From 077a76e250371c7a910cf395bfb9f48805c01ead Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Tue, 24 Sep 2024 10:10:58 +0200
Subject: [PATCH 01/14] Update `DESCRIPTION` to use latest 'easystats'
 dependencies (#766)

Co-authored-by: IndrajeetPatil <11330453+IndrajeetPatil@users.noreply.github.com>
---
 DESCRIPTION | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 842122309..f5cf4d81e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -73,9 +73,9 @@ BugReports: https://github.com/easystats/performance/issues
 Depends:
     R (>= 3.6)
 Imports:
-    bayestestR (>= 0.13.2),
-    insight (>= 0.20.2),
-    datawizard (>= 0.10.0),
+    bayestestR (>= 0.14.0),
+    insight (>= 0.20.3),
+    datawizard (>= 0.12.2),
     stats,
     utils
 Suggests:

From 0a047a7febccec49bd984862ba5436e721221aaf Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Fri, 27 Sep 2024 09:48:46 +0200
Subject: [PATCH 02/14] docs

---
 R/r2_nakagawa.R    | 3 ++-
 man/icc.Rd         | 3 ++-
 man/r2_nakagawa.Rd | 3 ++-
 3 files changed, 6 insertions(+), 3 deletions(-)

diff --git a/R/r2_nakagawa.R b/R/r2_nakagawa.R
index 1246a444a..aeb4df1c1 100644
--- a/R/r2_nakagawa.R
+++ b/R/r2_nakagawa.R
@@ -30,7 +30,7 @@
 #' - Bernoulli (logistic) regression
 #' - Binomial regression (with other than binary outcomes)
 #' - Poisson and Quasi-Poisson regression
-#' - Negative binomial regression (including nbinom1 and nbinom2 families)
+#' - Negative binomial regression (including nbinom1, nbinom2 and nbinom12 families)
 #' - Gaussian regression (linear models)
 #' - Gamma regression
 #' - Tweedie regression
@@ -44,6 +44,7 @@
 #' - Compound Poisson regression
 #' - Generalized Poisson regression
 #' - Log-normal regression
+#' - Skew-normal regression
 #'
 #' Extracting variance components for models with zero-inflation part is not
 #' straightforward, because it is not definitely clear how the distribution-specific
diff --git a/man/icc.Rd b/man/icc.Rd
index 071e1b617..8b38ece25 100644
--- a/man/icc.Rd
+++ b/man/icc.Rd
@@ -212,7 +212,7 @@ should be accurate and reliable for following mixed models or model families:
 \item Bernoulli (logistic) regression
 \item Binomial regression (with other than binary outcomes)
 \item Poisson and Quasi-Poisson regression
-\item Negative binomial regression (including nbinom1 and nbinom2 families)
+\item Negative binomial regression (including nbinom1, nbinom2 and nbinom12 families)
 \item Gaussian regression (linear models)
 \item Gamma regression
 \item Tweedie regression
@@ -227,6 +227,7 @@ Following model families are not yet validated, but should work:
 \item Compound Poisson regression
 \item Generalized Poisson regression
 \item Log-normal regression
+\item Skew-normal regression
 }
 
 Extracting variance components for models with zero-inflation part is not
diff --git a/man/r2_nakagawa.Rd b/man/r2_nakagawa.Rd
index 169af5709..75f2de3d0 100644
--- a/man/r2_nakagawa.Rd
+++ b/man/r2_nakagawa.Rd
@@ -111,7 +111,7 @@ should be accurate and reliable for following mixed models or model families:
 \item Bernoulli (logistic) regression
 \item Binomial regression (with other than binary outcomes)
 \item Poisson and Quasi-Poisson regression
-\item Negative binomial regression (including nbinom1 and nbinom2 families)
+\item Negative binomial regression (including nbinom1, nbinom2 and nbinom12 families)
 \item Gaussian regression (linear models)
 \item Gamma regression
 \item Tweedie regression
@@ -126,6 +126,7 @@ Following model families are not yet validated, but should work:
 \item Compound Poisson regression
 \item Generalized Poisson regression
 \item Log-normal regression
+\item Skew-normal regression
 }
 
 Extracting variance components for models with zero-inflation part is not

From f1d79148a6a6178afbac8e5fa3e4e77ee0bf7905 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Mon, 30 Sep 2024 13:23:57 +0200
Subject: [PATCH 03/14] Fix failing glmmTMB tests (#769)

---
 DESCRIPTION                                |  5 +++--
 NEWS.md                                    |  4 ++++
 R/check_model_diagnostics.R                |  2 +-
 tests/testthat/test-check_collinearity.R   |  2 --
 tests/testthat/test-check_convergence.R    |  1 -
 tests/testthat/test-check_model.R          |  1 -
 tests/testthat/test-check_normality.R      |  1 -
 tests/testthat/test-check_overdispersion.R |  4 ----
 tests/testthat/test-check_predictions.R    |  1 -
 tests/testthat/test-check_singularity.R    |  2 +-
 tests/testthat/test-check_zeroinflation.R  |  4 ----
 tests/testthat/test-r2.R                   | 19 ++++++++++---------
 12 files changed, 19 insertions(+), 27 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index f5cf4d81e..5d629a4b9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: performance
 Title: Assessment of Regression Models Performance
-Version: 0.12.3.3
+Version: 0.12.3.4
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",
@@ -103,7 +103,7 @@ Suggests:
     ftExtra,
     gamm4,
     ggdag,
-    glmmTMB,
+    glmmTMB (>= 1.1.10),
     graphics,
     Hmisc,
     httr2,
@@ -160,3 +160,4 @@ Config/Needs/website:
     r-lib/pkgdown,
     easystats/easystatstemplate
 Config/rcmdcheck/ignore-inconsequential-notes: true
+Remotes: easystats/insight, easystats/bayestestR, easystats/see, easystats/parameters
diff --git a/NEWS.md b/NEWS.md
index 81a8c5ad2..4f0984b48 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -7,6 +7,10 @@
 
 * Minor revisions to the printed output of `check_dag()`.
 
+## Bug fixes
+
+* Fixed failing tests that broke due to changes in latest *glmmTMB* update.
+
 # performance 0.12.3
 
 ## New functions
diff --git a/R/check_model_diagnostics.R b/R/check_model_diagnostics.R
index 431a2bc0f..8897c685e 100644
--- a/R/check_model_diagnostics.R
+++ b/R/check_model_diagnostics.R
@@ -460,7 +460,7 @@
   if (!is.na(match(faminfo$family, c("binomial", "poisson", "truncated_poisson")))) {
     return(1)
   }
-  betad <- model$fit$par["betad"]
+  betad <- model$fit$par["betadisp"]
   switch(faminfo$family,
     gaussian = exp(0.5 * betad),
     Gamma = exp(-0.5 * betad),
diff --git a/tests/testthat/test-check_collinearity.R b/tests/testthat/test-check_collinearity.R
index ba456ae6f..d62aec75d 100644
--- a/tests/testthat/test-check_collinearity.R
+++ b/tests/testthat/test-check_collinearity.R
@@ -24,7 +24,6 @@ test_that("check_collinearity, correct order in print", {
 
 
 test_that("check_collinearity", {
-  skip_if(getRversion() > "4.3.3")
   skip_if_not_installed("glmmTMB")
   skip_if_not(getRversion() >= "4.0.0")
 
@@ -51,7 +50,6 @@ test_that("check_collinearity", {
 
 
 test_that("check_collinearity", {
-  skip_if(getRversion() > "4.3.3")
   skip_if_not_installed("glmmTMB")
   skip_if_not(getRversion() >= "4.0.0")
 
diff --git a/tests/testthat/test-check_convergence.R b/tests/testthat/test-check_convergence.R
index 0bfadc8a6..8897b785d 100644
--- a/tests/testthat/test-check_convergence.R
+++ b/tests/testthat/test-check_convergence.R
@@ -29,7 +29,6 @@ test_that("check_convergence", {
 
 
 test_that("check_convergence, glmmTMB", {
-  skip_if(getRversion() > "4.3.3")
   skip_if_not_installed("glmmTMB")
   data(iris)
   model <- suppressWarnings(glmmTMB::glmmTMB(
diff --git a/tests/testthat/test-check_model.R b/tests/testthat/test-check_model.R
index 097f089a5..2b1141d26 100644
--- a/tests/testthat/test-check_model.R
+++ b/tests/testthat/test-check_model.R
@@ -52,7 +52,6 @@ test_that("`check_model()` works for quantreg", {
 })
 
 test_that("`check_model()` warnings for tweedie", {
-  skip_if(getRversion() > "4.3.3")
   skip_if_not_installed("glmmTMB")
   skip_if_not_installed("lme4")
   data(sleepstudy, package = "lme4")
diff --git a/tests/testthat/test-check_normality.R b/tests/testthat/test-check_normality.R
index 44b461aea..f166c6f03 100644
--- a/tests/testthat/test-check_normality.R
+++ b/tests/testthat/test-check_normality.R
@@ -35,7 +35,6 @@ test_that("check_normality | afex", {
 })
 
 test_that("check_normality | glmmTMB", {
-  skip_if(getRversion() > "4.3.3")
   skip_if_not_installed("glmmTMB")
   skip_if_not(getRversion() >= "4.0.0")
 
diff --git a/tests/testthat/test-check_overdispersion.R b/tests/testthat/test-check_overdispersion.R
index 06cc95dd0..2930322bb 100644
--- a/tests/testthat/test-check_overdispersion.R
+++ b/tests/testthat/test-check_overdispersion.R
@@ -1,5 +1,4 @@
 test_that("check_overdispersion, glmmTMB-poisson", {
-  skip_if(getRversion() > "4.3.3")
   skip_if_not_installed("glmmTMB")
   skip_if_not(getRversion() >= "4.0.0")
   data(Salamanders, package = "glmmTMB")
@@ -50,7 +49,6 @@ test_that("check_overdispersion, glmmTMB-poisson", {
 
 
 test_that("check_overdispersion, glmmTMB-poisson mixed", {
-  skip_if(getRversion() > "4.3.3")
   skip_if_not_installed("glmmTMB")
   skip_if_not(getRversion() >= "4.0.0")
   data(Salamanders, package = "glmmTMB")
@@ -78,7 +76,6 @@ test_that("check_overdispersion, glmmTMB-poisson mixed", {
 
 
 test_that("check_overdispersion, zero-inflated and negbin", {
-  skip_if(getRversion() > "4.3.3")
   skip_if_not_installed("glmmTMB")
   skip_if_not_installed("DHARMa")
   skip_if_not(getRversion() >= "4.0.0")
@@ -183,7 +180,6 @@ test_that("check_overdispersion, MASS::negbin", {
 
 
 test_that("check_overdispersion, genpois", {
-  skip_if(getRversion() > "4.3.3")
   skip_if_not_installed("glmmTMB")
   skip_if_not_installed("DHARMa")
   skip_if_not(getRversion() >= "4.0.0")
diff --git a/tests/testthat/test-check_predictions.R b/tests/testthat/test-check_predictions.R
index 04bc1d2cd..142a8b429 100644
--- a/tests/testthat/test-check_predictions.R
+++ b/tests/testthat/test-check_predictions.R
@@ -35,7 +35,6 @@ test_that("check_predictions", {
 
 
 test_that("check_predictions, glmmTMB", {
-  skip_if(getRversion() > "4.3.3")
   skip_if_not_installed("glmmTMB")
   data(mtcars)
   model <- glmmTMB::glmmTMB(vs ~ disp, data = mtcars, family = binomial())
diff --git a/tests/testthat/test-check_singularity.R b/tests/testthat/test-check_singularity.R
index dc0d56964..8a07b85e0 100644
--- a/tests/testthat/test-check_singularity.R
+++ b/tests/testthat/test-check_singularity.R
@@ -29,7 +29,7 @@ test_that("check_singularity", {
     newparam = list(
       beta = 0,
       theta = rep(0, 21),
-      betad = 0
+      betadisp = 0
     )
   )[[1]]
   expect_warning(expect_warning({
diff --git a/tests/testthat/test-check_zeroinflation.R b/tests/testthat/test-check_zeroinflation.R
index a7ff7cbbd..38a5c7726 100644
--- a/tests/testthat/test-check_zeroinflation.R
+++ b/tests/testthat/test-check_zeroinflation.R
@@ -1,5 +1,4 @@
 test_that("check_zeroinflation", {
-  skip_if(getRversion() > "4.3.3")
   skip_if_not_installed("glmmTMB")
   set.seed(123)
   data(Salamanders, package = "glmmTMB")
@@ -22,7 +21,6 @@ test_that("check_zeroinflation", {
 
 
 test_that("check_zeroinflation, glmmTMB with and without zero-inflation component", {
-  skip_if(getRversion() > "4.3.3")
   skip_if_not_installed("glmmTMB")
   skip_if_not_installed("DHARMa")
   set.seed(123)
@@ -109,7 +107,6 @@ test_that("check_zeroinflation, glmer.nb", {
 
 
 test_that("check_zeroinflation, glmmTMB nbinom", {
-  skip_if(getRversion() > "4.3.3")
   skip_if_not_installed("glmmTMB")
   skip_if_not_installed("DHARMa")
   skip_on_cran()
@@ -166,7 +163,6 @@ test_that("check_zeroinflation, MASS::negbin", {
 
 
 test_that("check_zeroinflation, genpois", {
-  skip_if(getRversion() > "4.3.3")
   skip_if_not_installed("glmmTMB")
   skip_if_not_installed("DHARMa")
   skip_if_not(getRversion() >= "4.0.0")
diff --git a/tests/testthat/test-r2.R b/tests/testthat/test-r2.R
index f521b3aab..d7ade6b29 100644
--- a/tests/testthat/test-r2.R
+++ b/tests/testthat/test-r2.R
@@ -46,8 +46,7 @@ skip_if_not_installed("withr")
 withr::with_environment(
   new.env(),
   test_that("r2 glmmTMB, no ranef", {
-    skip_if(getRversion() > "4.3.3")
-    skip_if_not_installed("glmmTMB")
+    skip_if_not_installed("glmmTMB", minimum_version = "1.1.10")
     data(Owls, package = "glmmTMB")
     # linear ---------------------------------------------------------------
     m <- glmmTMB::glmmTMB(NegPerChick ~ BroodSize + ArrivalTime, data = Owls)
@@ -89,14 +88,16 @@ withr::with_environment(
       data = bioChemists
     )
     out <- r2(m)
-    expect_equal(out[[1]], 0.1797549, tolerance = 1e-3, ignore_attr = TRUE)
+    expect_equal(out[[1]], 0.14943, tolerance = 1e-3, ignore_attr = TRUE)
+    ## FIXME: since glmmTMB 1.1.10(?) Pearson residuals differ and results
+    ## are no longer identical, see https://github.com/glmmTMB/glmmTMB/issues/1101
     # validate against pscl::zeroinfl
-    m2 <- pscl::zeroinfl(
-      art ~ fem + mar + kid5 + ment | kid5 + phd,
-      data = bioChemists
-    )
-    out2 <- r2(m2)
-    expect_equal(out[[1]], out2[[1]], tolerance = 1e-3, ignore_attr = TRUE)
+    # m2 <- pscl::zeroinfl(
+    #   art ~ fem + mar + kid5 + ment | kid5 + phd,
+    #   data = bioChemists
+    # )
+    # out2 <- r2(m2)
+    # expect_equal(out[[1]], out2[[1]], tolerance = 1e-3, ignore_attr = TRUE)
     # Gamma --------------------------------------------------------------
     clotting <<- data.frame(
       u = c(5, 10, 15, 20, 30, 40, 60, 80, 100),

From e24bdd83b3e69f41c80b2596dcb69fbd39f2fd7f Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Mon, 30 Sep 2024 14:05:23 +0200
Subject: [PATCH 04/14] desc

---
 DESCRIPTION | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 5d629a4b9..0e042c1db 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -48,9 +48,9 @@ Authors@R:
              role = "rev"),
       person(given = "gjo11",
              role = "rev"),
-      person("Etienne",
-             "Bacher", ,
-             "etienne.bacher@protonmail.com",
+      person(given = "Etienne",
+             family = "Bacher", ,
+             email = "etienne.bacher@protonmail.com",
              role = "ctb",
              comment = c(ORCID = "0000-0002-9271-5075")),
       person(given = "Joseph",
@@ -160,4 +160,3 @@ Config/Needs/website:
     r-lib/pkgdown,
     easystats/easystatstemplate
 Config/rcmdcheck/ignore-inconsequential-notes: true
-Remotes: easystats/insight, easystats/bayestestR, easystats/see, easystats/parameters

From 868144c09801877c52f58236fd09437b791d55a5 Mon Sep 17 00:00:00 2001
From: "github-actions[bot]"
 <41898282+github-actions[bot]@users.noreply.github.com>
Date: Tue, 1 Oct 2024 06:57:28 +0200
Subject: [PATCH 05/14] Update `DESCRIPTION` to use latest 'easystats'
 dependencies (#770)

Co-authored-by: IndrajeetPatil <11330453+IndrajeetPatil@users.noreply.github.com>
---
 DESCRIPTION | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 0e042c1db..a6e2a3069 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -74,8 +74,8 @@ Depends:
     R (>= 3.6)
 Imports:
     bayestestR (>= 0.14.0),
-    insight (>= 0.20.3),
-    datawizard (>= 0.12.2),
+    insight (>= 0.20.4),
+    datawizard (>= 0.12.3),
     stats,
     utils
 Suggests:

From 22971d617995a2f39831224e89529595e87acc0c Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Tue, 1 Oct 2024 22:06:52 +0200
Subject: [PATCH 06/14] new arg

---
 R/performance_aicc.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/performance_aicc.R b/R/performance_aicc.R
index 3c433161f..52cf3679c 100644
--- a/R/performance_aicc.R
+++ b/R/performance_aicc.R
@@ -265,7 +265,7 @@ performance_aicc.rma <- function(x, ...) {
 .adjust_ic_jacobian <- function(model, ic) {
   response_transform <- insight::find_transformation(model)
   if (!is.null(ic) && !is.null(response_transform) && !identical(response_transform, "identity")) {
-    adjustment <- .safe(.ll_analytic_adjustment(model, insight::get_weights(model, na_rm = TRUE)))
+    adjustment <- .safe(.ll_analytic_adjustment(model, insight::get_weights(model, remove_na = TRUE)))
     if (!is.null(adjustment)) {
       ic <- ic - 2 * adjustment
     }

From 35cd5d5006c23e98a578b501bcf5f9eabc7cbe8e Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Tue, 1 Oct 2024 22:46:40 +0200
Subject: [PATCH 07/14] lintr

---
 R/check_dag.R | 14 ++++++--------
 1 file changed, 6 insertions(+), 8 deletions(-)

diff --git a/R/check_dag.R b/R/check_dag.R
index 7a64ae4d0..272cc5814 100644
--- a/R/check_dag.R
+++ b/R/check_dag.R
@@ -285,15 +285,13 @@ check_dag <- function(...,
     adjustment_set <- unlist(dagitty::adjustmentSets(dag, effect = x), use.names = FALSE)
     adjustment_nodes <- unlist(dagitty::adjustedNodes(dag), use.names = FALSE)
     minimal_adjustments <- as.list(dagitty::adjustmentSets(dag, effect = x))
-    collider <- adjustment_nodes[vapply(adjustment_nodes, ggdag::is_collider, logical(1), .dag = dag, downstream = FALSE)]
-    if (!length(collider)) {
+    collider <- adjustment_nodes[vapply(adjustment_nodes, ggdag::is_collider, logical(1), .dag = dag, downstream = FALSE)] # nolint
+    if (length(collider)) {
+      # if we *have* colliders, remove them from minimal adjustments
+      minimal_adjustments <- lapply(minimal_adjustments, setdiff, y = collider)
+    } else {
       # if we don't have colliders, set to NULL
       collider <- NULL
-    } else {
-      # if we *have* colliders, remove them from minimal adjustments
-      minimal_adjustments <- lapply(minimal_adjustments, function(ma) {
-        setdiff(ma, collider)
-      })
     }
     list(
       # no adjustment needed when
@@ -303,7 +301,7 @@ check_dag <- function(...,
       # incorrect adjustment when
       # - required is NULL and current adjustment not NULL
       # - OR we have a collider in current adjustments
-      incorrectly_adjusted = (is.null(adjustment_set) && !is.null(adjustment_nodes)) || (!is.null(collider) && collider %in% adjustment_nodes),
+      incorrectly_adjusted = (is.null(adjustment_set) && !is.null(adjustment_nodes)) || (!is.null(collider) && collider %in% adjustment_nodes), # nolint
       current_adjustments = adjustment_nodes,
       minimal_adjustments = minimal_adjustments,
       collider = collider

From 8d5742ed418f579e50370f7e35dcf70997a7dbb6 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Wed, 2 Oct 2024 01:05:41 +0200
Subject: [PATCH 08/14] remove twitter handle

---
 DESCRIPTION | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a6e2a3069..9c2f7f969 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -7,22 +7,22 @@ Authors@R:
              family = "Lüdecke",
              role = c("aut", "cre"),
              email = "d.luedecke@uke.de",
-             comment = c(ORCID = "0000-0002-8895-3206", Twitter = "@strengejacke")),
+             comment = c(ORCID = "0000-0002-8895-3206")),
       person(given = "Dominique",
              family = "Makowski",
              role = c("aut", "ctb"),
              email = "dom.makowski@gmail.com",
-             comment = c(ORCID = "0000-0001-5375-9967", Twitter = "@Dom_Makowski")),
+             comment = c(ORCID = "0000-0001-5375-9967")),
      person(given = "Mattan S.",
              family = "Ben-Shachar",
              role = c("aut", "ctb"),
              email = "matanshm@post.bgu.ac.il",
-             comment = c(ORCID = "0000-0002-4287-4801", Twitter = "@mattansb")),
+             comment = c(ORCID = "0000-0002-4287-4801")),
       person(given = "Indrajeet",
              family = "Patil",
              role = c("aut", "ctb"),
              email = "patilindrajeet.science@gmail.com",
-             comment = c(ORCID = "0000-0003-1995-6531", Twitter = "@patilindrajeets")),
+             comment = c(ORCID = "0000-0003-1995-6531")),
       person(given = "Philip",
              family = "Waggoner",
              role = c("aut", "ctb"),
@@ -32,12 +32,12 @@ Authors@R:
              family = "Wiernik",
              role = c("aut", "ctb"),
              email = "brenton@wiernik.org",
-             comment = c(ORCID = "0000-0001-9560-6336", Twitter = "@bmwiernik")),
+             comment = c(ORCID = "0000-0001-9560-6336")),
       person(given = "Rémi",
              family = "Thériault",
              role = c("aut", "ctb"),
              email = "remi.theriault@mail.mcgill.ca",
-             comment = c(ORCID = "0000-0003-4315-6788", Twitter = "@rempsyc")),
+             comment = c(ORCID = "0000-0003-4315-6788")),
       person(given = "Vincent",
              family = "Arel-Bundock",
              email = "vincent.arel-bundock@umontreal.ca",

From c5a22290808f2200569e980592dc05d84cf4b9f9 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Wed, 2 Oct 2024 01:07:52 +0200
Subject: [PATCH 09/14] Update test based on glmmTMB fix (#771)

---
 DESCRIPTION                                   |  3 +-
 R/check_dag.R                                 | 68 +++++++++++++++++--
 R/check_heterogeneity_bias.R                  |  2 +-
 man/check_dag.Rd                              | 33 +++++++--
 man/check_heterogeneity_bias.Rd               |  2 -
 .../testthat/test-check_heterogeneity_bias.R  |  2 +-
 tests/testthat/test-icc.R                     |  2 +-
 tests/testthat/test-r2.R                      | 17 +++--
 8 files changed, 106 insertions(+), 23 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index a6e2a3069..8680fd5b9 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -142,7 +142,7 @@ Suggests:
     rstanarm,
     rstantools,
     sandwich,
-    see (>= 0.8.2),
+    see (>= 0.9.0),
     survey,
     survival,
     testthat (>= 3.2.1),
@@ -160,3 +160,4 @@ Config/Needs/website:
     r-lib/pkgdown,
     easystats/easystatstemplate
 Config/rcmdcheck/ignore-inconsequential-notes: true
+Remotes: glmmTMB/glmmTMB/glmmTMB#1102
diff --git a/R/check_dag.R b/R/check_dag.R
index 272cc5814..c8b53533f 100644
--- a/R/check_dag.R
+++ b/R/check_dag.R
@@ -37,9 +37,17 @@
 #' @param latent A character vector with names of latent variables in the model.
 #' @param effect Character string, indicating which effect to check. Can be
 #' `"all"` (default), `"total"`, or `"direct"`.
-#' @param coords A list with two elements, `x` and `y`, which both are named
-#' vectors of numerics. The names correspond to the variable names in the DAG,
-#' and the values for `x` and `y` indicate the x/y coordinates in the plot.
+#' @param coords Coordinates of the variables when plotting the DAG. The
+#' coordinates can be provided in three different ways:
+#'
+#' - a list with two elements, `x` and `y`, which both are named vectors of
+#'   numerics. The names correspond to the variable names in the DAG, and the
+#'   values for `x` and `y` indicate the x/y coordinates in the plot.
+#' - a list with elements that correspond to the variables in the DAG. Each
+#'   element is a numeric vector of length two with x- and y-coordinate.
+#' - a data frame with three columns: `x`, `y` and `name` (which contains the
+#'   variable names).
+#'
 #' See 'Examples'.
 #' @param x An object of class `check_dag`, as returned by `check_dag()`.
 #'
@@ -111,7 +119,7 @@
 #'   Interpreting Confounder and Modifier Coefficients. American Journal of
 #'   Epidemiology, 177(4), 292–298. \doi{10.1093/aje/kws412}
 #'
-#' @examplesIf require("ggdag", quietly = TRUE) && require("dagitty", quietly = TRUE) && require("see", quietly = TRUE) && packageVersion("see") > "0.8.5"
+#' @examplesIf require("ggdag", quietly = TRUE) && require("dagitty", quietly = TRUE) && require("see", quietly = TRUE)
 #' # no adjustment needed
 #' check_dag(
 #'   y ~ x + b,
@@ -171,6 +179,22 @@
 #' )
 #' plot(dag)
 #'
+#' # alternative way of providing the coordinates
+#' dag <- check_dag(
+#'   score ~ exp + b + c,
+#'   exp ~ b,
+#'   outcome = "score",
+#'   exposure = "exp",
+#'   coords = list(
+#'     # x/y coordinates for each node
+#'     score = c(5, 3),
+#'     exp = c(4, 3),
+#'     b = c(3, 2),
+#'     c = c(3, 4)
+#'   )
+#' )
+#' plot(dag)
+#'
 #' # Objects returned by `check_dag()` can be used with "ggdag" or "dagitty"
 #' ggdag::ggdag_status(dag)
 #'
@@ -248,6 +272,9 @@ check_dag <- function(...,
     adjusted <- all.vars(adjusted)
   }
 
+  # process coords-argument
+  coords <- .process_coords(coords)
+
   # convert to dag
   dag_args <- c(formulas, list(
     exposure = exposure,
@@ -338,6 +365,39 @@ check_dag <- function(...,
 }
 
 
+.process_coords <- function(coords) {
+  # check if the coords are not provided as list with x/y elements, but instead
+  # as list x/y coordinates for each element. This means, "coords" is provided as
+  #
+  # coords <- list(
+  #   score = c(5, 3),
+  #   exp = c(4, 3),
+  #   b = c(3, 2),
+  #   c = c(3, 4)
+  # )
+  #
+  # but we want
+  #
+  # coords = list(
+  #   x = c(score = 5, exp = 4, b = 3, c = 3),
+  #   y = c(score = 3, exp = 3, b = 2, c = 4)
+  # )
+  #
+  # we have to check that it's not a data frame and that it is a list -
+  # values like `ggdag::time_ordered_coords()` returns a function, not a list
+  if (!is.null(coords) && !is.data.frame(coords) && is.list(coords) && (length(coords) != 2 || !identical(names(coords), c("x", "y")))) { # nolint
+    # transform list into data frame, split x and y coordinates into columns
+    coords <- datawizard::rownames_as_column(
+      stats::setNames(as.data.frame(do.call(rbind, coords)), c("x", "y")),
+      "name"
+    )
+    # reorder
+    coords <- coords[c("x", "y", "name")]
+  }
+  coords
+}
+
+
 # methods --------------------------------------------------------------------
 
 #' @rdname check_dag
diff --git a/R/check_heterogeneity_bias.R b/R/check_heterogeneity_bias.R
index 3c9b502ce..755f47dfa 100644
--- a/R/check_heterogeneity_bias.R
+++ b/R/check_heterogeneity_bias.R
@@ -39,7 +39,7 @@
 #'   Modeling of Time-Series Cross-Sectional and Panel Data. Political Science
 #'   Research and Methods, 3(1), 133–153.
 #'
-#' @examplesIf insight::check_if_installed("datawizard", minimum_version = "0.12.0", quietly = TRUE)
+#' @examples
 #' data(iris)
 #' iris$ID <- sample(1:4, nrow(iris), replace = TRUE) # fake-ID
 #' check_heterogeneity_bias(iris, select = c("Sepal.Length", "Petal.Length"), by = "ID")
diff --git a/man/check_dag.Rd b/man/check_dag.Rd
index fa7e92207..e366ff07a 100644
--- a/man/check_dag.Rd
+++ b/man/check_dag.Rd
@@ -42,9 +42,18 @@ are adjusted for in the model, e.g. \code{adjusted = c("x1", "x2")} or
 \item{effect}{Character string, indicating which effect to check. Can be
 \code{"all"} (default), \code{"total"}, or \code{"direct"}.}
 
-\item{coords}{A list with two elements, \code{x} and \code{y}, which both are named
-vectors of numerics. The names correspond to the variable names in the DAG,
-and the values for \code{x} and \code{y} indicate the x/y coordinates in the plot.
+\item{coords}{Coordinates of the variables when plotting the DAG. The
+coordinates can be provided in three different ways:
+\itemize{
+\item a list with two elements, \code{x} and \code{y}, which both are named vectors of
+numerics. The names correspond to the variable names in the DAG, and the
+values for \code{x} and \code{y} indicate the x/y coordinates in the plot.
+\item a list with elements that correspond to the variables in the DAG. Each
+element is a numeric vector of length two with x- and y-coordinate.
+\item a data frame with three columns: \code{x}, \code{y} and \code{name} (which contains the
+variable names).
+}
+
 See 'Examples'.}
 
 \item{x}{An object of class \code{check_dag}, as returned by \code{check_dag()}.}
@@ -137,7 +146,7 @@ adjustments or over-adjustment.
 }
 
 \examples{
-\dontshow{if (require("ggdag", quietly = TRUE) && require("dagitty", quietly = TRUE) && require("see", quietly = TRUE) && packageVersion("see") > "0.8.5") (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
+\dontshow{if (require("ggdag", quietly = TRUE) && require("dagitty", quietly = TRUE) && require("see", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 # no adjustment needed
 check_dag(
   y ~ x + b,
@@ -197,6 +206,22 @@ dag <- check_dag(
 )
 plot(dag)
 
+# alternative way of providing the coordinates
+dag <- check_dag(
+  score ~ exp + b + c,
+  exp ~ b,
+  outcome = "score",
+  exposure = "exp",
+  coords = list(
+    # x/y coordinates for each node
+    score = c(5, 3),
+    exp = c(4, 3),
+    b = c(3, 2),
+    c = c(3, 4)
+  )
+)
+plot(dag)
+
 # Objects returned by `check_dag()` can be used with "ggdag" or "dagitty"
 ggdag::ggdag_status(dag)
 
diff --git a/man/check_heterogeneity_bias.Rd b/man/check_heterogeneity_bias.Rd
index 228d26510..40b2b66ca 100644
--- a/man/check_heterogeneity_bias.Rd
+++ b/man/check_heterogeneity_bias.Rd
@@ -50,11 +50,9 @@ cause a heterogeneity bias, i.e. if variables have a within- and/or
 between-effect (\emph{Bell and Jones, 2015}).
 }
 \examples{
-\dontshow{if (insight::check_if_installed("datawizard", minimum_version = "0.12.0", quietly = TRUE)) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}
 data(iris)
 iris$ID <- sample(1:4, nrow(iris), replace = TRUE) # fake-ID
 check_heterogeneity_bias(iris, select = c("Sepal.Length", "Petal.Length"), by = "ID")
-\dontshow{\}) # examplesIf}
 }
 \references{
 \itemize{
diff --git a/tests/testthat/test-check_heterogeneity_bias.R b/tests/testthat/test-check_heterogeneity_bias.R
index e01ecf3ff..9701a7c03 100644
--- a/tests/testthat/test-check_heterogeneity_bias.R
+++ b/tests/testthat/test-check_heterogeneity_bias.R
@@ -1,5 +1,5 @@
 test_that("check_heterogeneity_bias", {
-  skip_if_not_installed("datawizard", minimum_version = "0.12.0")
+  skip_if_not_installed("datawizard")
   data(iris)
   set.seed(123)
   iris$ID <- sample.int(4, nrow(iris), replace = TRUE) # fake-ID
diff --git a/tests/testthat/test-icc.R b/tests/testthat/test-icc.R
index 82da6a3eb..73f8b6e3f 100644
--- a/tests/testthat/test-icc.R
+++ b/tests/testthat/test-icc.R
@@ -121,7 +121,7 @@ test_that("icc", {
 
 
 test_that("icc, glmmTMB 1.1.9+", {
-  skip_if_not_installed("glmmTMB", minimum_version = "1.1.9")
+  skip_if_not_installed("glmmTMB")
   set.seed(101)
   dd <- data.frame(
     z = rnorm(1000),
diff --git a/tests/testthat/test-r2.R b/tests/testthat/test-r2.R
index d7ade6b29..6b4ac0b05 100644
--- a/tests/testthat/test-r2.R
+++ b/tests/testthat/test-r2.R
@@ -79,6 +79,7 @@ withr::with_environment(
     out2 <- r2(m2)
     expect_equal(out[[1]], out2[[1]], tolerance = 1e-3, ignore_attr = TRUE)
     # zero-inflated --------------------------------------------------------------
+    skip_if_not(packageVersion("glmmTMB") > "1.1.10")
     skip_if_not_installed("pscl")
     data(bioChemists, package = "pscl")
     m <- glmmTMB::glmmTMB(
@@ -88,16 +89,14 @@ withr::with_environment(
       data = bioChemists
     )
     out <- r2(m)
-    expect_equal(out[[1]], 0.14943, tolerance = 1e-3, ignore_attr = TRUE)
-    ## FIXME: since glmmTMB 1.1.10(?) Pearson residuals differ and results
-    ## are no longer identical, see https://github.com/glmmTMB/glmmTMB/issues/1101
+    expect_equal(out[[1]], 0.1797549, tolerance = 1e-3, ignore_attr = TRUE)
     # validate against pscl::zeroinfl
-    # m2 <- pscl::zeroinfl(
-    #   art ~ fem + mar + kid5 + ment | kid5 + phd,
-    #   data = bioChemists
-    # )
-    # out2 <- r2(m2)
-    # expect_equal(out[[1]], out2[[1]], tolerance = 1e-3, ignore_attr = TRUE)
+    m2 <- pscl::zeroinfl(
+      art ~ fem + mar + kid5 + ment | kid5 + phd,
+      data = bioChemists
+    )
+    out2 <- r2(m2)
+    expect_equal(out[[1]], out2[[1]], tolerance = 1e-3, ignore_attr = TRUE)
     # Gamma --------------------------------------------------------------
     clotting <<- data.frame(
       u = c(5, 10, 15, 20, 30, 40, 60, 80, 100),

From 6b1020eb802072348253dcbcab38c27a9c2ea495 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Fri, 18 Oct 2024 20:39:52 +0200
Subject: [PATCH 10/14] Prepare CRAN submission (#772)

---
 DESCRIPTION | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 883790eab..826abc7b3 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: performance
 Title: Assessment of Regression Models Performance
-Version: 0.12.3.4
+Version: 0.12.4
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",
@@ -73,9 +73,9 @@ BugReports: https://github.com/easystats/performance/issues
 Depends:
     R (>= 3.6)
 Imports:
-    bayestestR (>= 0.14.0),
-    insight (>= 0.20.4),
-    datawizard (>= 0.12.3),
+    bayestestR (>= 0.15.0),
+    insight (>= 0.20.5),
+    datawizard (>= 0.13.0),
     stats,
     utils
 Suggests:
@@ -160,4 +160,3 @@ Config/Needs/website:
     r-lib/pkgdown,
     easystats/easystatstemplate
 Config/rcmdcheck/ignore-inconsequential-notes: true
-Remotes: glmmTMB/glmmTMB/glmmTMB#1102

From 8b52f6cabf7ed3c855bc27fc77f09d984a4c79a7 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Mon, 21 Oct 2024 10:24:28 +0200
Subject: [PATCH 11/14] update test, due to changes in DHARMa::createData()

---
 tests/testthat/test-check_residuals.R | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/testthat/test-check_residuals.R b/tests/testthat/test-check_residuals.R
index 9be029c0c..dbaebe447 100644
--- a/tests/testthat/test-check_residuals.R
+++ b/tests/testthat/test-check_residuals.R
@@ -19,13 +19,13 @@ test_that("check_residuals and simulate_residuals", {
   # check raw residuals
   expect_equal(
     head(residuals(res)),
-    c(0.55349, 0.44012, 0.39826, 0.9825, 0.90753, 0.05809),
+    c(0.01815, 0.7062, 0.56076, 0.19282, 0.31423, 0.10115),
     tolerance = 1e-4,
     ignore_attr = TRUE
   )
   expect_equal(
     head(residuals(res, quantile_function = stats::qnorm)),
-    c(0.13448, -0.15068, -0.25785, 2.10826, 1.3257, -1.57097),
+    c(-2.09365, 0.54232, 0.1529, -0.86756, -0.4839, -1.27504),
     tolerance = 1e-4,
     ignore_attr = TRUE
   )
@@ -57,10 +57,10 @@ test_that("check_residuals and simulate_residuals", {
 
   # check_residuals
   out <- check_residuals(res)
-  expect_equal(out, 0.01884602, ignore_attr = TRUE, tolerance = 1e-4)
+  expect_equal(out, 0.02574286, ignore_attr = TRUE, tolerance = 1e-4)
   expect_identical(
     capture.output(print(out)),
-    "Warning: Non-uniformity of simulated residuals detected (p = 0.019)."
+    "Warning: Non-uniformity of simulated residuals detected (p = 0.026)."
   )
   expect_error(simulate_residuals(m, iterations = 1), "`iterations` must be")
 

From 90d000834997fa1a593afc8db5d0628c23c2b113 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Tue, 22 Oct 2024 10:41:12 +0200
Subject: [PATCH 12/14] docs

---
 R/performance_aicc.R       | 10 ++++++++++
 man/performance-package.Rd | 12 ++++++------
 man/performance_aicc.Rd    | 10 ++++++++++
 3 files changed, 26 insertions(+), 6 deletions(-)

diff --git a/R/performance_aicc.R b/R/performance_aicc.R
index 52cf3679c..bc1f3e0ab 100644
--- a/R/performance_aicc.R
+++ b/R/performance_aicc.R
@@ -28,6 +28,9 @@
 #' scale. To get back to the original scale, the likelihood of the model is
 #' multiplied by the Jacobian/derivative of the transformation.
 #'
+#' In case it is not possible to return the corrected AIC value, a waring
+#' is given that the corrected log-likelihood value could not be computed.
+#'
 #' @references
 #' - Akaike, H. (1973) Information theory as an extension of the maximum
 #' likelihood principle. In: Second International Symposium on Information
@@ -52,6 +55,13 @@
 #' # performance_aic() correctly detects transformed response and
 #' # returns corrected AIC
 #' performance_aic(model)
+#'
+#' \dontrun{
+#' # there are a few exceptions where the corrected log-likelihood values
+#' # cannot be returned. The following exampe gives a warning.
+#' model <- lm(1 / mpg ~ factor(cyl), mtcars)
+#' performance_aic(model)
+#' }
 #' @export
 performance_aicc <- function(x, ...) {
   UseMethod("performance_aicc")
diff --git a/man/performance-package.Rd b/man/performance-package.Rd
index f7a05c369..4644e6443 100644
--- a/man/performance-package.Rd
+++ b/man/performance-package.Rd
@@ -34,16 +34,16 @@ Useful links:
 
 }
 \author{
-\strong{Maintainer}: Daniel Lüdecke \email{d.luedecke@uke.de} (\href{https://orcid.org/0000-0002-8895-3206}{ORCID}) (@strengejacke)
+\strong{Maintainer}: Daniel Lüdecke \email{d.luedecke@uke.de} (\href{https://orcid.org/0000-0002-8895-3206}{ORCID})
 
 Authors:
 \itemize{
-  \item Dominique Makowski \email{dom.makowski@gmail.com} (\href{https://orcid.org/0000-0001-5375-9967}{ORCID}) (@Dom_Makowski) [contributor]
-  \item Mattan S. Ben-Shachar \email{matanshm@post.bgu.ac.il} (\href{https://orcid.org/0000-0002-4287-4801}{ORCID}) (@mattansb) [contributor]
-  \item Indrajeet Patil \email{patilindrajeet.science@gmail.com} (\href{https://orcid.org/0000-0003-1995-6531}{ORCID}) (@patilindrajeets) [contributor]
+  \item Dominique Makowski \email{dom.makowski@gmail.com} (\href{https://orcid.org/0000-0001-5375-9967}{ORCID}) [contributor]
+  \item Mattan S. Ben-Shachar \email{matanshm@post.bgu.ac.il} (\href{https://orcid.org/0000-0002-4287-4801}{ORCID}) [contributor]
+  \item Indrajeet Patil \email{patilindrajeet.science@gmail.com} (\href{https://orcid.org/0000-0003-1995-6531}{ORCID}) [contributor]
   \item Philip Waggoner \email{philip.waggoner@gmail.com} (\href{https://orcid.org/0000-0002-7825-7573}{ORCID}) [contributor]
-  \item Brenton M. Wiernik \email{brenton@wiernik.org} (\href{https://orcid.org/0000-0001-9560-6336}{ORCID}) (@bmwiernik) [contributor]
-  \item Rémi Thériault \email{remi.theriault@mail.mcgill.ca} (\href{https://orcid.org/0000-0003-4315-6788}{ORCID}) (@rempsyc) [contributor]
+  \item Brenton M. Wiernik \email{brenton@wiernik.org} (\href{https://orcid.org/0000-0001-9560-6336}{ORCID}) [contributor]
+  \item Rémi Thériault \email{remi.theriault@mail.mcgill.ca} (\href{https://orcid.org/0000-0003-4315-6788}{ORCID}) [contributor]
 }
 
 Other contributors:
diff --git a/man/performance_aicc.Rd b/man/performance_aicc.Rd
index 0bf2120b7..529ee53aa 100644
--- a/man/performance_aicc.Rd
+++ b/man/performance_aicc.Rd
@@ -46,6 +46,9 @@ incorporates a correction for small sample sizes.
 unlike \code{stats::AIC()}, returns the "corrected" AIC value on the original
 scale. To get back to the original scale, the likelihood of the model is
 multiplied by the Jacobian/derivative of the transformation.
+
+In case it is not possible to return the corrected AIC value, a waring
+is given that the corrected log-likelihood value could not be computed.
 }
 \examples{
 m <- lm(mpg ~ wt + cyl + gear + disp, data = mtcars)
@@ -63,6 +66,13 @@ AIC(model)
 # performance_aic() correctly detects transformed response and
 # returns corrected AIC
 performance_aic(model)
+
+\dontrun{
+# there are a few exceptions where the corrected log-likelihood values
+# cannot be returned. The following exampe gives a warning.
+model <- lm(1 / mpg ~ factor(cyl), mtcars)
+performance_aic(model)
+}
 }
 \references{
 \itemize{

From c8c81200c91a7339fcc65314081895de12078a71 Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Tue, 22 Oct 2024 11:05:53 +0200
Subject: [PATCH 13/14] DRY

---
 DESCRIPTION          |  3 +-
 R/performance_aicc.R | 65 +++-----------------------------------------
 2 files changed, 6 insertions(+), 62 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 826abc7b3..2b7fe815a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: performance
 Title: Assessment of Regression Models Performance
-Version: 0.12.4
+Version: 0.12.4.1
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",
@@ -160,3 +160,4 @@ Config/Needs/website:
     r-lib/pkgdown,
     easystats/easystatstemplate
 Config/rcmdcheck/ignore-inconsequential-notes: true
+Remotes: easystats/insight
diff --git a/R/performance_aicc.R b/R/performance_aicc.R
index bc1f3e0ab..eb10bc40f 100644
--- a/R/performance_aicc.R
+++ b/R/performance_aicc.R
@@ -266,8 +266,6 @@ performance_aicc.rma <- function(x, ...) {
 }
 
 
-
-
 # jacobian / derivate for log models and other transformations ----------------
 
 
@@ -275,68 +273,13 @@ performance_aicc.rma <- function(x, ...) {
 .adjust_ic_jacobian <- function(model, ic) {
   response_transform <- insight::find_transformation(model)
   if (!is.null(ic) && !is.null(response_transform) && !identical(response_transform, "identity")) {
-    adjustment <- .safe(.ll_analytic_adjustment(model, insight::get_weights(model, remove_na = TRUE)))
+    adjustment <- .safe(insight::get_loglikelihood_adjustment(
+      model,
+      insight::get_weights(model, remove_na = TRUE)
+    ))
     if (!is.null(adjustment)) {
       ic <- ic - 2 * adjustment
     }
   }
   ic
 }
-
-
-# copied from `insight`
-.ll_analytic_adjustment <- function(x, model_weights = NULL) {
-  tryCatch(
-    {
-      trans <- insight::find_transformation(x)
-      switch(trans,
-        identity = .weighted_sum(log(insight::get_response(x)), w = model_weights),
-        log = .weighted_sum(log(1 / insight::get_response(x)), w = model_weights),
-        log1p = .weighted_sum(log(1 / (insight::get_response(x) + 1)), w = model_weights),
-        log2 = .weighted_sum(log(1 / (insight::get_response(x) * log(2))), w = model_weights),
-        log10 = .weighted_sum(log(1 / (insight::get_response(x) * log(10))), w = model_weights),
-        exp = .weighted_sum(insight::get_response(x), w = model_weights),
-        expm1 = .weighted_sum((insight::get_response(x) - 1), w = model_weights),
-        sqrt = .weighted_sum(log(0.5 / sqrt(insight::get_response(x))), w = model_weights),
-        .ll_jacobian_adjustment(x, model_weights)
-      )
-    },
-    error = function(e) {
-      NULL
-    }
-  )
-}
-
-
-# this function calculates the adjustment for the log-likelihood of a model
-# with transformed response
-.ll_jacobian_adjustment <- function(model, weights = NULL) {
-  tryCatch(
-    {
-      trans <- insight::get_transformation(model)$transformation
-      .weighted_sum(log(
-        diag(attr(with(
-          insight::get_data(model, verbose = FALSE),
-          stats::numericDeriv(
-            expr = quote(trans(
-              get(insight::find_response(model))
-            )),
-            theta = insight::find_response(model)
-          )
-        ), "gradient"))
-      ), weights)
-    },
-    error = function(e) {
-      NULL
-    }
-  )
-}
-
-
-.weighted_sum <- function(x, w = NULL, ...) {
-  if (is.null(w)) {
-    mean(x) * length(x)
-  } else {
-    stats::weighted.mean(x, w) * length(x)
-  }
-}

From 0aa349233fd2ba62399f5caf16cbe89511b999ac Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Tue, 22 Oct 2024 12:59:00 +0200
Subject: [PATCH 14/14] Remove deprecated functions and arguments (#774)

---
 DESCRIPTION                               |  6 +++---
 NAMESPACE                                 |  2 --
 NEWS.md                                   | 10 ++++++++++
 R/check_convergence.R                     |  5 +++--
 R/check_heterogeneity_bias.R              |  9 +--------
 R/check_predictions.R                     | 20 --------------------
 R/performance_aicc.R                      |  2 +-
 R/simulate_residuals.R                    |  7 ++++---
 man/check_heterogeneity_bias.Rd           | 10 +---------
 man/check_predictions.Rd                  |  6 ------
 man/performance_aicc.Rd                   |  2 +-
 tests/testthat/test-check_zeroinflation.R | 22 +++++++++++-----------
 12 files changed, 35 insertions(+), 66 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 2b7fe815a..abac13053 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: performance
 Title: Assessment of Regression Models Performance
-Version: 0.12.4.1
+Version: 0.12.4.2
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",
@@ -95,7 +95,7 @@ Suggests:
     cplm,
     dagitty,
     dbscan,
-    DHARMa,
+    DHARMa (>= 0.4.7),
     estimatr,
     fixest,
     flextable,
@@ -129,7 +129,7 @@ Suggests:
     nonnest2,
     ordinal,
     parallel,
-    parameters (>= 0.21.6),
+    parameters (>= 0.22.0),
     patchwork,
     pscl,
     psych,
diff --git a/NAMESPACE b/NAMESPACE
index 08f6bcc15..d35d82547 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -566,7 +566,6 @@ export(check_multimodal)
 export(check_normality)
 export(check_outliers)
 export(check_overdispersion)
-export(check_posterior_predictions)
 export(check_predictions)
 export(check_residuals)
 export(check_singularity)
@@ -602,7 +601,6 @@ export(performance_rmse)
 export(performance_roc)
 export(performance_rse)
 export(performance_score)
-export(posterior_predictive_check)
 export(print_html)
 export(print_md)
 export(r2)
diff --git a/NEWS.md b/NEWS.md
index 4f0984b48..9eb5ded26 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,13 @@
+# performance 0.12.5
+
+## Breaking changes
+
+* Deprecated arguments and alias-function-names have been removed.
+
+## Changes
+
+* Increased accuracy for `check_convergence()` for *glmmTMB* models.
+
 # performance 0.12.4
 
 ## Changes
diff --git a/R/check_convergence.R b/R/check_convergence.R
index 6f7628a12..f60a7e298 100644
--- a/R/check_convergence.R
+++ b/R/check_convergence.R
@@ -98,9 +98,10 @@ check_convergence.merMod <- function(x, tolerance = 0.001, ...) {
 
 
 #' @export
-check_convergence.glmmTMB <- function(x, ...) {
+check_convergence.glmmTMB <- function(x, tolerance = 0.001, ...) {
   # https://github.com/glmmTMB/glmmTMB/issues/275
-  isTRUE(x$sdr$pdHess)
+  # https://stackoverflow.com/q/79110546/2094622
+  isTRUE(all.equal(x$fit$convergence, 0, tolerance = tolerance)) && isTRUE(x$sdr$pdHess)
 }
 
 
diff --git a/R/check_heterogeneity_bias.R b/R/check_heterogeneity_bias.R
index 755f47dfa..2414873cc 100644
--- a/R/check_heterogeneity_bias.R
+++ b/R/check_heterogeneity_bias.R
@@ -27,7 +27,6 @@
 #' @param nested Logical, if `TRUE`, the data is treated as nested. If `FALSE`,
 #'   the data is treated as cross-classified. Only applies if `by` contains more
 #'   than one variable.
-#' @param group Deprecated. Use `by` instead.
 #'
 #' @seealso
 #' For further details, read the vignette
@@ -44,15 +43,9 @@
 #' iris$ID <- sample(1:4, nrow(iris), replace = TRUE) # fake-ID
 #' check_heterogeneity_bias(iris, select = c("Sepal.Length", "Petal.Length"), by = "ID")
 #' @export
-check_heterogeneity_bias <- function(x, select = NULL, by = NULL, nested = FALSE, group = NULL) {
+check_heterogeneity_bias <- function(x, select = NULL, by = NULL, nested = FALSE) {
   insight::check_if_installed("datawizard", minimum_version = "0.12.0")
 
-  ## TODO: deprecate later
-  if (!is.null(group)) {
-    insight::format_warning("Argument `group` is deprecated and will be removed in a future release. Please use `by` instead.") # nolint
-    by <- group
-  }
-
   if (insight::is_model(x)) {
     by <- insight::find_random(x, split_nested = TRUE, flatten = TRUE)
     if (is.null(by)) {
diff --git a/R/check_predictions.R b/R/check_predictions.R
index fbc3b5eaf..c903f4309 100644
--- a/R/check_predictions.R
+++ b/R/check_predictions.R
@@ -423,26 +423,6 @@ pp_check.glmmTMB   <-
 #' S3method(bayesplot::pp_check, BFBayesFactor)
 
 
-
-# aliases --------------------------
-
-#' @rdname check_predictions
-#' @export
-posterior_predictive_check <- function(object, ...) {
-  .Deprecated("check_predictions()")
-  check_predictions(object, ...)
-}
-
-#' @rdname check_predictions
-#' @export
-check_posterior_predictions <- function(object, ...) {
-  .Deprecated("check_predictions()")
-  check_predictions(object, ...)
-}
-
-
-
-
 # methods -----------------------
 
 
diff --git a/R/performance_aicc.R b/R/performance_aicc.R
index eb10bc40f..74041ac1b 100644
--- a/R/performance_aicc.R
+++ b/R/performance_aicc.R
@@ -28,7 +28,7 @@
 #' scale. To get back to the original scale, the likelihood of the model is
 #' multiplied by the Jacobian/derivative of the transformation.
 #'
-#' In case it is not possible to return the corrected AIC value, a waring
+#' In case it is not possible to return the corrected AIC value, a warning
 #' is given that the corrected log-likelihood value could not be computed.
 #'
 #' @references
diff --git a/R/simulate_residuals.R b/R/simulate_residuals.R
index 7312c196f..1f58218c0 100644
--- a/R/simulate_residuals.R
+++ b/R/simulate_residuals.R
@@ -65,9 +65,10 @@
 #' @export
 simulate_residuals <- function(x, iterations = 250, ...) {
   insight::check_if_installed("DHARMa")
-  # TODO (low priority): Note that DHARMa::simulateResiduals(x, ...) does its own checks for whether
-  # or not the model passed to it is supported, do we want to use this or do our
-  # own checks so we can supply our own error message?
+  # TODO (low priority): Note that DHARMa::simulateResiduals(x, ...) does its
+  # own checks for whether or not the model passed to it is supported, do we
+  # want to use this or do our own checks so we can supply our own error
+  # message?
   if (iterations < 2) {
     insight::format_error("`iterations` must be at least 2.")
   }
diff --git a/man/check_heterogeneity_bias.Rd b/man/check_heterogeneity_bias.Rd
index 40b2b66ca..db18ae7ef 100644
--- a/man/check_heterogeneity_bias.Rd
+++ b/man/check_heterogeneity_bias.Rd
@@ -4,13 +4,7 @@
 \alias{check_heterogeneity_bias}
 \title{Check model predictor for heterogeneity bias}
 \usage{
-check_heterogeneity_bias(
-  x,
-  select = NULL,
-  by = NULL,
-  nested = FALSE,
-  group = NULL
-)
+check_heterogeneity_bias(x, select = NULL, by = NULL, nested = FALSE)
 }
 \arguments{
 \item{x}{A data frame or a mixed model object.}
@@ -41,8 +35,6 @@ See also section \emph{De-meaning for cross-classified designs} and
 \item{nested}{Logical, if \code{TRUE}, the data is treated as nested. If \code{FALSE},
 the data is treated as cross-classified. Only applies if \code{by} contains more
 than one variable.}
-
-\item{group}{Deprecated. Use \code{by} instead.}
 }
 \description{
 \code{check_heterogeneity_bias()} checks if model predictors or variables may
diff --git a/man/check_predictions.Rd b/man/check_predictions.Rd
index 148df6994..6c13fc0d5 100644
--- a/man/check_predictions.Rd
+++ b/man/check_predictions.Rd
@@ -3,8 +3,6 @@
 \name{check_predictions}
 \alias{check_predictions}
 \alias{check_predictions.default}
-\alias{posterior_predictive_check}
-\alias{check_posterior_predictions}
 \title{Posterior predictive checks}
 \usage{
 check_predictions(object, ...)
@@ -19,10 +17,6 @@ check_predictions(object, ...)
   verbose = TRUE,
   ...
 )
-
-posterior_predictive_check(object, ...)
-
-check_posterior_predictions(object, ...)
 }
 \arguments{
 \item{object}{A statistical model.}
diff --git a/man/performance_aicc.Rd b/man/performance_aicc.Rd
index 529ee53aa..b1d9a1255 100644
--- a/man/performance_aicc.Rd
+++ b/man/performance_aicc.Rd
@@ -47,7 +47,7 @@ unlike \code{stats::AIC()}, returns the "corrected" AIC value on the original
 scale. To get back to the original scale, the likelihood of the model is
 multiplied by the Jacobian/derivative of the transformation.
 
-In case it is not possible to return the corrected AIC value, a waring
+In case it is not possible to return the corrected AIC value, a warning
 is given that the corrected log-likelihood value could not be computed.
 }
 \examples{
diff --git a/tests/testthat/test-check_zeroinflation.R b/tests/testthat/test-check_zeroinflation.R
index 38a5c7726..53f8af9f5 100644
--- a/tests/testthat/test-check_zeroinflation.R
+++ b/tests/testthat/test-check_zeroinflation.R
@@ -111,22 +111,22 @@ test_that("check_zeroinflation, glmmTMB nbinom", {
   skip_if_not_installed("DHARMa")
   skip_on_cran()
 
+  data(Salamanders, package = "glmmTMB")
+  m <- glmmTMB::glmmTMB(
+    count ~ spp + mined + (1 | site),
+    family = glmmTMB::nbinom1(),
+    data = Salamanders
+  )
   set.seed(1234)
-  dat <- DHARMa::createData(sampleSize = 1000)
-  fit <- suppressWarnings(glmmTMB::glmmTMB(
-    observedResponse ~ Environment1 + (1 | group),
-    data = dat,
-    family = glmmTMB::nbinom1()
-  ))
   expect_equal(
-    check_zeroinflation(fit),
+    check_zeroinflation(m),
     structure(
       list(
-        predicted.zeros = 462,
-        observed.zeros = 482L,
-        ratio = 0.95850622406639,
+        predicted.zeros = 389,
+        observed.zeros = 387L,
+        ratio = 1.00635658914729,
         tolerance = 0.1,
-        p.value = 0.776
+        p.value = 0.944
       ),
       class = "check_zi"
     ),