From 5842c1534cd01b71ed65a99352431a133feceb1d Mon Sep 17 00:00:00 2001
From: Daniel <mail@danielluedecke.de>
Date: Fri, 15 Mar 2024 18:32:01 +0100
Subject: [PATCH] fixes

---
 R/check_residuals.R        |  4 ++--
 R/check_zeroinflation.R    | 14 ++++++++++----
 man/check_zeroinflation.Rd | 10 +++++++++-
 3 files changed, 21 insertions(+), 7 deletions(-)

diff --git a/R/check_residuals.R b/R/check_residuals.R
index 628c5cfd0..b04328f25 100644
--- a/R/check_residuals.R
+++ b/R/check_residuals.R
@@ -42,7 +42,7 @@ check_residuals.default <- function(x, alternative = c("two.sided", "less", "gre
 #' @export
 check_residuals.performance_simres <- function(x, alternative = c("two.sided", "less", "greater"), ...) {
   alternative <- match.arg(alternative)
-  ts <- suppressWarnings(
+  ts_test <- suppressWarnings(
     stats::ks.test(
       stats::residuals(x),
       "punif",
@@ -51,7 +51,7 @@ check_residuals.performance_simres <- function(x, alternative = c("two.sided", "
     )
   )
 
-  p.val <- ts$p.value
+  p.val <- ts_test$p.value
 
   attr(p.val, "data") <- x
   attr(p.val, "object_name") <- insight::safe_deparse_symbol(substitute(x))
diff --git a/R/check_zeroinflation.R b/R/check_zeroinflation.R
index d8e42fbe0..e392137d1 100644
--- a/R/check_zeroinflation.R
+++ b/R/check_zeroinflation.R
@@ -7,9 +7,13 @@
 #' @param x Fitted model of class `merMod`, `glmmTMB`, `glm`, or `glm.nb`
 #' (package **MASS**).
 #' @param tolerance The tolerance for the ratio of observed and predicted
-#'  zeros to considered as over- or underfitting zeros. A ratio
-#'  between 1 +/- `tolerance` is considered as OK, while a ratio
-#'  beyond or below this threshold would indicate over- or underfitting.
+#' zeros to considered as over- or underfitting zeros. A ratio
+#' between 1 +/- `tolerance` is considered as OK, while a ratio
+#' beyond or below this threshold would indicate over- or underfitting.
+#' @param alternative A character string specifying the alternative hypothesis.
+#' @param ... Arguments passed down to [`simulate_residuals()`]. This only applies
+#' for models with zero-inflation component, or for models of class `glmmTMB`
+#' from `nbinom1` or `nbinom2` family.
 #'
 #' @return A list with information about the amount of predicted and observed
 #'  zeros in the outcome, as well as the ratio between these two values.
@@ -23,7 +27,9 @@
 #' or hurdle models, the results from `check_zeroinflation()` are likely to be
 #' unreliable. In such cases, it is recommended to use `simulate_residuals()`
 #' first, followed by `check_zeroinflation()` to check for zero-inflation,
-#' e.g.: `check_zeroinflation(simulate_residuals(model))`.
+#' e.g.: `check_zeroinflation(simulate_residuals(model))`. Usually, such models
+#' are detected automatically and `check_zeroinflation()` internally calls
+#' `simulate_residuals()` if necessary.
 #'
 #' @family functions to check model assumptions and and assess model quality
 #'
diff --git a/man/check_zeroinflation.Rd b/man/check_zeroinflation.Rd
index 724e2be00..32a2c2143 100644
--- a/man/check_zeroinflation.Rd
+++ b/man/check_zeroinflation.Rd
@@ -21,10 +21,16 @@ check_zeroinflation(x, ...)
 \item{x}{Fitted model of class \code{merMod}, \code{glmmTMB}, \code{glm}, or \code{glm.nb}
 (package \strong{MASS}).}
 
+\item{...}{Arguments passed down to \code{\link[=simulate_residuals]{simulate_residuals()}}. This only applies
+for models with zero-inflation component, or for models of class \code{glmmTMB}
+from \code{nbinom1} or \code{nbinom2} family.}
+
 \item{tolerance}{The tolerance for the ratio of observed and predicted
 zeros to considered as over- or underfitting zeros. A ratio
 between 1 +/- \code{tolerance} is considered as OK, while a ratio
 beyond or below this threshold would indicate over- or underfitting.}
+
+\item{alternative}{A character string specifying the alternative hypothesis.}
 }
 \value{
 A list with information about the amount of predicted and observed
@@ -44,7 +50,9 @@ In case of negative binomial models, models with zero-inflation component,
 or hurdle models, the results from \code{check_zeroinflation()} are likely to be
 unreliable. In such cases, it is recommended to use \code{simulate_residuals()}
 first, followed by \code{check_zeroinflation()} to check for zero-inflation,
-e.g.: \code{check_zeroinflation(simulate_residuals(model))}.
+e.g.: \code{check_zeroinflation(simulate_residuals(model))}. Usually, such models
+are detected automatically and \code{check_zeroinflation()} internally calls
+\code{simulate_residuals()} if necessary.
 }
 \examples{
 \dontshow{if (require("glmmTMB") && require("DHARMa")) (if (getRversion() >= "3.4") withAutoprint else force)(\{ # examplesIf}