support for quantile regression and mixed effects quantile regression (…

…#685)
easystats · Feb 16, 2024 · 41d60d0 · 41d60d0
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diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,7 +1,7 @@
 Type: Package
 Package: performance
 Title: Assessment of Regression Models Performance
-Version: 0.10.8.14
+Version: 0.10.8.15
 Authors@R: 
     c(person(given = "Daniel",
              family = "Lüdecke",
@@ -128,6 +128,7 @@ Suggests:
     patchwork,
     pscl,
     psych,
+    quantreg,
     qqplotr (>= 0.0.6),
     randomForest,
     rempsyc,

diff --git a/NAMESPACE b/NAMESPACE
@@ -89,6 +89,9 @@ S3method(check_outliers,metagen)
 S3method(check_outliers,numeric)
 S3method(check_outliers,rma)
 S3method(check_outliers,rma.uni)
+S3method(check_outliers,rq)
+S3method(check_outliers,rqs)
+S3method(check_outliers,rqss)
 S3method(check_overdispersion,default)
 S3method(check_overdispersion,fixest)
 S3method(check_overdispersion,fixest_multi)

diff --git a/NEWS.md b/NEWS.md
@@ -42,6 +42,8 @@
 * Fixed edge cases in `check_collinearity()` and `check_outliers()` for models
   with response variables of classes `Date`, `POSIXct`, `POSIXlt` or `difftime`.
 
+* Fixed issue with `check_model()` for models of package *quantreg*.
+
 # performance 0.10.8
 
 ## Changes

diff --git a/R/check_outliers.R b/R/check_outliers.R
@@ -1987,3 +1987,12 @@ check_outliers.lmrob <- check_outliers.glmmTMB
 
 #' @export
 check_outliers.glmrob <- check_outliers.glmmTMB
+
+#' @export
+check_outliers.rq <- check_outliers.glmmTMB
+
+#' @export
+check_outliers.rqs <- check_outliers.glmmTMB
+
+#' @export
+check_outliers.rqss <- check_outliers.glmmTMB
diff --git a/R/model_performance.bayesian.R b/R/model_performance.bayesian.R
@@ -40,7 +40,7 @@
 #'
 #'   - **PCP**: percentage of correct predictions, see [performance_pcp()].
 #'
-#' @examplesIf require("rstanarm") && require("rstantools") && require("BayesFactor")
+#' @examplesIf require("rstanarm") && require("rstantools")
 #' \donttest{
 #' model <- suppressWarnings(rstanarm::stan_glm(
 #'   mpg ~ wt + cyl,
@@ -59,12 +59,6 @@
 #'   refresh = 0
 #' ))
 #' model_performance(model)
-#'
-#' model <- BayesFactor::generalTestBF(carb ~ am + mpg, mtcars)
-#'
-#' model_performance(model)
-#' model_performance(model[3])
-#' model_performance(model, average = TRUE)
 #' }
 #' @seealso [r2_bayes]
 #' @references Gelman, A., Goodrich, B., Gabry, J., and Vehtari, A. (2018).

diff --git a/R/r2_bayes.R b/R/r2_bayes.R
@@ -30,7 +30,7 @@
 #'   `r2_posterior()` is the actual workhorse for `r2_bayes()` and
 #'   returns a posterior sample of Bayesian R2 values.
 #'
-#' @examplesIf require("rstanarm") && require("rstantools") && require("BayesFactor") && require("brms")
+#' @examplesIf require("rstanarm") && require("rstantools") && require("brms")
 #' library(performance)
 #' \donttest{
 #' model <- suppressWarnings(rstanarm::stan_glm(
@@ -53,24 +53,6 @@
 #' r2_bayes(model)
 #' }
 #'
-#' BFM <- BayesFactor::generalTestBF(mpg ~ qsec + gear, data = mtcars, progress = FALSE)
-#' FM <- BayesFactor::lmBF(mpg ~ qsec + gear, data = mtcars)
-#'
-#' r2_bayes(FM)
-#' r2_bayes(BFM[3])
-#' r2_bayes(BFM, average = TRUE) # across all models
-#'
-#' # with random effects:
-#' mtcars$gear <- factor(mtcars$gear)
-#' model <- BayesFactor::lmBF(
-#'   mpg ~ hp + cyl + gear + gear:wt,
-#'   mtcars,
-#'   progress = FALSE,
-#'   whichRandom = c("gear", "gear:wt")
-#' )
-#'
-#' r2_bayes(model)
-#'
 #' \donttest{
 #' model <- suppressWarnings(brms::brm(
 #'   mpg ~ wt + cyl,

diff --git a/man/model_performance.stanreg.Rd b/man/model_performance.stanreg.Rd
diff --git a/man/r2_bayes.Rd b/man/r2_bayes.Rd
diff --git a/tests/testthat/test-check_model.R b/tests/testthat/test-check_model.R
@@ -43,3 +43,11 @@ test_that("`check_model()` for invalid models", {
   m1 <- lm(y ~ 1, data = dd)
   expect_error(check_model(m1))
 })
+
+test_that("`check_model()` works for quantreg", {
+  skip_if_not_installed("quantreg")
+  data(engel, package = "quantreg")
+  qm <- quantreg::rq(foodexp ~ income, data = engel)
+  x <- check_model(qm, verbose = FALSE)
+  expect_s3_class(x, "check_model")
+})
diff --git a/vignettes/r2.Rmd b/vignettes/r2.Rmd
@@ -29,14 +29,11 @@ knitr::opts_chunk$set(
 )
 options(digits = 2)
 
-pkgs <- c(
-  "effectsize", "BayesFactor", "lme4", "rstanarm"
-)
+pkgs <- c("effectsize", "lme4", "rstanarm")
 successfully_loaded <- sapply(pkgs, requireNamespace, quietly = TRUE)
 if (all(successfully_loaded)) {
   library(performance)
   library(effectsize)
-  library(BayesFactor)
   library(lme4)
   library(rstanarm)
 }
@@ -147,27 +144,6 @@ model <- stan_lmer(Petal.Length ~ Petal.Width + (1 | Species), data = iris, refr
 r2(model)
 ```
 
-Let's look at another regression analysis carried out with `{BayesFactor}` package.
-
-```{r, eval=successfully_loaded["BayesFactor"] && utils::packageVersion("BayesFactor") >= package_version("0.9.12-4.3")}
-library(BayesFactor)
-data(puzzles)
-
-m1 <- anovaBF(extra ~ group + ID,
-  data = sleep,
-  whichRandom = "ID", progress = FALSE
-)
-
-r2(m1)
-
-m2 <- generalTestBF(RT ~ shape * color + ID,
-  data = puzzles, whichRandom = "ID",
-  neverExclude = "ID", progress = FALSE
-)
-
-r2(m2)
-```
-
 # Comparing change in R2 using Cohen's *f*
 
 Cohen's $f$ (of [ANOVA fame](https://easystats.github.io/effectsize/articles/anovaES.html)) can be used as a measure of effect size in the context of sequential multiple regression (i.e., [**nested models**](https://easystats.github.io/performance/reference/test_performance.html)).