms",
+      "model", "response", "ci", "p_adjust", "backend", "call", "focal_terms",
       "adjusted_for", "predict", "comparison", "contrast", "estimate",
       "transform", "datagrid", "preserve_range", "coef_name", "model_info",
       "keep_iterations", "joint_test"
     )
   )
+  # fmt: skip
   expect_named(
     out,
     c(
@@ -81,16 +87,18 @@ test_that("estimate_contrasts() - posterior draws", {
   expect_identical(dim(out), c(3L, 4010L))
 
   out <- estimate_contrasts(m, "wt=c(3,4,5)")
+  # fmt: skip
   expect_named(
     attributes(out),
     c(
       "names", "row.names", "class", "table_title", "table_footer",
-      "model", "response", "ci", "p_adjust", "backend", "focal_terms",
+      "model", "response", "ci", "p_adjust", "backend", "call", "focal_terms",
       "adjusted_for", "predict", "comparison", "contrast", "estimate",
       "transform", "datagrid", "preserve_range", "coef_name", "model_info",
       "keep_iterations", "joint_test"
     )
   )
+  # fmt: skip
   expect_named(
     out,
     c(
@@ -106,14 +114,16 @@ test_that("estimate_slopes() - posterior draws", {
   m <- insight::download_model("brms_1")
   skip_if(is.null(m))
   out <- estimate_slopes(m, "wt", keep_iterations = 5)
+  # fmt: skip
   expect_named(
     attributes(out),
     c(
       "names", "class", "row.names", "trend", "p_adjust", "transform",
       "coef_name", "slope", "ci", "model_info", "keep_iterations",
-      "table_title", "table_footer", "model", "response"
+      "table_title", "table_footer", "model", "response", "call"
     )
   )
+  # fmt: skip
   expect_named(
     out,
     c(
@@ -125,14 +135,16 @@ test_that("estimate_slopes() - posterior draws", {
   expect_identical(dim(out), c(1L, 13L))
 
   out <- estimate_slopes(m, "wt")
+  # fmt: skip
   expect_named(
     attributes(out),
     c(
       "names", "class", "row.names", "trend", "p_adjust", "transform",
       "coef_name", "slope", "ci", "model_info", "keep_iterations",
-      "table_title", "table_footer", "model", "response"
+      "table_title", "table_footer", "model", "response", "call"
     )
   )
+  # fmt: skip
   expect_named(
     out,
     c(
@@ -148,14 +160,16 @@ test_that("estimate_means() - posterior draws, emmeans", {
   m <- insight::download_model("brms_1")
   skip_if(is.null(m))
   out <- estimate_means(m, by = "wt", keep_iterations = 5, backend = "emmeans")
+  # fmt: skip
   expect_named(
     attributes(out),
     c(
       "names", "class", "row.names", "table_title", "table_footer",
-      "model", "response", "ci", "backend", "coef_name", "at", "by",
+      "model", "response", "ci", "backend", "coef_name", "call", "at", "by",
       "focal_terms", "predict", "transform", "keep_iterations"
     )
   )
+  # fmt: skip
   expect_named(
     out,
     c(
@@ -166,11 +180,12 @@ test_that("estimate_means() - posterior draws, emmeans", {
   expect_identical(dim(out), c(10L, 10L))
 
   out <- estimate_means(m, by = "wt", keep_iterations = TRUE, backend = "emmeans")
+  # fmt: skip
   expect_named(
     attributes(out),
     c(
       "names", "class", "row.names", "table_title", "table_footer",
-      "model", "response", "ci", "backend", "coef_name", "at", "by",
+      "model", "response", "ci", "backend", "coef_name", "call", "at", "by",
       "focal_terms", "predict", "transform", "keep_iterations"
     )
   )
@@ -182,15 +197,17 @@ test_that("estimate_contrasts() - posterior draws, emmeans", {
   m <- insight::download_model("brms_1")
   skip_if(is.null(m))
   out <- estimate_contrasts(m, by = "wt=c(3,4,5)", keep_iterations = 5, backend = "emmeans")
+  # fmt: skip
   expect_named(
     attributes(out),
     c(
       "names", "class", "row.names", "table_title", "table_footer",
-      "model", "response", "ci", "p_adjust", "backend", "at", "by",
+      "model", "response", "ci", "p_adjust", "backend", "call", "at", "by",
       "predict", "comparison", "contrast", "transform", "keep_iterations",
       "joint_test"
     )
   )
+  # fmt: skip
   expect_named(
     out,
     c(
@@ -201,11 +218,12 @@ test_that("estimate_contrasts() - posterior draws, emmeans", {
   expect_identical(dim(out), c(3L, 12L))
 
   out <- estimate_contrasts(m, by = "wt=c(3,4,5)", keep_iterations = TRUE, backend = "emmeans")
+  # fmt: skip
   expect_named(
     attributes(out),
     c(
       "names", "class", "row.names", "table_title", "table_footer",
-      "model", "response", "ci", "p_adjust", "backend", "at", "by",
+      "model", "response", "ci", "p_adjust", "backend", "call", "at", "by",
       "predict", "comparison", "contrast", "transform", "keep_iterations",
       "joint_test"
     )
@@ -218,14 +236,16 @@ test_that("estimate_slopes() - posterior draws, emmeans", {
   m <- insight::download_model("brms_1")
   skip_if(is.null(m))
   out <- estimate_slopes(m, "wt", keep_iterations = 5, backend = "emmeans")
+  # fmt: skip
   expect_named(
     attributes(out),
     c(
       "names", "class", "row.names", "table_title", "table_footer",
-      "model", "response", "ci", "trend", "transform", "coef_name",
+      "model", "response", "ci", "call", "trend", "transform", "coef_name",
       "keep_iterations"
     )
   )
+  # fmt: skip
   expect_named(
     out,
     c(
@@ -236,11 +256,12 @@ test_that("estimate_slopes() - posterior draws, emmeans", {
   expect_identical(dim(out), c(1L, 10L))
 
   out <- estimate_slopes(m, "wt", keep_iterations = TRUE, backend = "emmeans")
+  # fmt: skip
   expect_named(
     attributes(out),
     c(
       "names", "class", "row.names", "table_title", "table_footer",
-      "model", "response", "ci", "trend", "transform", "coef_name",
+      "model", "response", "ci", "call", "trend", "transform", "coef_name",
       "keep_iterations"
     )
   )
@@ -252,6 +273,7 @@ test_that("estimate_slopes() - posterior draws, get_predicted", {
   m <- insight::download_model("brms_1")
   skip_if(is.null(m))
   out <- estimate_relation(m, by = "wt", keep_iterations = 5)
+  # fmt: skip
   expect_named(
     attributes(out),
     c(
@@ -261,6 +283,7 @@ test_that("estimate_slopes() - posterior draws, get_predicted", {
       "adjusted_for", "at_specs", "at", "by", "reference", "data"
     )
   )
+  # fmt: skip
   expect_named(
     out,
     c(