Merge branch 'main' into strengejacke/issue697

DESCRIPTION

@@ -1,28 +1,28 @@
 Type: Package
 Package: performance
 Title: Assessment of Regression Models Performance
-Version: 0.12.3.3
+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]",
@@ -48,9 +48,9 @@ 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")),
       person(given = "Joseph",
@@ -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 (>= 0.15.0),
+    insight (>= 0.20.5),
+    datawizard (>= 0.13.0),
     stats,
     utils
 Suggests:
@@ -95,15 +95,15 @@ Suggests:
     cplm,
     dagitty,
     dbscan,
-    DHARMa,
+    DHARMa (>= 0.4.7),
     estimatr,
     fixest,
     flextable,
     forecast,
     ftExtra,
     gamm4,
     ggdag,
-    glmmTMB,
+    glmmTMB (>= 1.1.10),
     graphics,
     Hmisc,
     httr2,
@@ -129,7 +129,7 @@ Suggests:
     nonnest2,
     ordinal,
     parallel,
-    parameters (>= 0.21.6),
+    parameters (>= 0.22.0),
     patchwork,
     pscl,
     psych,
@@ -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: easystats/insight

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)

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
@@ -7,6 +17,10 @@
 
 * 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

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)
 }
 
 

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,
@@ -285,15 +312,13 @@ 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 +328,7 @@ 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
@@ -340,6 +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

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
@@ -39,20 +38,14 @@
 #'   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")
 #' @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)) {

R/check_model_diagnostics.R

@@ -478,7 +478,7 @@
   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),

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 -----------------------