Merge branch 'main' into update_outlier_vignette

easystats · Oct 24, 2024 · 584fb7b · 584fb7b
2 parents b38efd9 + 0aa3492
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diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION
@@ -1,3 +1,3 @@
-Version: 0.12.2
-Date: 2024-07-17 21:02:38 UTC
-SHA: d4c45126ca666644785dc64d2af6b87eee9ca39b
+Version: 0.12.3
+Date: 2024-09-02 16:10:51 UTC
+SHA: dfbe03fd4961ee9049d5169275248a4ef7a5a21e
diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,28 +1,28 @@
 Type: Package
 Package: performance
 Title: Assessment of Regression Models Performance
-Version: 0.12.2
+Version: 0.12.4.2
 Authors@R:
     c(person(given = "Daniel",
              family = "Lüdecke",
              role = c("aut", "cre"),
              email = "[email protected]",
-             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 = "[email protected]",
-             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 = "[email protected]",
-             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 = "[email protected]",
-             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 = "[email protected]",
-             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 = "[email protected]",
-             comment = c(ORCID = "0000-0003-4315-6788", Twitter = "@rempsyc")),
+             comment = c(ORCID = "0000-0003-4315-6788")),
       person(given = "Vincent",
              family = "Arel-Bundock",
              email = "[email protected]",
@@ -48,11 +48,15 @@ Authors@R:
              role = "rev"),
       person(given = "gjo11",
              role = "rev"),
-      person("Etienne",
-             "Bacher", ,
-             "[email protected]",
+      person(given = "Etienne",
+             family = "Bacher", ,
+             email = "[email protected]",
              role = "ctb",
-             comment = c(ORCID = "0000-0002-9271-5075")))
+             comment = c(ORCID = "0000-0002-9271-5075")),
+      person(given = "Joseph",
+             family = "Luchman",
+             role = "ctb",
+             comment = c(ORCID = "0000-0002-8886-9717")))
 Maintainer: Daniel Lüdecke <[email protected]>
 Description: Utilities for computing measures to assess model quality,
     which are not directly provided by R's 'base' or 'stats' packages.
@@ -69,9 +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 (>= 0.15.0),
+    insight (>= 0.20.5),
+    datawizard (>= 0.13.0),
     stats,
     utils
 Suggests:
@@ -89,16 +93,18 @@ Suggests:
     CompQuadForm,
     correlation,
     cplm,
+    dagitty,
     dbscan,
-    DHARMa,
+    DHARMa (>= 0.4.7),
     estimatr,
     fixest,
     flextable,
     forecast,
     gamm4,
     geomtextpath,
     ggplot2,
-    glmmTMB,
+    ggdag,
+    glmmTMB (>= 1.1.10),
     graphics,
     Hmisc,
     httr2,
@@ -124,7 +130,7 @@ Suggests:
     nonnest2,
     ordinal,
     parallel,
-    parameters (>= 0.21.6),
+    parameters (>= 0.22.0),
     patchwork,
     pscl,
     psych,
@@ -137,7 +143,7 @@ Suggests:
     rstanarm,
     rstantools,
     sandwich,
-    see (>= 0.8.2),
+    see (>= 0.9.0),
     survey,
     survival,
     testthat (>= 3.2.1),
@@ -155,3 +161,4 @@ Config/Needs/website:
     r-lib/pkgdown,
     easystats/easystatstemplate
 Config/rcmdcheck/ignore-inconsequential-notes: true
+Remotes: easystats/insight
diff --git a/NAMESPACE b/NAMESPACE
@@ -170,12 +170,14 @@ S3method(model_performance,censReg)
 S3method(model_performance,clm)
 S3method(model_performance,clm2)
 S3method(model_performance,coxph)
+S3method(model_performance,coxph_weightit)
 S3method(model_performance,default)
 S3method(model_performance,felm)
 S3method(model_performance,fixest)
 S3method(model_performance,fixest_multi)
 S3method(model_performance,flexsurvreg)
 S3method(model_performance,glm)
+S3method(model_performance,glm_weightit)
 S3method(model_performance,glmmTMB)
 S3method(model_performance,glmmadmb)
 S3method(model_performance,glmx)
@@ -197,9 +199,11 @@ S3method(model_performance,mixor)
 S3method(model_performance,mlogit)
 S3method(model_performance,model_fit)
 S3method(model_performance,multinom)
+S3method(model_performance,multinom_weightit)
 S3method(model_performance,negbinirr)
 S3method(model_performance,negbinmfx)
 S3method(model_performance,nestedLogit)
+S3method(model_performance,ordinal_weightit)
 S3method(model_performance,plm)
 S3method(model_performance,poissonirr)
 S3method(model_performance,poissonmfx)
@@ -269,6 +273,7 @@ S3method(plot,binned_residuals)
 S3method(plot,check_autocorrelation)
 S3method(plot,check_clusterstructure)
 S3method(plot,check_collinearity)
+S3method(plot,check_dag)
 S3method(plot,check_distribution)
 S3method(plot,check_distribution_numeric)
 S3method(plot,check_heteroscedasticity)
@@ -289,6 +294,7 @@ S3method(print,binned_residuals)
 S3method(print,check_autocorrelation)
 S3method(print,check_collinearity)
 S3method(print,check_concurvity)
+S3method(print,check_dag)
 S3method(print,check_distribution)
 S3method(print,check_distribution_numeric)
 S3method(print,check_heterogeneity_bias)
@@ -484,6 +490,7 @@ S3method(r2_mcfadden,serp)
 S3method(r2_mcfadden,truncreg)
 S3method(r2_mcfadden,vglm)
 S3method(r2_mckelvey,default)
+S3method(r2_mlm,mlm)
 S3method(r2_nagelkerke,BBreg)
 S3method(r2_nagelkerke,DirichletRegModel)
 S3method(r2_nagelkerke,bife)
@@ -538,12 +545,14 @@ S3method(test_vuong,default)
 S3method(test_wald,ListNestedRegressions)
 S3method(test_wald,ListNonNestedRegressions)
 S3method(test_wald,default)
+export(as.dag)
 export(binned_residuals)
 export(check_autocorrelation)
 export(check_clusterstructure)
 export(check_collinearity)
 export(check_concurvity)
 export(check_convergence)
+export(check_dag)
 export(check_distribution)
 export(check_factorstructure)
 export(check_heterogeneity_bias)
@@ -557,7 +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)
@@ -593,7 +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)
@@ -606,6 +613,7 @@ export(r2_loo)
 export(r2_loo_posterior)
 export(r2_mcfadden)
 export(r2_mckelvey)
+export(r2_mlm)
 export(r2_nagelkerke)
 export(r2_nakagawa)
 export(r2_posterior)

diff --git a/NEWS.md b/NEWS.md
@@ -1,3 +1,38 @@
+# 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
+
+* `check_dag()` now also checks for colliders, and suggests removing it in the
+  printed output.
+
+* 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
+
+* `check_dag()`, to check DAGs for correct adjustment sets.
+
+## Changes
+
+* `check_heterogeneity_bias()` gets a `nested` argument. Furthermore, `by` can
+  specify more than one variable, meaning that nested or cross-classified
+  model designs can also be tested for heterogeneity bias.
+
 # performance 0.12.2
 
 Patch release, to ensure that _performance_ runs with older version of

diff --git 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)
 }