From 734187721299428546ea2b0e124f86e523b91865 Mon Sep 17 00:00:00 2001
From: Sebastian Jentschke <Sebastian.Jentschke@gmail.com>
Date: Tue, 9 Sep 2025 08:43:42 +1000
Subject: [PATCH 1/5] Added UI elements for data summary in EFA and PCA

---
 R/efa.h.R         | 76 +++++++++++++++++++++++++++++--------------
 R/pca.h.R         | 82 +++++++++++++++++++++++++++++++----------------
 jamovi/efa.a.yaml | 56 ++++++++++++++++++++++----------
 jamovi/efa.u.yaml |  9 ++++++
 jamovi/pca.a.yaml | 56 ++++++++++++++++++++++----------
 jamovi/pca.u.yaml |  9 ++++++
 6 files changed, 203 insertions(+), 85 deletions(-)

diff --git a/R/efa.h.R b/R/efa.h.R
index 030cbb58..83b887b7 100644
--- a/R/efa.h.R
+++ b/R/efa.h.R
@@ -12,6 +12,10 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             minEigen = 0,
             extraction = "minres",
             rotation = "oblimin",
+            minCorrThr = 0.3,
+            maxCorrThr = 0.9,
+            kmo = FALSE,
+            bartlett = FALSE,
             hideLoadings = 0.3,
             sortLoadings = FALSE,
             screePlot = FALSE,
@@ -19,8 +23,6 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             factorCor = FALSE,
             factorSummary = FALSE,
             modelFit = FALSE,
-            kmo = FALSE,
-            bartlett = FALSE,
             factorScoreMethod = "Thurstone", ...) {
 
             super$initialize(
@@ -75,6 +77,26 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "oblimin",
                     "simplimax"),
                 default="oblimin")
+            private$..minCorrThr <- jmvcore::OptionNumber$new(
+                "minCorrThr",
+                minCorrThr,
+                min=0,
+                max=1,
+                default=0.3)
+            private$..maxCorrThr <- jmvcore::OptionNumber$new(
+                "maxCorrThr",
+                maxCorrThr,
+                min=0,
+                max=1,
+                default=0.9)
+            private$..kmo <- jmvcore::OptionBool$new(
+                "kmo",
+                kmo,
+                default=FALSE)
+            private$..bartlett <- jmvcore::OptionBool$new(
+                "bartlett",
+                bartlett,
+                default=FALSE)
             private$..hideLoadings <- jmvcore::OptionNumber$new(
                 "hideLoadings",
                 hideLoadings,
@@ -103,14 +125,6 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                 "modelFit",
                 modelFit,
                 default=FALSE)
-            private$..kmo <- jmvcore::OptionBool$new(
-                "kmo",
-                kmo,
-                default=FALSE)
-            private$..bartlett <- jmvcore::OptionBool$new(
-                "bartlett",
-                bartlett,
-                default=FALSE)
             private$..factorScoresOV <- jmvcore::OptionOutput$new(
                 "factorScoresOV")
             private$..factorScoreMethod <- jmvcore::OptionList$new(
@@ -130,6 +144,10 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             self$.addOption(private$..minEigen)
             self$.addOption(private$..extraction)
             self$.addOption(private$..rotation)
+            self$.addOption(private$..minCorrThr)
+            self$.addOption(private$..maxCorrThr)
+            self$.addOption(private$..kmo)
+            self$.addOption(private$..bartlett)
             self$.addOption(private$..hideLoadings)
             self$.addOption(private$..sortLoadings)
             self$.addOption(private$..screePlot)
@@ -137,8 +155,6 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             self$.addOption(private$..factorCor)
             self$.addOption(private$..factorSummary)
             self$.addOption(private$..modelFit)
-            self$.addOption(private$..kmo)
-            self$.addOption(private$..bartlett)
             self$.addOption(private$..factorScoresOV)
             self$.addOption(private$..factorScoreMethod)
         }),
@@ -149,6 +165,10 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
         minEigen = function() private$..minEigen$value,
         extraction = function() private$..extraction$value,
         rotation = function() private$..rotation$value,
+        minCorrThr = function() private$..minCorrThr$value,
+        maxCorrThr = function() private$..maxCorrThr$value,
+        kmo = function() private$..kmo$value,
+        bartlett = function() private$..bartlett$value,
         hideLoadings = function() private$..hideLoadings$value,
         sortLoadings = function() private$..sortLoadings$value,
         screePlot = function() private$..screePlot$value,
@@ -156,8 +176,6 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
         factorCor = function() private$..factorCor$value,
         factorSummary = function() private$..factorSummary$value,
         modelFit = function() private$..modelFit$value,
-        kmo = function() private$..kmo$value,
-        bartlett = function() private$..bartlett$value,
         factorScoresOV = function() private$..factorScoresOV$value,
         factorScoreMethod = function() private$..factorScoreMethod$value),
     private = list(
@@ -167,6 +185,10 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
         ..minEigen = NA,
         ..extraction = NA,
         ..rotation = NA,
+        ..minCorrThr = NA,
+        ..maxCorrThr = NA,
+        ..kmo = NA,
+        ..bartlett = NA,
         ..hideLoadings = NA,
         ..sortLoadings = NA,
         ..screePlot = NA,
@@ -174,8 +196,6 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
         ..factorCor = NA,
         ..factorSummary = NA,
         ..modelFit = NA,
-        ..kmo = NA,
-        ..bartlett = NA,
         ..factorScoresOV = NA,
         ..factorScoreMethod = NA)
 )
@@ -263,6 +283,14 @@ efaBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' @param rotation \code{'none'}, \code{'varimax'}, \code{'quartimax'},
 #'   \code{'promax'}, \code{'oblimin'} (default), or \code{'simplimax'}, the
 #'   rotation to use in estimation
+#' @param minCorrThr a number (default: 0.3), count correlations between
+#'   variables that are above this threshold
+#' @param maxCorrThr a number (default: 0.9), count correlations between
+#'   variables that are above this threshold
+#' @param kmo \code{TRUE} or \code{FALSE} (default), show Kaiser-Meyer-Olkin
+#'   (KMO) measure of sampling adequacy (MSA) results
+#' @param bartlett \code{TRUE} or \code{FALSE} (default), show Bartlett's test
+#'   of sphericity results
 #' @param hideLoadings a number (default: 0.3), hide factor loadings below
 #'   this value
 #' @param sortLoadings \code{TRUE} or \code{FALSE} (default), sort the factor
@@ -275,10 +303,6 @@ efaBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #'   summary
 #' @param modelFit \code{TRUE} or \code{FALSE} (default), show model fit
 #'   measures and test
-#' @param kmo \code{TRUE} or \code{FALSE} (default), show Kaiser-Meyer-Olkin
-#'   (KMO) measure of sampling adequacy (MSA) results
-#' @param bartlett \code{TRUE} or \code{FALSE} (default), show Bartlett's test
-#'   of sphericity results
 #' @param factorScoreMethod \code{'Thurstone'} (default), \code{'Bartlett'},
 #'   \code{'tenBerge'}, \code{'Anderson'}, or \code{'Harman'} use respectively
 #'   'Thurstone', 'Bartlett', 'ten Berge', 'Anderson & Rubin', or 'Harman'
@@ -297,6 +321,10 @@ efa <- function(
     minEigen = 0,
     extraction = "minres",
     rotation = "oblimin",
+    minCorrThr = 0.3,
+    maxCorrThr = 0.9,
+    kmo = FALSE,
+    bartlett = FALSE,
     hideLoadings = 0.3,
     sortLoadings = FALSE,
     screePlot = FALSE,
@@ -304,8 +332,6 @@ efa <- function(
     factorCor = FALSE,
     factorSummary = FALSE,
     modelFit = FALSE,
-    kmo = FALSE,
-    bartlett = FALSE,
     factorScoreMethod = "Thurstone") {
 
     if ( ! requireNamespace("jmvcore", quietly=TRUE))
@@ -326,6 +352,10 @@ efa <- function(
         minEigen = minEigen,
         extraction = extraction,
         rotation = rotation,
+        minCorrThr = minCorrThr,
+        maxCorrThr = maxCorrThr,
+        kmo = kmo,
+        bartlett = bartlett,
         hideLoadings = hideLoadings,
         sortLoadings = sortLoadings,
         screePlot = screePlot,
@@ -333,8 +363,6 @@ efa <- function(
         factorCor = factorCor,
         factorSummary = factorSummary,
         modelFit = modelFit,
-        kmo = kmo,
-        bartlett = bartlett,
         factorScoreMethod = factorScoreMethod)
 
     analysis <- efaClass$new(
diff --git a/R/pca.h.R b/R/pca.h.R
index 3ad569d4..12dbad57 100644
--- a/R/pca.h.R
+++ b/R/pca.h.R
@@ -11,14 +11,16 @@ pcaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             nFactors = 1,
             minEigen = 1,
             rotation = "varimax",
+            minCorrThr = 0.3,
+            maxCorrThr = 0.9,
+            kmo = FALSE,
+            bartlett = FALSE,
             hideLoadings = 0.3,
             sortLoadings = FALSE,
             screePlot = FALSE,
             eigen = FALSE,
             factorCor = FALSE,
-            factorSummary = FALSE,
-            kmo = FALSE,
-            bartlett = FALSE, ...) {
+            factorSummary = FALSE, ...) {
 
             super$initialize(
                 package="jmv",
@@ -64,6 +66,26 @@ pcaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "oblimin",
                     "simplimax"),
                 default="varimax")
+            private$..minCorrThr <- jmvcore::OptionNumber$new(
+                "minCorrThr",
+                minCorrThr,
+                min=0,
+                max=1,
+                default=0.3)
+            private$..maxCorrThr <- jmvcore::OptionNumber$new(
+                "maxCorrThr",
+                maxCorrThr,
+                min=0,
+                max=1,
+                default=0.9)
+            private$..kmo <- jmvcore::OptionBool$new(
+                "kmo",
+                kmo,
+                default=FALSE)
+            private$..bartlett <- jmvcore::OptionBool$new(
+                "bartlett",
+                bartlett,
+                default=FALSE)
             private$..hideLoadings <- jmvcore::OptionNumber$new(
                 "hideLoadings",
                 hideLoadings,
@@ -88,14 +110,6 @@ pcaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                 "factorSummary",
                 factorSummary,
                 default=FALSE)
-            private$..kmo <- jmvcore::OptionBool$new(
-                "kmo",
-                kmo,
-                default=FALSE)
-            private$..bartlett <- jmvcore::OptionBool$new(
-                "bartlett",
-                bartlett,
-                default=FALSE)
             private$..factorScoresOV <- jmvcore::OptionOutput$new(
                 "factorScoresOV")
 
@@ -104,14 +118,16 @@ pcaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             self$.addOption(private$..nFactors)
             self$.addOption(private$..minEigen)
             self$.addOption(private$..rotation)
+            self$.addOption(private$..minCorrThr)
+            self$.addOption(private$..maxCorrThr)
+            self$.addOption(private$..kmo)
+            self$.addOption(private$..bartlett)
             self$.addOption(private$..hideLoadings)
             self$.addOption(private$..sortLoadings)
             self$.addOption(private$..screePlot)
             self$.addOption(private$..eigen)
             self$.addOption(private$..factorCor)
             self$.addOption(private$..factorSummary)
-            self$.addOption(private$..kmo)
-            self$.addOption(private$..bartlett)
             self$.addOption(private$..factorScoresOV)
         }),
     active = list(
@@ -120,14 +136,16 @@ pcaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
         nFactors = function() private$..nFactors$value,
         minEigen = function() private$..minEigen$value,
         rotation = function() private$..rotation$value,
+        minCorrThr = function() private$..minCorrThr$value,
+        maxCorrThr = function() private$..maxCorrThr$value,
+        kmo = function() private$..kmo$value,
+        bartlett = function() private$..bartlett$value,
         hideLoadings = function() private$..hideLoadings$value,
         sortLoadings = function() private$..sortLoadings$value,
         screePlot = function() private$..screePlot$value,
         eigen = function() private$..eigen$value,
         factorCor = function() private$..factorCor$value,
         factorSummary = function() private$..factorSummary$value,
-        kmo = function() private$..kmo$value,
-        bartlett = function() private$..bartlett$value,
         factorScoresOV = function() private$..factorScoresOV$value),
     private = list(
         ..vars = NA,
@@ -135,14 +153,16 @@ pcaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
         ..nFactors = NA,
         ..minEigen = NA,
         ..rotation = NA,
+        ..minCorrThr = NA,
+        ..maxCorrThr = NA,
+        ..kmo = NA,
+        ..bartlett = NA,
         ..hideLoadings = NA,
         ..sortLoadings = NA,
         ..screePlot = NA,
         ..eigen = NA,
         ..factorCor = NA,
         ..factorSummary = NA,
-        ..kmo = NA,
-        ..bartlett = NA,
         ..factorScoresOV = NA)
 )
 
@@ -480,6 +500,14 @@ pcaBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' @param rotation \code{'none'}, \code{'varimax'} (default),
 #'   \code{'quartimax'}, \code{'promax'}, \code{'oblimin'}, or
 #'   \code{'simplimax'}, the rotation to use in estimation
+#' @param minCorrThr a number (default: 0.3), count correlations between
+#'   variables that are above this threshold
+#' @param maxCorrThr a number (default: 0.9), count correlations between
+#'   variables that are above this threshold
+#' @param kmo \code{TRUE} or \code{FALSE} (default), show Kaiser-Meyer-Olkin
+#'   (KMO) measure of sampling adequacy (MSA) results
+#' @param bartlett \code{TRUE} or \code{FALSE} (default), show Bartlett's test
+#'   of sphericity results
 #' @param hideLoadings a number (default: 0.3), hide loadings below this value
 #' @param sortLoadings \code{TRUE} or \code{FALSE} (default), sort the factor
 #'   loadings by size
@@ -489,10 +517,6 @@ pcaBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #'   correlations
 #' @param factorSummary \code{TRUE} or \code{FALSE} (default), show factor
 #'   summary
-#' @param kmo \code{TRUE} or \code{FALSE} (default), show Kaiser-Meyer-Olkin
-#'   (KMO) measure of sampling adequacy (MSA) results
-#' @param bartlett \code{TRUE} or \code{FALSE} (default), show Bartlett's test
-#'   of sphericity results
 #' @return A results object containing:
 #' \tabular{llllll}{
 #'   \code{results$loadings} \tab \tab \tab \tab \tab a table \cr
@@ -520,14 +544,16 @@ pca <- function(
     nFactors = 1,
     minEigen = 1,
     rotation = "varimax",
+    minCorrThr = 0.3,
+    maxCorrThr = 0.9,
+    kmo = FALSE,
+    bartlett = FALSE,
     hideLoadings = 0.3,
     sortLoadings = FALSE,
     screePlot = FALSE,
     eigen = FALSE,
     factorCor = FALSE,
-    factorSummary = FALSE,
-    kmo = FALSE,
-    bartlett = FALSE) {
+    factorSummary = FALSE) {
 
     if ( ! requireNamespace("jmvcore", quietly=TRUE))
         stop("pca requires jmvcore to be installed (restart may be required)")
@@ -546,14 +572,16 @@ pca <- function(
         nFactors = nFactors,
         minEigen = minEigen,
         rotation = rotation,
+        minCorrThr = minCorrThr,
+        maxCorrThr = maxCorrThr,
+        kmo = kmo,
+        bartlett = bartlett,
         hideLoadings = hideLoadings,
         sortLoadings = sortLoadings,
         screePlot = screePlot,
         eigen = eigen,
         factorCor = factorCor,
-        factorSummary = factorSummary,
-        kmo = kmo,
-        bartlett = bartlett)
+        factorSummary = factorSummary)
 
     analysis <- pcaClass$new(
         options = options,
diff --git a/jamovi/efa.a.yaml b/jamovi/efa.a.yaml
index 3fc74cd5..1b38f55b 100644
--- a/jamovi/efa.a.yaml
+++ b/jamovi/efa.a.yaml
@@ -121,6 +121,45 @@ options:
             `'oblimin'` (default), or `'simplimax'`, the rotation to use
             in estimation
 
+    - name: minCorrThr
+      title: ''
+      type: Number
+      min: 0
+      max: 1
+      default: 0.3
+      description:
+          R: >
+            a number (default: 0.3), count correlations between variables that
+            are above this threshold
+
+    - name: maxCorrThr
+      title: ''
+      type: Number
+      min: 0
+      max: 1
+      default: 0.9
+      description:
+          R: >
+            a number (default: 0.9), count correlations between variables that
+            are above this threshold
+
+    - name: kmo
+      title: KMO measure of sampling adequacy
+      type: Bool
+      default: false
+      description:
+          R: >
+            `TRUE` or `FALSE` (default), show Kaiser-Meyer-Olkin (KMO) measure of
+            sampling adequacy (MSA) results
+
+    - name: bartlett
+      title: Bartlett's test of sphericity
+      type: Bool
+      default: false
+      description:
+          R: >
+            `TRUE` or `FALSE` (default), show Bartlett's test of sphericity results
+
     - name: hideLoadings
       title: Hide loadings below
       type: Number
@@ -177,23 +216,6 @@ options:
           R: >
             `TRUE` or `FALSE` (default), show model fit measures and test
 
-    - name: kmo
-      title: KMO measure of sampling adequacy
-      type: Bool
-      default: false
-      description:
-          R: >
-            `TRUE` or `FALSE` (default), show Kaiser-Meyer-Olkin (KMO) measure of
-            sampling adequacy (MSA) results
-
-    - name: bartlett
-      title: Bartlett's test of sphericity
-      type: Bool
-      default: false
-      description:
-          R: >
-            `TRUE` or `FALSE` (default), show Bartlett's test of sphericity results
-
     - name: factorScoresOV
       title: Factor scores
       type: Output
diff --git a/jamovi/efa.u.yaml b/jamovi/efa.u.yaml
index 5d570680..313ab563 100644
--- a/jamovi/efa.u.yaml
+++ b/jamovi/efa.u.yaml
@@ -64,6 +64,15 @@ children:
                     suffix: factor(s)
                     format: number
                     enable: (nFactorMethod_fixed)
+          - type: Label
+            label: Data Summary
+            children:
+              - name: minCorrThr
+                type: TextBox
+                format: number
+              - name: maxCorrThr
+                type: TextBox
+                format: number
       - type: LayoutBox
         margin: large
         cell:
diff --git a/jamovi/pca.a.yaml b/jamovi/pca.a.yaml
index af81ec76..9b535272 100644
--- a/jamovi/pca.a.yaml
+++ b/jamovi/pca.a.yaml
@@ -101,6 +101,45 @@ options:
             `'oblimin'`, or `'simplimax'`, the rotation to use
             in estimation
 
+    - name: minCorrThr
+      title: ''
+      type: Number
+      min: 0
+      max: 1
+      default: 0.3
+      description:
+          R: >
+            a number (default: 0.3), count correlations between variables that
+            are above this threshold
+
+    - name: maxCorrThr
+      title: ''
+      type: Number
+      min: 0
+      max: 1
+      default: 0.9
+      description:
+          R: >
+            a number (default: 0.9), count correlations between variables that
+            are above this threshold
+
+    - name: kmo
+      title: KMO measure of sampling adequacy
+      type: Bool
+      default: false
+      description:
+          R: >
+            `TRUE` or `FALSE` (default), show Kaiser-Meyer-Olkin (KMO) measure of
+            sampling adequacy (MSA) results
+
+    - name: bartlett
+      title: Bartlett's test of sphericity
+      type: Bool
+      default: false
+      description:
+          R: >
+            `TRUE` or `FALSE` (default), show Bartlett's test of sphericity results
+
     - name: hideLoadings
       title: Hide loadings below
       type: Number
@@ -149,23 +188,6 @@ options:
           R: >
             `TRUE` or `FALSE` (default), show factor summary
 
-    - name: kmo
-      title: KMO measure of sampling adequacy
-      type: Bool
-      default: false
-      description:
-          R: >
-            `TRUE` or `FALSE` (default), show Kaiser-Meyer-Olkin (KMO) measure of
-            sampling adequacy (MSA) results
-
-    - name: bartlett
-      title: Bartlett's test of sphericity
-      type: Bool
-      default: false
-      description:
-          R: >
-            `TRUE` or `FALSE` (default), show Bartlett's test of sphericity results
-
     - name: factorScoresOV
       title: Component scores
       type: Output
diff --git a/jamovi/pca.u.yaml b/jamovi/pca.u.yaml
index 4584a816..41b68bfb 100644
--- a/jamovi/pca.u.yaml
+++ b/jamovi/pca.u.yaml
@@ -65,6 +65,15 @@ children:
                     suffix: component(s)
                     format: number
                     enable: (nFactorMethod_fixed)
+          - type: Label
+            label: Data Summary
+            children:
+              - name: minCorrThr
+                type: TextBox
+                format: number
+              - name: maxCorrThr
+                type: TextBox
+                format: number
       - type: LayoutBox
         margin: large
         cell:

From c6053f06e0356ad673d1dea4729bf26564d1e807 Mon Sep 17 00:00:00 2001
From: Sebastian Jentschke <Sebastian.Jentschke@gmail.com>
Date: Tue, 9 Sep 2025 12:05:27 +1000
Subject: [PATCH 2/5] Adjusted UI elements for data summary in EFA and PCA

---
 R/efa.h.R         | 20 ++++++++++----------
 R/pca.b.R         |  2 ++
 R/pca.h.R         | 41 +++++++++++++++++++++++++++++++++++++++++
 jamovi/efa.a.yaml | 12 ++++++------
 jamovi/efa.u.yaml |  1 +
 jamovi/pca.r.yaml | 27 +++++++++++++++++++++++++++
 jamovi/pca.u.yaml |  1 +
 7 files changed, 88 insertions(+), 16 deletions(-)

diff --git a/R/efa.h.R b/R/efa.h.R
index 83b887b7..b0e15820 100644
--- a/R/efa.h.R
+++ b/R/efa.h.R
@@ -12,8 +12,8 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             minEigen = 0,
             extraction = "minres",
             rotation = "oblimin",
-            minCorrThr = 0.3,
-            maxCorrThr = 0.9,
+            minCorrThr = 0,
+            maxCorrThr = 0,
             kmo = FALSE,
             bartlett = FALSE,
             hideLoadings = 0.3,
@@ -82,13 +82,13 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                 minCorrThr,
                 min=0,
                 max=1,
-                default=0.3)
+                default=0)
             private$..maxCorrThr <- jmvcore::OptionNumber$new(
                 "maxCorrThr",
                 maxCorrThr,
                 min=0,
                 max=1,
-                default=0.9)
+                default=0)
             private$..kmo <- jmvcore::OptionBool$new(
                 "kmo",
                 kmo,
@@ -283,10 +283,10 @@ efaBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' @param rotation \code{'none'}, \code{'varimax'}, \code{'quartimax'},
 #'   \code{'promax'}, \code{'oblimin'} (default), or \code{'simplimax'}, the
 #'   rotation to use in estimation
-#' @param minCorrThr a number (default: 0.3), count correlations between
-#'   variables that are above this threshold
-#' @param maxCorrThr a number (default: 0.9), count correlations between
-#'   variables that are above this threshold
+#' @param minCorrThr a number (default: 0), count correlations between
+#'   variables that are above this threshold (if 0, no output is produced)
+#' @param maxCorrThr a number (default: 0), count correlations between
+#'   variables that are above this threshold (if 0, no output is produced)
 #' @param kmo \code{TRUE} or \code{FALSE} (default), show Kaiser-Meyer-Olkin
 #'   (KMO) measure of sampling adequacy (MSA) results
 #' @param bartlett \code{TRUE} or \code{FALSE} (default), show Bartlett's test
@@ -321,8 +321,8 @@ efa <- function(
     minEigen = 0,
     extraction = "minres",
     rotation = "oblimin",
-    minCorrThr = 0.3,
-    maxCorrThr = 0.9,
+    minCorrThr = 0,
+    maxCorrThr = 0,
     kmo = FALSE,
     bartlett = FALSE,
     hideLoadings = 0.3,
diff --git a/R/pca.b.R b/R/pca.b.R
index 4dd47850..e423b4a8 100644
--- a/R/pca.b.R
+++ b/R/pca.b.R
@@ -116,6 +116,8 @@ pcaClass <- R6::R6Class(
         .run = function() {
             if (is.null(self$options$vars) || length(self$options$vars) < 2)
                 return()
+print(self$options$minCorrThr)
+print(self$options$maxCorrThr)
 
             private$.errorCheck()
 
diff --git a/R/pca.h.R b/R/pca.h.R
index 12dbad57..3c062f8c 100644
--- a/R/pca.h.R
+++ b/R/pca.h.R
@@ -173,6 +173,7 @@ pcaResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
         loadings = function() private$.items[["loadings"]],
         factorStats = function() private$.items[["factorStats"]],
         modelFit = function() private$.items[["modelFit"]],
+        dataSummary = function() private$.items[["dataSummary"]],
         assump = function() private$.items[["assump"]],
         eigen = function() private$.items[["eigen"]],
         factorScoresOV = function() private$.items[["factorScoresOV"]]),
@@ -331,6 +332,44 @@ pcaResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                                     `type`="number", 
                                     `format`="zto,pvalue", 
                                     `superTitle`="Model Test"))))}))$new(options=options))
+            self$add(R6::R6Class(
+                inherit = jmvcore::Group,
+                active = list(
+                    corrAboveMin = function() private$.items[["corrAboveMin"]],
+                    corrAboveMax = function() private$.items[["corrAboveMax"]]),
+                private = list(),
+                public=list(
+                    initialize=function(options) {
+                        super$initialize(
+                            options=options,
+                            name="dataSummary",
+                            title="Data Summary")
+                        self$add(jmvcore::Table$new(
+                            options=options,
+                            name="corrAboveMin",
+                            title="Correlations Above Minimum Threshold",
+                            visible="(minCorrThr > 0)",
+                            rows=1,
+                            clearWith=list(
+                                "vars"),
+                            columns=list(
+                                list(
+                                    `name`="header", 
+                                    `title`="", 
+                                    `type`="text"))))
+                        self$add(jmvcore::Table$new(
+                            options=options,
+                            name="corrAboveMax",
+                            title="Correlations Above Maximum Threshold",
+                            visible="(maxCorrThr > 0)",
+                            rows=1,
+                            clearWith=list(
+                                "vars"),
+                            columns=list(
+                                list(
+                                    `name`="header", 
+                                    `title`="", 
+                                    `type`="text"))))}))$new(options=options))
             self$add(R6::R6Class(
                 inherit = jmvcore::Group,
                 active = list(
@@ -523,6 +562,8 @@ pcaBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #'   \code{results$factorStats$factorSummary} \tab \tab \tab \tab \tab a table \cr
 #'   \code{results$factorStats$factorCor} \tab \tab \tab \tab \tab a table \cr
 #'   \code{results$modelFit$fit} \tab \tab \tab \tab \tab a table \cr
+#'   \code{results$dataSummary$corrAboveMin} \tab \tab \tab \tab \tab a table \cr
+#'   \code{results$dataSummary$corrAboveMax} \tab \tab \tab \tab \tab a table \cr
 #'   \code{results$assump$bartlett} \tab \tab \tab \tab \tab a table \cr
 #'   \code{results$assump$kmo} \tab \tab \tab \tab \tab a table \cr
 #'   \code{results$eigen$initEigen} \tab \tab \tab \tab \tab a table \cr
diff --git a/jamovi/efa.a.yaml b/jamovi/efa.a.yaml
index 1b38f55b..5ee4026b 100644
--- a/jamovi/efa.a.yaml
+++ b/jamovi/efa.a.yaml
@@ -126,22 +126,22 @@ options:
       type: Number
       min: 0
       max: 1
-      default: 0.3
+      default: 0
       description:
           R: >
-            a number (default: 0.3), count correlations between variables that
-            are above this threshold
+            a number (default: 0), count correlations between variables that
+            are above this threshold (if 0, no output is produced)
 
     - name: maxCorrThr
       title: ''
       type: Number
       min: 0
       max: 1
-      default: 0.9
+      default: 0
       description:
           R: >
-            a number (default: 0.9), count correlations between variables that
-            are above this threshold
+            a number (default: 0), count correlations between variables that
+            are above this threshold (if 0, no output is produced)
 
     - name: kmo
       title: KMO measure of sampling adequacy
diff --git a/jamovi/efa.u.yaml b/jamovi/efa.u.yaml
index 313ab563..117f342a 100644
--- a/jamovi/efa.u.yaml
+++ b/jamovi/efa.u.yaml
@@ -66,6 +66,7 @@ children:
                     enable: (nFactorMethod_fixed)
           - type: Label
             label: Data Summary
+            style: inline
             children:
               - name: minCorrThr
                 type: TextBox
diff --git a/jamovi/pca.r.yaml b/jamovi/pca.r.yaml
index 16fb38a2..b7b9dcfc 100644
--- a/jamovi/pca.r.yaml
+++ b/jamovi/pca.r.yaml
@@ -123,6 +123,33 @@ items:
               format: zto,pvalue
               superTitle: Model Test
 
+    - name: dataSummary
+      title: Data Summary
+      type: Group
+      items:
+        - name: corrAboveMin
+          title: Correlations Above Minimum Threshold
+          type: Table
+          visible: (minCorrThr > 0)
+          rows: 1
+          clearWith:
+            - vars
+          columns:
+            - name: header
+              title: ""
+              type: text
+        - name: corrAboveMax
+          title: Correlations Above Maximum Threshold
+          type: Table
+          visible: (maxCorrThr > 0)
+          rows: 1
+          clearWith:
+            - vars
+          columns:
+            - name: header
+              title: ""
+              type: text
+
     - name: assump
       title: Assumption Checks
       type: Group
diff --git a/jamovi/pca.u.yaml b/jamovi/pca.u.yaml
index 41b68bfb..b2382561 100644
--- a/jamovi/pca.u.yaml
+++ b/jamovi/pca.u.yaml
@@ -67,6 +67,7 @@ children:
                     enable: (nFactorMethod_fixed)
           - type: Label
             label: Data Summary
+            style: inline
             children:
               - name: minCorrThr
                 type: TextBox

From 463a8e8e857ccb1d5d596876dbc4345091bcaa98 Mon Sep 17 00:00:00 2001
From: Sebastian Jentschke <Sebastian.Jentschke@gmail.com>
Date: Tue, 9 Sep 2025 18:02:17 +1000
Subject: [PATCH 3/5] Implemented Data Summary showing number of correlations
 above a minimum and maximum threshold

---
 R/efa.h.R         | 46 ++++++++++++++++---------------
 R/pca.b.R         | 40 +++++++++++++++++++++++++--
 R/pca.h.R         | 70 +++++++++++++++++++++++++----------------------
 jamovi/efa.a.yaml | 14 ++++------
 jamovi/efa.u.yaml | 34 ++++++++++++++++++-----
 jamovi/pca.a.yaml | 20 +++++++-------
 jamovi/pca.r.yaml | 12 +++++---
 jamovi/pca.u.yaml | 34 ++++++++++++++++++-----
 8 files changed, 178 insertions(+), 92 deletions(-)

diff --git a/R/efa.h.R b/R/efa.h.R
index b0e15820..eb7656c4 100644
--- a/R/efa.h.R
+++ b/R/efa.h.R
@@ -12,8 +12,8 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             minEigen = 0,
             extraction = "minres",
             rotation = "oblimin",
-            minCorrThr = 0,
-            maxCorrThr = 0,
+            countCorrMin = 0,
+            countCorrMax = 0,
             kmo = FALSE,
             bartlett = FALSE,
             hideLoadings = 0.3,
@@ -77,15 +77,15 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "oblimin",
                     "simplimax"),
                 default="oblimin")
-            private$..minCorrThr <- jmvcore::OptionNumber$new(
-                "minCorrThr",
-                minCorrThr,
+            private$..countCorrMin <- jmvcore::OptionNumber$new(
+                "countCorrMin",
+                countCorrMin,
                 min=0,
                 max=1,
                 default=0)
-            private$..maxCorrThr <- jmvcore::OptionNumber$new(
-                "maxCorrThr",
-                maxCorrThr,
+            private$..countCorrMax <- jmvcore::OptionNumber$new(
+                "countCorrMax",
+                countCorrMax,
                 min=0,
                 max=1,
                 default=0)
@@ -144,8 +144,8 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             self$.addOption(private$..minEigen)
             self$.addOption(private$..extraction)
             self$.addOption(private$..rotation)
-            self$.addOption(private$..minCorrThr)
-            self$.addOption(private$..maxCorrThr)
+            self$.addOption(private$..countCorrMin)
+            self$.addOption(private$..countCorrMax)
             self$.addOption(private$..kmo)
             self$.addOption(private$..bartlett)
             self$.addOption(private$..hideLoadings)
@@ -165,8 +165,8 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
         minEigen = function() private$..minEigen$value,
         extraction = function() private$..extraction$value,
         rotation = function() private$..rotation$value,
-        minCorrThr = function() private$..minCorrThr$value,
-        maxCorrThr = function() private$..maxCorrThr$value,
+        countCorrMin = function() private$..countCorrMin$value,
+        countCorrMax = function() private$..countCorrMax$value,
         kmo = function() private$..kmo$value,
         bartlett = function() private$..bartlett$value,
         hideLoadings = function() private$..hideLoadings$value,
@@ -185,8 +185,8 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
         ..minEigen = NA,
         ..extraction = NA,
         ..rotation = NA,
-        ..minCorrThr = NA,
-        ..maxCorrThr = NA,
+        ..countCorrMin = NA,
+        ..countCorrMax = NA,
         ..kmo = NA,
         ..bartlett = NA,
         ..hideLoadings = NA,
@@ -283,10 +283,12 @@ efaBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' @param rotation \code{'none'}, \code{'varimax'}, \code{'quartimax'},
 #'   \code{'promax'}, \code{'oblimin'} (default), or \code{'simplimax'}, the
 #'   rotation to use in estimation
-#' @param minCorrThr a number (default: 0), count correlations between
-#'   variables that are above this threshold (if 0, no output is produced)
-#' @param maxCorrThr a number (default: 0), count correlations between
-#'   variables that are above this threshold (if 0, no output is produced)
+#' @param countCorrMin a number (default: 0), returns the number of
+#'   correlations between variables above this minimum (if 0, no output is
+#'   produced)
+#' @param countCorrMax a number (default: 0), returns the number of
+#'   correlations between variables above this maxmimum (if 0, no output is
+#'   produced)
 #' @param kmo \code{TRUE} or \code{FALSE} (default), show Kaiser-Meyer-Olkin
 #'   (KMO) measure of sampling adequacy (MSA) results
 #' @param bartlett \code{TRUE} or \code{FALSE} (default), show Bartlett's test
@@ -321,8 +323,8 @@ efa <- function(
     minEigen = 0,
     extraction = "minres",
     rotation = "oblimin",
-    minCorrThr = 0,
-    maxCorrThr = 0,
+    countCorrMin = 0,
+    countCorrMax = 0,
     kmo = FALSE,
     bartlett = FALSE,
     hideLoadings = 0.3,
@@ -352,8 +354,8 @@ efa <- function(
         minEigen = minEigen,
         extraction = extraction,
         rotation = rotation,
-        minCorrThr = minCorrThr,
-        maxCorrThr = maxCorrThr,
+        countCorrMin = countCorrMin,
+        countCorrMax = countCorrMax,
         kmo = kmo,
         bartlett = bartlett,
         hideLoadings = hideLoadings,
diff --git a/R/pca.b.R b/R/pca.b.R
index e423b4a8..9a6c4b37 100644
--- a/R/pca.b.R
+++ b/R/pca.b.R
@@ -110,14 +110,13 @@ pcaClass <- R6::R6Class(
             private$.initLoadingsTable()
             private$.initModelFitTable()
             private$.initEigenTable()
+            private$.initCorrCountTable()
             private$.initKMOTable()
             private$.initFactorCor()
         },
         .run = function() {
             if (is.null(self$options$vars) || length(self$options$vars) < 2)
                 return()
-print(self$options$minCorrThr)
-print(self$options$maxCorrThr)
 
             private$.errorCheck()
 
@@ -126,6 +125,7 @@ print(self$options$maxCorrThr)
             private$.populateFactorSummaryTable()
             private$.populateFactorCorTable()
             private$.populateModelFitTable()
+            private$.populateCorrCountTable()
             private$.populateKMOTable()
             private$.populateBartlettTable()
             private$.prepareScreePlot()
@@ -252,6 +252,21 @@ print(self$options$maxCorrThr)
             for (i in seq_along(self$options$vars))
                 table$addRow(rowKey=i, values=list(comp = as.character(i)))
         },
+        .initCorrCountTable = function() {
+            group <- self$results$dataSummary
+            vars <- self$options$vars
+
+            for (t in c("Min", "Max")) {
+                table <- group[[paste0("corrAbove", t)]]
+                title <- jmvcore::format(.("Correlations Above {} Threshold ({})"),
+                                         ifelse(t == "Min", .("Minimum"), .("Maximum")),
+                                         self$options[[paste0("countCorr", t)]])
+                table$setTitle(title)
+                for (i in seq_along(vars)) {
+                    table$addColumn(name = sprintf("c%d", i), title = ".", type = 'integer')
+                }
+            }
+        },
         .initKMOTable = function() {
             table <- self$results$assump$kmo
             vars <- self$options$vars
@@ -415,6 +430,27 @@ print(self$options$maxCorrThr)
                 table$setRow(rowNo=1, values=row)
             }
         },
+        .populateCorrCountTable = function() {
+            group <- self$results$dataSummary
+            vars <- self$options$vars
+            if (length(vars) >= 1) {
+                corrMatrix = abs(cor(sapply(self$data[, vars], jmvcore::toNumeric), use = "pairwise"))
+                diag(corrMatrix) <- NA
+
+                for (t in c("Min", "Max")) {
+                    thresh <- self$options[[paste0("countCorr", t)]]
+                    if (thresh > 0) {
+                        table  <- group[[paste0("corrAbove", t)]]
+                        counts <- sort(colSums(corrMatrix > thresh, na.rm = TRUE))
+                        cnames <- names(counts)
+                        table$setRow(rowNo = 1, setNames(as.list(counts), sprintf("c%d", seq_along(vars))))
+                        for (i in seq_along(cnames)) {
+                            table$columns[[i + 1]]$setTitle(cnames[i])
+                        }
+                    }
+                }
+            }
+        },
         .populateKMOTable = function() {
             if (! self$options$kmo)
                 return()
diff --git a/R/pca.h.R b/R/pca.h.R
index 3c062f8c..2a3cff42 100644
--- a/R/pca.h.R
+++ b/R/pca.h.R
@@ -11,8 +11,8 @@ pcaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             nFactors = 1,
             minEigen = 1,
             rotation = "varimax",
-            minCorrThr = 0.3,
-            maxCorrThr = 0.9,
+            countCorrMin = 0,
+            countCorrMax = 0,
             kmo = FALSE,
             bartlett = FALSE,
             hideLoadings = 0.3,
@@ -66,18 +66,18 @@ pcaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "oblimin",
                     "simplimax"),
                 default="varimax")
-            private$..minCorrThr <- jmvcore::OptionNumber$new(
-                "minCorrThr",
-                minCorrThr,
+            private$..countCorrMin <- jmvcore::OptionNumber$new(
+                "countCorrMin",
+                countCorrMin,
                 min=0,
                 max=1,
-                default=0.3)
-            private$..maxCorrThr <- jmvcore::OptionNumber$new(
-                "maxCorrThr",
-                maxCorrThr,
+                default=0)
+            private$..countCorrMax <- jmvcore::OptionNumber$new(
+                "countCorrMax",
+                countCorrMax,
                 min=0,
                 max=1,
-                default=0.9)
+                default=0)
             private$..kmo <- jmvcore::OptionBool$new(
                 "kmo",
                 kmo,
@@ -118,8 +118,8 @@ pcaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             self$.addOption(private$..nFactors)
             self$.addOption(private$..minEigen)
             self$.addOption(private$..rotation)
-            self$.addOption(private$..minCorrThr)
-            self$.addOption(private$..maxCorrThr)
+            self$.addOption(private$..countCorrMin)
+            self$.addOption(private$..countCorrMax)
             self$.addOption(private$..kmo)
             self$.addOption(private$..bartlett)
             self$.addOption(private$..hideLoadings)
@@ -136,8 +136,8 @@ pcaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
         nFactors = function() private$..nFactors$value,
         minEigen = function() private$..minEigen$value,
         rotation = function() private$..rotation$value,
-        minCorrThr = function() private$..minCorrThr$value,
-        maxCorrThr = function() private$..maxCorrThr$value,
+        countCorrMin = function() private$..countCorrMin$value,
+        countCorrMax = function() private$..countCorrMax$value,
         kmo = function() private$..kmo$value,
         bartlett = function() private$..bartlett$value,
         hideLoadings = function() private$..hideLoadings$value,
@@ -153,8 +153,8 @@ pcaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
         ..nFactors = NA,
         ..minEigen = NA,
         ..rotation = NA,
-        ..minCorrThr = NA,
-        ..maxCorrThr = NA,
+        ..countCorrMin = NA,
+        ..countCorrMax = NA,
         ..kmo = NA,
         ..bartlett = NA,
         ..hideLoadings = NA,
@@ -347,29 +347,33 @@ pcaResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                         self$add(jmvcore::Table$new(
                             options=options,
                             name="corrAboveMin",
-                            title="Correlations Above Minimum Threshold",
-                            visible="(minCorrThr > 0)",
+                            title="",
+                            visible="(countCorrMin > 0)",
                             rows=1,
                             clearWith=list(
-                                "vars"),
+                                "vars",
+                                "countCorrMin"),
                             columns=list(
                                 list(
                                     `name`="header", 
                                     `title`="", 
-                                    `type`="text"))))
+                                    `type`="text", 
+                                    `content`="N"))))
                         self$add(jmvcore::Table$new(
                             options=options,
                             name="corrAboveMax",
-                            title="Correlations Above Maximum Threshold",
-                            visible="(maxCorrThr > 0)",
+                            title="",
+                            visible="(countCorrMax > 0)",
                             rows=1,
                             clearWith=list(
-                                "vars"),
+                                "vars",
+                                "countCorrMax"),
                             columns=list(
                                 list(
                                     `name`="header", 
                                     `title`="", 
-                                    `type`="text"))))}))$new(options=options))
+                                    `type`="text", 
+                                    `content`="N"))))}))$new(options=options))
             self$add(R6::R6Class(
                 inherit = jmvcore::Group,
                 active = list(
@@ -539,10 +543,12 @@ pcaBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' @param rotation \code{'none'}, \code{'varimax'} (default),
 #'   \code{'quartimax'}, \code{'promax'}, \code{'oblimin'}, or
 #'   \code{'simplimax'}, the rotation to use in estimation
-#' @param minCorrThr a number (default: 0.3), count correlations between
-#'   variables that are above this threshold
-#' @param maxCorrThr a number (default: 0.9), count correlations between
-#'   variables that are above this threshold
+#' @param countCorrMin a number (default: 0), returns the number of
+#'   correlations between variables above this minimum (if 0, no output is
+#'   produced)
+#' @param countCorrMax a number (default: 0), returns the number of
+#'   correlations between variables above this maxmimum (if 0, no output is
+#'   produced)
 #' @param kmo \code{TRUE} or \code{FALSE} (default), show Kaiser-Meyer-Olkin
 #'   (KMO) measure of sampling adequacy (MSA) results
 #' @param bartlett \code{TRUE} or \code{FALSE} (default), show Bartlett's test
@@ -585,8 +591,8 @@ pca <- function(
     nFactors = 1,
     minEigen = 1,
     rotation = "varimax",
-    minCorrThr = 0.3,
-    maxCorrThr = 0.9,
+    countCorrMin = 0,
+    countCorrMax = 0,
     kmo = FALSE,
     bartlett = FALSE,
     hideLoadings = 0.3,
@@ -613,8 +619,8 @@ pca <- function(
         nFactors = nFactors,
         minEigen = minEigen,
         rotation = rotation,
-        minCorrThr = minCorrThr,
-        maxCorrThr = maxCorrThr,
+        countCorrMin = countCorrMin,
+        countCorrMax = countCorrMax,
         kmo = kmo,
         bartlett = bartlett,
         hideLoadings = hideLoadings,
diff --git a/jamovi/efa.a.yaml b/jamovi/efa.a.yaml
index 5ee4026b..f555c190 100644
--- a/jamovi/efa.a.yaml
+++ b/jamovi/efa.a.yaml
@@ -121,27 +121,25 @@ options:
             `'oblimin'` (default), or `'simplimax'`, the rotation to use
             in estimation
 
-    - name: minCorrThr
-      title: ''
+    - name: countCorrMin
       type: Number
       min: 0
       max: 1
       default: 0
       description:
           R: >
-            a number (default: 0), count correlations between variables that
-            are above this threshold (if 0, no output is produced)
+            a number (default: 0), returns the number of correlations between
+            variables above this minimum (if 0, no output is produced)
 
-    - name: maxCorrThr
-      title: ''
+    - name: countCorrMax
       type: Number
       min: 0
       max: 1
       default: 0
       description:
           R: >
-            a number (default: 0), count correlations between variables that
-            are above this threshold (if 0, no output is produced)
+            a number (default: 0), returns the number of correlations between
+            variables above this maxmimum (if 0, no output is produced)
 
     - name: kmo
       title: KMO measure of sampling adequacy
diff --git a/jamovi/efa.u.yaml b/jamovi/efa.u.yaml
index 117f342a..a2754971 100644
--- a/jamovi/efa.u.yaml
+++ b/jamovi/efa.u.yaml
@@ -66,14 +66,34 @@ children:
                     enable: (nFactorMethod_fixed)
           - type: Label
             label: Data Summary
-            style: inline
             children:
-              - name: minCorrThr
-                type: TextBox
-                format: number
-              - name: maxCorrThr
-                type: TextBox
-                format: number
+              - type: Label
+                label: Count Correlations Above Min.
+                cell:
+                  column: 0
+                  row: 0
+              - type: LayoutBox
+                cell:
+                  column: 1
+                  row: 0
+                children:
+                  - name: countCorrMin
+                    type: TextBox
+                    format: number
+              - type: Label
+                label: And Above Max.
+                horizontalAlignment: right
+                cell:
+                  column: 0
+                  row: 1
+              - type: LayoutBox
+                cell:
+                  column: 1
+                  row: 1
+                children:
+                  - name: countCorrMax
+                    type: TextBox
+                    format: number
       - type: LayoutBox
         margin: large
         cell:
diff --git a/jamovi/pca.a.yaml b/jamovi/pca.a.yaml
index 9b535272..57c2331a 100644
--- a/jamovi/pca.a.yaml
+++ b/jamovi/pca.a.yaml
@@ -101,27 +101,27 @@ options:
             `'oblimin'`, or `'simplimax'`, the rotation to use
             in estimation
 
-    - name: minCorrThr
-      title: ''
+    - name: countCorrMin
+      title: ""
       type: Number
       min: 0
       max: 1
-      default: 0.3
+      default: 0
       description:
           R: >
-            a number (default: 0.3), count correlations between variables that
-            are above this threshold
+            a number (default: 0), returns the number of correlations between
+            variables above this minimum (if 0, no output is produced)
 
-    - name: maxCorrThr
-      title: ''
+    - name: countCorrMax
+      title: ""
       type: Number
       min: 0
       max: 1
-      default: 0.9
+      default: 0
       description:
           R: >
-            a number (default: 0.9), count correlations between variables that
-            are above this threshold
+            a number (default: 0), returns the number of correlations between
+            variables above this maxmimum (if 0, no output is produced)
 
     - name: kmo
       title: KMO measure of sampling adequacy
diff --git a/jamovi/pca.r.yaml b/jamovi/pca.r.yaml
index b7b9dcfc..351166e6 100644
--- a/jamovi/pca.r.yaml
+++ b/jamovi/pca.r.yaml
@@ -128,27 +128,31 @@ items:
       type: Group
       items:
         - name: corrAboveMin
-          title: Correlations Above Minimum Threshold
+          title: ""
           type: Table
-          visible: (minCorrThr > 0)
+          visible: (countCorrMin > 0)
           rows: 1
           clearWith:
             - vars
+            - countCorrMin
           columns:
             - name: header
               title: ""
               type: text
+              content: N
         - name: corrAboveMax
-          title: Correlations Above Maximum Threshold
+          title: ""
           type: Table
-          visible: (maxCorrThr > 0)
+          visible: (countCorrMax > 0)
           rows: 1
           clearWith:
             - vars
+            - countCorrMax
           columns:
             - name: header
               title: ""
               type: text
+              content: N
 
     - name: assump
       title: Assumption Checks
diff --git a/jamovi/pca.u.yaml b/jamovi/pca.u.yaml
index b2382561..261b2946 100644
--- a/jamovi/pca.u.yaml
+++ b/jamovi/pca.u.yaml
@@ -67,14 +67,34 @@ children:
                     enable: (nFactorMethod_fixed)
           - type: Label
             label: Data Summary
-            style: inline
             children:
-              - name: minCorrThr
-                type: TextBox
-                format: number
-              - name: maxCorrThr
-                type: TextBox
-                format: number
+              - type: Label
+                label: Count Correlations Above Min.
+                cell:
+                  column: 0
+                  row: 0
+              - type: LayoutBox
+                cell:
+                  column: 1
+                  row: 0
+                children:
+                  - name: countCorrMin
+                    type: TextBox
+                    format: number
+              - type: Label
+                label: And Above Max.
+                horizontalAlignment: right
+                cell:
+                  column: 0
+                  row: 1
+              - type: LayoutBox
+                cell:
+                  column: 1
+                  row: 1
+                children:
+                  - name: countCorrMax
+                    type: TextBox
+                    format: number
       - type: LayoutBox
         margin: large
         cell:

From 5f3ece5282a38a0f4e5ccda465367ffac851ef7f Mon Sep 17 00:00:00 2001
From: Sebastian Jentschke <Sebastian.Jentschke@gmail.com>
Date: Wed, 10 Sep 2025 08:29:57 +1000
Subject: [PATCH 4/5] Implemented Data Summary showing number of correlations
 above a minimum and maximum threshold

---
 R/efa.h.R         | 28 ++++++++++++----------------
 R/pca.b.R         | 21 +++++++++++----------
 R/pca.h.R         | 32 ++++++++++++++------------------
 jamovi/efa.a.yaml | 20 ++++++++------------
 jamovi/efa.u.yaml |  4 ++--
 jamovi/pca.a.yaml | 20 ++++++++------------
 jamovi/pca.r.yaml |  4 ++--
 jamovi/pca.u.yaml |  4 ++--
 8 files changed, 59 insertions(+), 74 deletions(-)

diff --git a/R/efa.h.R b/R/efa.h.R
index eb7656c4..20a4a167 100644
--- a/R/efa.h.R
+++ b/R/efa.h.R
@@ -12,8 +12,8 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             minEigen = 0,
             extraction = "minres",
             rotation = "oblimin",
-            countCorrMin = 0,
-            countCorrMax = 0,
+            countCorrMin = "",
+            countCorrMax = "",
             kmo = FALSE,
             bartlett = FALSE,
             hideLoadings = 0.3,
@@ -77,18 +77,14 @@ efaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "oblimin",
                     "simplimax"),
                 default="oblimin")
-            private$..countCorrMin <- jmvcore::OptionNumber$new(
+            private$..countCorrMin <- jmvcore::OptionString$new(
                 "countCorrMin",
                 countCorrMin,
-                min=0,
-                max=1,
-                default=0)
-            private$..countCorrMax <- jmvcore::OptionNumber$new(
+                default="")
+            private$..countCorrMax <- jmvcore::OptionString$new(
                 "countCorrMax",
                 countCorrMax,
-                min=0,
-                max=1,
-                default=0)
+                default="")
             private$..kmo <- jmvcore::OptionBool$new(
                 "kmo",
                 kmo,
@@ -283,11 +279,11 @@ efaBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' @param rotation \code{'none'}, \code{'varimax'}, \code{'quartimax'},
 #'   \code{'promax'}, \code{'oblimin'} (default), or \code{'simplimax'}, the
 #'   rotation to use in estimation
-#' @param countCorrMin a number (default: 0), returns the number of
-#'   correlations between variables above this minimum (if 0, no output is
+#' @param countCorrMin a number (default: NA), returns the number of
+#'   correlations between variables above this minimum (if NA, no output is
 #'   produced)
-#' @param countCorrMax a number (default: 0), returns the number of
-#'   correlations between variables above this maxmimum (if 0, no output is
+#' @param countCorrMax a number (default: NA), returns the number of
+#'   correlations between variables above this maxmimum (if NA, no output is
 #'   produced)
 #' @param kmo \code{TRUE} or \code{FALSE} (default), show Kaiser-Meyer-Olkin
 #'   (KMO) measure of sampling adequacy (MSA) results
@@ -323,8 +319,8 @@ efa <- function(
     minEigen = 0,
     extraction = "minres",
     rotation = "oblimin",
-    countCorrMin = 0,
-    countCorrMax = 0,
+    countCorrMin = "",
+    countCorrMax = "",
     kmo = FALSE,
     bartlett = FALSE,
     hideLoadings = 0.3,
diff --git a/R/pca.b.R b/R/pca.b.R
index 9a6c4b37..23cadbee 100644
--- a/R/pca.b.R
+++ b/R/pca.b.R
@@ -263,7 +263,7 @@ pcaClass <- R6::R6Class(
                                          self$options[[paste0("countCorr", t)]])
                 table$setTitle(title)
                 for (i in seq_along(vars)) {
-                    table$addColumn(name = sprintf("c%d", i), title = ".", type = 'integer')
+                    table$addColumn(name = sprintf("c%d", i), title = "", type = 'integer')
                 }
             }
         },
@@ -438,15 +438,16 @@ pcaClass <- R6::R6Class(
                 diag(corrMatrix) <- NA
 
                 for (t in c("Min", "Max")) {
-                    thresh <- self$options[[paste0("countCorr", t)]]
-                    if (thresh > 0) {
-                        table  <- group[[paste0("corrAbove", t)]]
-                        counts <- sort(colSums(corrMatrix > thresh, na.rm = TRUE))
-                        cnames <- names(counts)
-                        table$setRow(rowNo = 1, setNames(as.list(counts), sprintf("c%d", seq_along(vars))))
-                        for (i in seq_along(cnames)) {
-                            table$columns[[i + 1]]$setTitle(cnames[i])
-                        }
+                    thresh <- as.numeric(self$options[[paste0("countCorr", t)]])
+                    if (is.na(thresh)) next
+                    if (thresh <= 0 || thresh >= 1)
+                        jmvcore::reject(.("Values for the Correlation Min. / Max. need to be Numeric and Between 0 and 1"))
+                    table  <- group[[paste0("corrAbove", t)]]
+                    counts <- sort(colSums(corrMatrix > thresh, na.rm = TRUE))
+                    cnames <- names(counts)
+                    table$setRow(rowNo = 1, setNames(as.list(counts), sprintf("c%d", seq_along(vars))))
+                    for (i in seq_along(cnames)) {
+                         table$columns[[i + 1]]$setTitle(cnames[i])
                     }
                 }
             }
diff --git a/R/pca.h.R b/R/pca.h.R
index 2a3cff42..1f89ffa1 100644
--- a/R/pca.h.R
+++ b/R/pca.h.R
@@ -11,8 +11,8 @@ pcaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
             nFactors = 1,
             minEigen = 1,
             rotation = "varimax",
-            countCorrMin = 0,
-            countCorrMax = 0,
+            countCorrMin = "",
+            countCorrMax = "",
             kmo = FALSE,
             bartlett = FALSE,
             hideLoadings = 0.3,
@@ -66,18 +66,14 @@ pcaOptions <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                     "oblimin",
                     "simplimax"),
                 default="varimax")
-            private$..countCorrMin <- jmvcore::OptionNumber$new(
+            private$..countCorrMin <- jmvcore::OptionString$new(
                 "countCorrMin",
                 countCorrMin,
-                min=0,
-                max=1,
-                default=0)
-            private$..countCorrMax <- jmvcore::OptionNumber$new(
+                default="")
+            private$..countCorrMax <- jmvcore::OptionString$new(
                 "countCorrMax",
                 countCorrMax,
-                min=0,
-                max=1,
-                default=0)
+                default="")
             private$..kmo <- jmvcore::OptionBool$new(
                 "kmo",
                 kmo,
@@ -348,7 +344,7 @@ pcaResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                             options=options,
                             name="corrAboveMin",
                             title="",
-                            visible="(countCorrMin > 0)",
+                            visible="(countCorrMin != \"\")",
                             rows=1,
                             clearWith=list(
                                 "vars",
@@ -363,7 +359,7 @@ pcaResults <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
                             options=options,
                             name="corrAboveMax",
                             title="",
-                            visible="(countCorrMax > 0)",
+                            visible="(countCorrMax != \"\")",
                             rows=1,
                             clearWith=list(
                                 "vars",
@@ -543,11 +539,11 @@ pcaBase <- if (requireNamespace("jmvcore", quietly=TRUE)) R6::R6Class(
 #' @param rotation \code{'none'}, \code{'varimax'} (default),
 #'   \code{'quartimax'}, \code{'promax'}, \code{'oblimin'}, or
 #'   \code{'simplimax'}, the rotation to use in estimation
-#' @param countCorrMin a number (default: 0), returns the number of
-#'   correlations between variables above this minimum (if 0, no output is
+#' @param countCorrMin a number (default: NA), returns the number of
+#'   correlations between variables above this minimum (if NA, no output is
 #'   produced)
-#' @param countCorrMax a number (default: 0), returns the number of
-#'   correlations between variables above this maxmimum (if 0, no output is
+#' @param countCorrMax a number (default: NA), returns the number of
+#'   correlations between variables above this maxmimum (if NA, no output is
 #'   produced)
 #' @param kmo \code{TRUE} or \code{FALSE} (default), show Kaiser-Meyer-Olkin
 #'   (KMO) measure of sampling adequacy (MSA) results
@@ -591,8 +587,8 @@ pca <- function(
     nFactors = 1,
     minEigen = 1,
     rotation = "varimax",
-    countCorrMin = 0,
-    countCorrMax = 0,
+    countCorrMin = "",
+    countCorrMax = "",
     kmo = FALSE,
     bartlett = FALSE,
     hideLoadings = 0.3,
diff --git a/jamovi/efa.a.yaml b/jamovi/efa.a.yaml
index f555c190..09370645 100644
--- a/jamovi/efa.a.yaml
+++ b/jamovi/efa.a.yaml
@@ -122,24 +122,20 @@ options:
             in estimation
 
     - name: countCorrMin
-      type: Number
-      min: 0
-      max: 1
-      default: 0
+      type: String
+      default: ""
       description:
           R: >
-            a number (default: 0), returns the number of correlations between
-            variables above this minimum (if 0, no output is produced)
+            a number (default: NA), returns the number of correlations between
+            variables above this minimum (if NA, no output is produced)
 
     - name: countCorrMax
-      type: Number
-      min: 0
-      max: 1
-      default: 0
+      type: String
+      default: ""
       description:
           R: >
-            a number (default: 0), returns the number of correlations between
-            variables above this maxmimum (if 0, no output is produced)
+            a number (default: NA), returns the number of correlations between
+            variables above this maxmimum (if NA, no output is produced)
 
     - name: kmo
       title: KMO measure of sampling adequacy
diff --git a/jamovi/efa.u.yaml b/jamovi/efa.u.yaml
index a2754971..855ba5f2 100644
--- a/jamovi/efa.u.yaml
+++ b/jamovi/efa.u.yaml
@@ -79,7 +79,7 @@ children:
                 children:
                   - name: countCorrMin
                     type: TextBox
-                    format: number
+                    format: string
               - type: Label
                 label: And Above Max.
                 horizontalAlignment: right
@@ -93,7 +93,7 @@ children:
                 children:
                   - name: countCorrMax
                     type: TextBox
-                    format: number
+                    format: string
       - type: LayoutBox
         margin: large
         cell:
diff --git a/jamovi/pca.a.yaml b/jamovi/pca.a.yaml
index 57c2331a..2c65e9c9 100644
--- a/jamovi/pca.a.yaml
+++ b/jamovi/pca.a.yaml
@@ -103,25 +103,21 @@ options:
 
     - name: countCorrMin
       title: ""
-      type: Number
-      min: 0
-      max: 1
-      default: 0
+      type: String
+      default: ""
       description:
           R: >
-            a number (default: 0), returns the number of correlations between
-            variables above this minimum (if 0, no output is produced)
+            a number (default: NA), returns the number of correlations between
+            variables above this minimum (if NA, no output is produced)
 
     - name: countCorrMax
       title: ""
-      type: Number
-      min: 0
-      max: 1
-      default: 0
+      type: String
+      default: ""
       description:
           R: >
-            a number (default: 0), returns the number of correlations between
-            variables above this maxmimum (if 0, no output is produced)
+            a number (default: NA), returns the number of correlations between
+            variables above this maxmimum (if NA, no output is produced)
 
     - name: kmo
       title: KMO measure of sampling adequacy
diff --git a/jamovi/pca.r.yaml b/jamovi/pca.r.yaml
index 351166e6..c6507e76 100644
--- a/jamovi/pca.r.yaml
+++ b/jamovi/pca.r.yaml
@@ -130,7 +130,7 @@ items:
         - name: corrAboveMin
           title: ""
           type: Table
-          visible: (countCorrMin > 0)
+          visible: (countCorrMin != "")
           rows: 1
           clearWith:
             - vars
@@ -143,7 +143,7 @@ items:
         - name: corrAboveMax
           title: ""
           type: Table
-          visible: (countCorrMax > 0)
+          visible: (countCorrMax != "")
           rows: 1
           clearWith:
             - vars
diff --git a/jamovi/pca.u.yaml b/jamovi/pca.u.yaml
index 261b2946..db0651bf 100644
--- a/jamovi/pca.u.yaml
+++ b/jamovi/pca.u.yaml
@@ -80,7 +80,7 @@ children:
                 children:
                   - name: countCorrMin
                     type: TextBox
-                    format: number
+                    format: string
               - type: Label
                 label: And Above Max.
                 horizontalAlignment: right
@@ -94,7 +94,7 @@ children:
                 children:
                   - name: countCorrMax
                     type: TextBox
-                    format: number
+                    format: string
       - type: LayoutBox
         margin: large
         cell:

From 16e78956a72a62f893ecb9f47aa2fd79285d519c Mon Sep 17 00:00:00 2001
From: Sebastian Jentschke <Sebastian.Jentschke@gmail.com>
Date: Fri, 24 Oct 2025 14:06:42 +1100
Subject: [PATCH 5/5] Fixed sorting the correlation counts

---
 R/pca.b.R | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/R/pca.b.R b/R/pca.b.R
index 23cadbee..d2370f3f 100644
--- a/R/pca.b.R
+++ b/R/pca.b.R
@@ -443,7 +443,9 @@ pcaClass <- R6::R6Class(
                     if (thresh <= 0 || thresh >= 1)
                         jmvcore::reject(.("Values for the Correlation Min. / Max. need to be Numeric and Between 0 and 1"))
                     table  <- group[[paste0("corrAbove", t)]]
-                    counts <- sort(colSums(corrMatrix > thresh, na.rm = TRUE))
+                    # sort the columns by the number of correlations above threshold (increasing for min: lower counts
+                    # on the left, decreasing for max: higher counts on the left)
+                    counts <- sort(colSums(corrMatrix > thresh, na.rm = TRUE), decreasing = (t == "Max"))
                     cnames <- names(counts)
                     table$setRow(rowNo = 1, setNames(as.list(counts), sprintf("c%d", seq_along(vars))))
                     for (i in seq_along(cnames)) {