Housekeeping (fix GH action warnings, lintr, code-style, ...) (#611)

* fix warnings in tests * fix * vig * fx vig * fix * fix * fix, lintr * fix * lintr, code-style, fix vignette * fix vignette? * fix * fix * fix * fix?
easystats · Jun 30, 2023 · 6090d1c · 6090d1c
1 parent 5af07e4
commit 6090d1c
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Showing 27 changed files with 357 additions and 160 deletions.
diff --git a/R/bayesfactor_models.R b/R/bayesfactor_models.R
@@ -204,9 +204,7 @@ bayesfactor_models.default <- function(..., denominator = 1, verbose = TRUE) {
     supported_models[!has_terms] <- FALSE
   }
 
-  objects <- tryCatch(do.call(insight::ellipsis_info, c(mods, verbose = FALSE)),
-    error = function(...) NULL
-  )
+  objects <- .safe(do.call(insight::ellipsis_info, c(mods, verbose = FALSE)))
   if (!is.null(objects)) {
     were_checked <- inherits(objects, "ListModels")
 
@@ -219,9 +217,9 @@ bayesfactor_models.default <- function(..., denominator = 1, verbose = TRUE) {
 
     # Get BIC
     if (were_checked && estimator == "REML" &&
-      any(vapply(mods, insight::is_mixed_model, TRUE)) &&
-      !isTRUE(attr(objects, "same_fixef")) &&
-      verbose) {
+          any(vapply(mods, insight::is_mixed_model, TRUE)) &&
+          !isTRUE(attr(objects, "same_fixef")) &&
+          verbose) {
       insight::format_warning(
         "Information criteria (like BIC) based on REML fits (i.e. `estimator=\"REML\"`)",
         "are not recommended for comparison between models with different fixed effects.",

diff --git a/R/bci.R b/R/bci.R
@@ -227,7 +227,17 @@ bci.brmsfit <- function(x, ci = 0.95, effects = c("fixed", "random", "all"),
   component <- match.arg(component)
 
   out <- .prepare_output(
-    bci(insight::get_parameters(x, effects = effects, component = component, parameters = parameters), ci = ci, verbose = verbose, ...),
+    bci(
+      insight::get_parameters(
+        x,
+        effects = effects,
+        component = component,
+        parameters = parameters
+      ),
+      ci = ci,
+      verbose = verbose,
+      ...
+    ),
     insight::clean_parameters(x)
   )
 

diff --git a/R/bic_to_bf.R b/R/bic_to_bf.R
@@ -10,7 +10,8 @@
 #' @param log If `TRUE`, return the `log(BF)`.
 #'
 #' @references
-#' Wagenmakers, E. J. (2007). A practical solution to the pervasive problems of p values. Psychonomic bulletin & review, 14(5), 779-804
+#' Wagenmakers, E. J. (2007). A practical solution to the pervasive problems of
+#' p values. Psychonomic bulletin & review, 14(5), 779-804
 #'
 #' @examples
 #' bic1 <- BIC(lm(Sepal.Length ~ 1, data = iris))

diff --git a/R/check_prior.R b/R/check_prior.R
@@ -147,16 +147,16 @@ check_prior.blavaan <- check_prior.brmsfit
     priors <- priors[common_columns]
     posteriors <- posteriors[common_columns]
     if (verbose) {
-      insight::format_warning("Parameters and priors could not be fully matched. Only returning results for parameters with matching priors.")
+      insight::format_warning(
+        "Parameters and priors could not be fully matched. Only returning results for parameters with matching priors."
+      )
     }
   }
 
 
   # for priors whose distribution cannot be simulated, prior values are
   # all NA. Catch those, and warn user
-  all_missing <- sapply(priors, function(i) {
-    all(is.na(i))
-  })
+  all_missing <- vapply(priors, function(i) all(is.na(i)), TRUE)
 
   if (any(all_missing) && verbose) {
     insight::format_warning("Some priors could not be simulated.")

diff --git a/R/diagnostic_draws.R b/R/diagnostic_draws.R
@@ -8,7 +8,7 @@
 #' set.seed(333)
 #'
 #' if (require("brms", quietly = TRUE)) {
-#'   model <- suppressWarning(brm(mpg ~ wt * cyl * vs,
+#'   model <- suppressWarnings(brm(mpg ~ wt * cyl * vs,
 #'     data = mtcars,
 #'     iter = 100, control = list(adapt_delta = 0.80),
 #'     refresh = 0