From 0f43a929c78b806cd7fb89fb8dc914738a73177e Mon Sep 17 00:00:00 2001
From: JTPetter <61797391+JTPetter@users.noreply.github.com>
Date: Wed, 20 Nov 2024 15:51:32 +0100
Subject: [PATCH 1/3] Missing packages added to DESCRIPTION

---
 DESCRIPTION | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 447a684..6f2b8ee 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -18,7 +18,9 @@ Imports:
   jaspTTests,
   ggforce,
   tidyr,
-  igraph
+  igraph,
+  HDInterval,
+  metafor
 Remotes:
   jasp-stats/jaspBase,
   jasp-stats/jaspGraphs,

From 91674869ac2e3844d312ebe1eea278eee799821b Mon Sep 17 00:00:00 2001
From: JTPetter <61797391+JTPetter@users.noreply.github.com>
Date: Wed, 20 Nov 2024 16:24:27 +0100
Subject: [PATCH 2/3] Fixes for effect sizes

---
 R/LSeffectSizes.R | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/R/LSeffectSizes.R b/R/LSeffectSizes.R
index b6bbe25..66b11bb 100644
--- a/R/LSeffectSizes.R
+++ b/R/LSeffectSizes.R
@@ -517,7 +517,7 @@ switchOptions <- function(options) {
   rhoTable <- createJaspContainer()
   rhoTable$position <- 3
   rhoTable$dependOn(c("effectSize", "effectSizeValueRho", "simulateData", "simulateDataN",
-                      "rhoSharedVariance", "setSeed", "seed"))
+                      "rhoSharedVariance", "setSeed", "seed", "explanatoryTexts"))
   jaspResults[["rhoTable"]] <- rhoTable
 
 
@@ -712,7 +712,7 @@ switchOptions <- function(options) {
 
   if (options[["plotRhoRegression"]]) {
     plot <- plot + ggplot2::geom_abline(
-      intercept = mu2,
+      intercept = mu2 - (rho * (sigma2/sigma1)) * mu1,
       slope     = rho * (sigma2/sigma1)
     )
   }
@@ -936,7 +936,7 @@ switchOptions <- function(options) {
 
   phiTable <-  createJaspContainer()
   phiTable$position <- 3
-  phiTable$dependOn(c("effectSize", "effectSizeValuePhi", "simulateData", "simulateDataN", "pX", "pY", "inputPopulation", "pX1Y1", "pX1Y0", "pX0Y1", "pX0Y0", "setSeed", "seed", "phiOR", "phiRR", "phiRD"))
+  phiTable$dependOn(c("effectSize", "effectSizeValuePhi", "simulateData", "simulateDataN", "pX", "pY", "inputPopulation", "pX1Y1", "pX1Y0", "pX0Y1", "pX0Y0", "setSeed", "seed", "phiOR", "phiRR", "phiRD", "explanatoryTexts"))
   jaspResults[["phiTable"]] <- phiTable
 
 

From 54c83fb3c63a05ec9edee00be93e88442a1721ad Mon Sep 17 00:00:00 2001
From: JTPetter <61797391+JTPetter@users.noreply.github.com>
Date: Wed, 20 Nov 2024 16:42:50 +0100
Subject: [PATCH 3/3] Fix bug in descriptive statistics

---
 R/LSTdescriptives.R | 15 +++++++++++----
 1 file changed, 11 insertions(+), 4 deletions(-)

diff --git a/R/LSTdescriptives.R b/R/LSTdescriptives.R
index 11b8335..b994ddc 100644
--- a/R/LSTdescriptives.R
+++ b/R/LSTdescriptives.R
@@ -24,12 +24,18 @@ LSTdescriptives <- function(jaspResults, dataset, options, state = NULL) {
   data <- .getDataLSTdesc(jaspResults, options, inputType)
 
   #checking whether data is discrete or continuous, whereas only integers are treated as discrete
-  discrete <- ifelse(all(data$x == as.integer(data$x)), TRUE, FALSE)
+  integerData <- as.integer(data$x)
+  # conversion to integers fails with extreme values, if it failed for any value just treat it as continuous
+  if (any(is.na(integerData))) {
+    discrete <- FALSE
+  } else {
+    discrete <- ifelse(all(data$x == integerData), TRUE, FALSE)
+  }
 
   stats <- switch(options[["LSdescStatistics"]],
-                            "LSdescMean" = "ct", "LSdescMedian" = "ct", "LSdescMode" = "ct", "LSdescMMM" = "ct",
-                            "LSdescRange" = "spread", "LSdescQR" = "spread", "LSdescSD" = "spread",
-                            "none" = "none")
+                  "LSdescMean" = "ct", "LSdescMedian" = "ct", "LSdescMode" = "ct", "LSdescMMM" = "ct",
+                  "LSdescRange" = "spread", "LSdescQR" = "spread", "LSdescSD" = "spread",
+                  "none" = "none")
 
 
   if (options[["LSdescHistBar"]])
@@ -497,6 +503,7 @@ LSTdescriptives <- function(jaspResults, dataset, options, state = NULL) {
   variable <- variable[variable != ""]
   dataset <- .readDataSetToEnd(columns.as.numeric = variable)
   df <- data.frame(x = unlist(dataset))
+  df <- na.omit(df)
   return(df)
 }