easystats · strengejacke · Mar 31, 2023 · Jan 12, 2023 · Jan 12, 2023 · Jan 18, 2023
diff --git a/.Rbuildignore b/.Rbuildignore
@@ -16,7 +16,7 @@
 ^vignettes/.
 ^pkgdown/.
 ^WIP/.
-^paper/.
+^papers/.
 ^.github/.
 ^CODE_OF_CONDUCT\.md$
 ^revdep$

diff --git a/R/check_outliers.R b/R/check_outliers.R
@@ -197,13 +197,13 @@
 #'
 #' ```
 #' list(
-#'   zscore = stats::qnorm(p = 1 - 0.001),
-#'   zscore_robust = stats::qnorm(p = 1 - 0.001),
+#'   zscore = stats::qnorm(p = 1 - 0.001 / 2),
+#'   zscore_robust = stats::qnorm(p = 1 - 0.001 / 2),
 #'   iqr = 1.7,
-#'   ci = 0.999,
-#'   eti = 0.999,
-#'   hdi = 0.999,
-#'   bci = 0.999,
+#'   ci = 1 - 0.001,
+#'   eti = 1 - 0.001,
+#'   hdi = 1 - 0.001,
+#'   bci = 1 - 0.001,
 #'   cook = stats::qf(0.5, ncol(x), nrow(x) - ncol(x)),
 #'   pareto = 0.7,
 #'   mahalanobis = stats::qchisq(p = 1 - 0.001, df = ncol(x)),
@@ -1233,13 +1233,13 @@ check_outliers.geeglm <- check_outliers.gls
 }
 
 .check_outliers_thresholds_nowarn <- function(x) {
-  zscore <- stats::qnorm(p = 1 - 0.001)
-  zscore_robust <- stats::qnorm(p = 1 - 0.001)
+  zscore <- stats::qnorm(p = 1 - 0.001 / 2)
+  zscore_robust <- stats::qnorm(p = 1 - 0.001 / 2)
   iqr <- 1.7
-  ci <- 0.999
-  eti <- 0.999
-  hdi <- 0.999
-  bci <- 0.999
+  ci <- 1 - 0.001
+  eti <- 1 - 0.001
+  hdi <- 1 - 0.001
+  bci <- 1 - 0.001
   cook <- stats::qf(0.5, ncol(x), nrow(x) - ncol(x))
   pareto <- 0.7
   mahalanobis <- stats::qchisq(p = 1 - 0.001, df = ncol(x))
@@ -1273,7 +1273,7 @@ check_outliers.geeglm <- check_outliers.gls
 # utilities --------------------
 
 .check_outliers_zscore <- function(x,
-                                   threshold = stats::qnorm(p = 1 - 0.001),
+                                   threshold = stats::qnorm(p = 1 - 0.001 / 2),
                                    robust = TRUE,
                                    method = "max",
                                    ID.names = NULL) {
@@ -1382,7 +1382,7 @@ check_outliers.geeglm <- check_outliers.gls
 
 
 .check_outliers_ci <- function(x,
-                               threshold = 0.999,
+                               threshold = 1 - 0.001,
                                method = "ci",
                                ID.names = NULL) {
   # Run through columns

diff --git a/man/check_outliers.Rd b/man/check_outliers.Rd
diff --git a/paper/apa.csl → papers/JOSS/apa.csl b/paper/apa.csl → papers/JOSS/apa.csl
diff --git a/paper/figure1.png → papers/JOSS/figure1.png b/paper/figure1.png → papers/JOSS/figure1.png
diff --git a/paper/figure2.png → papers/JOSS/figure2.png b/paper/figure2.png → papers/JOSS/figure2.png
diff --git a/paper/figure_workflow.png → papers/JOSS/figure_workflow.png b/paper/figure_workflow.png → papers/JOSS/figure_workflow.png
diff --git a/paper/figures.pptx → papers/JOSS/figures.pptx b/paper/figures.pptx → papers/JOSS/figures.pptx
diff --git a/paper/make_figs.R → papers/JOSS/make_figs.R b/paper/make_figs.R → papers/JOSS/make_figs.R
diff --git a/paper/paper.bib → papers/JOSS/paper.bib b/paper/paper.bib → papers/JOSS/paper.bib
diff --git a/paper/paper.md → papers/JOSS/paper.md b/paper/paper.md → papers/JOSS/paper.md
diff --git a/paper/paper.pdf → papers/JOSS/paper.pdf b/paper/paper.pdf → papers/JOSS/paper.pdf
diff --git a/papers/Mathematics/journalnames.tex b/papers/Mathematics/journalnames.tex
diff --git a/papers/Mathematics/logo-mdpi.pdf b/papers/Mathematics/logo-mdpi.pdf
diff --git a/papers/Mathematics/logo-orcid.pdf b/papers/Mathematics/logo-orcid.pdf
diff --git a/papers/Mathematics/logo-updates.pdf b/papers/Mathematics/logo-updates.pdf