From ae642cae2d172c5eae8f10a639556413c9e23086 Mon Sep 17 00:00:00 2001
From: Joseph Larmarange <joseph@larmarange.net>
Date: Sat, 27 Jul 2024 13:45:25 +0200
Subject: [PATCH] improving doc, examples and adding NEWS

fix #260
---
 DESCRIPTION                          |  2 +-
 NEWS.md                              |  2 ++
 R/custom_tidiers.R                   | 14 ++++++++++++--
 man/tidy_multgee.Rd                  | 14 ++++++++++++--
 tests/testthat/test-tidy_plus_plus.R | 14 ++++++++++----
 5 files changed, 37 insertions(+), 9 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index c6a5dfe3..6208c775 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -86,4 +86,4 @@ Encoding: UTF-8
 Language: en-US
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
diff --git a/NEWS.md b/NEWS.md
index 27e957bd..e142cad8 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -19,6 +19,8 @@
   
 **Fixes**
 
+- `tidy_multgee()` has been fixed to properly identify the different `y.levels`
+  (#260 @jackmwolf)
 - `tidy_marginal_predictions()` has been updated to avoid the use of the
   deprecated function `marginaleffects::datagridcf()` (#256)
 
diff --git a/R/custom_tidiers.R b/R/custom_tidiers.R
index 4e53c625..0ce95079 100644
--- a/R/custom_tidiers.R
+++ b/R/custom_tidiers.R
@@ -258,15 +258,25 @@ tidy_broom <- function(x, ...) {
 #' interval in the tidied output
 #' @param conf.level the confidence level to use for the confidence interval
 #' @param ... additional parameters passed to `parameters::model_parameters()`
+#' @details
+#' To be noted, for `multgee::nomLORgee()`, the baseline `y` category is the
+#' latest modality of `y`.
+#'
 #' @export
 #' @family custom_tieders
 #' @examplesIf interactive()
 #' if (.assert_package("multgee", boolean = TRUE)) {
 #'   library(multgee)
 #'
+#'   h <- housing
+#'   h$status <- factor(
+#'     h$y,
+#'     labels = c("street", "community", "independant")
+#'   )
+#'
 #'   mod <- multgee::nomLORgee(
-#'     y ~ factor(time) * sec,
-#'     data = multgee::housing,
+#'     status ~ factor(time) * sec,
+#'     data = h,
 #'     id = id,
 #'     repeated = time,
 #'   )
diff --git a/man/tidy_multgee.Rd b/man/tidy_multgee.Rd
index a7995da9..dce63148 100644
--- a/man/tidy_multgee.Rd
+++ b/man/tidy_multgee.Rd
@@ -22,14 +22,24 @@ A tidier for models generated with \code{multgee::nomLORgee()} or \code{multgee:
 Term names will be updated to be consistent with generic models. The original
 term names are preserved in an \code{"original_term"} column.
 }
+\details{
+To be noted, for \code{multgee::nomLORgee()}, the baseline \code{y} category is the
+latest modality of \code{y}.
+}
 \examples{
 \dontshow{if (interactive()) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 if (.assert_package("multgee", boolean = TRUE)) {
   library(multgee)
 
+  h <- housing
+  h$status <- factor(
+    h$y,
+    labels = c("street", "community", "independant")
+  )
+
   mod <- multgee::nomLORgee(
-    y ~ factor(time) * sec,
-    data = multgee::housing,
+    status ~ factor(time) * sec,
+    data = h,
     id = id,
     repeated = time,
   )
diff --git a/tests/testthat/test-tidy_plus_plus.R b/tests/testthat/test-tidy_plus_plus.R
index 0ef6d5e4..ca0585f2 100644
--- a/tests/testthat/test-tidy_plus_plus.R
+++ b/tests/testthat/test-tidy_plus_plus.R
@@ -715,9 +715,14 @@ test_that("tidy_plus_plus() works with multgee models", {
   skip_if_not_installed("parameters")
 
   library(multgee)
+  h <- housing
+  h$status <- factor(
+    h$y,
+    labels = c("street", "community", "independant")
+  )
   mod <- multgee::nomLORgee(
-    y ~ factor(time) * sec,
-    data = multgee::housing,
+    status ~ factor(time) * sec,
+    data = h,
     id = id,
     repeated = time,
   )
@@ -728,8 +733,9 @@ test_that("tidy_plus_plus() works with multgee models", {
   expect_equivalent(
     res$y.level,
     c(
-      "0", "0", "0", "0", "0", "0", "0", "0",
-      "1", "1", "1", "1", "1", "1", "1", "1"
+      "street", "street", "street", "street", "street", "street",
+      "street", "street", "community", "community", "community", "community",
+      "community", "community", "community", "community"
     )
   )
   expect_equivalent(