From 1f712f66ad1a1219e3f548ded40d62efcc315d79 Mon Sep 17 00:00:00 2001
From: yh202109 <yh202109@gmail.com>
Date: Sun, 7 Jul 2024 15:31:07 -0400
Subject: [PATCH] v0.2.14

---
 docs/_static/fig/statlab_kappa_fig1.svg | 424 +++++++++------
 docs/_static/fig/statlab_kappa_fig2.svg | 675 +++++++++++++-----------
 docs/_static/fig/statlab_kappa_fig3.svg | 675 +++++++++++++-----------
 docs/statlab_kappa.rst                  |  14 +-
 mtbp3/statlab/kappa.py                  |  15 +-
 5 files changed, 1032 insertions(+), 771 deletions(-)

diff --git a/docs/_static/fig/statlab_kappa_fig1.svg b/docs/_static/fig/statlab_kappa_fig1.svg
index dd6ca44c..fcb9d74f 100644
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diff --git a/docs/statlab_kappa.rst b/docs/statlab_kappa.rst
index 9ba770f4..bbc165c0 100644
--- a/docs/statlab_kappa.rst
+++ b/docs/statlab_kappa.rst
@@ -395,8 +395,10 @@ To create a bubble plot using ``mtbp3.statlab``:
 
     from mtbp3.statlab import kappa
 
-    r1 = random.choices(fruits, k=100)
-    r2 = random.choices(fruits, k=100)
+    fruits = ['Apple', 'Orange', 'Pear']
+    np.random.seed(100)
+    r1 = np.random.choice(fruits, size=100).tolist()
+    r2 = np.random.choice(fruits, size=100).tolist()
 
     kappa = KappaCalculator([r1,r2], stringna='NA')
     print("Cohen's kappa (mtbp3.statlab): "+str(kappa.cohen_kappa))
@@ -410,10 +412,10 @@ Output:
 
 .. testoutput::
 
-    Cohen's kappa (mtbp3.statlab): 0.06864954183566166
-    Number of raters per sample: 2.0
-    Number of rating categories: 3
-    Number of sample: 100
+Cohen's kappa (mtbp3.statlab): 0.06513872135102527
+Number of raters per sample: 2.0
+Number of rating categories: 3
+Number of sample: 100
 
 .. figure:: /_static/fig/statlab_kappa_fig1.svg
     :scale: 70%
diff --git a/mtbp3/statlab/kappa.py b/mtbp3/statlab/kappa.py
index 0a771640..7233e41e 100644
--- a/mtbp3/statlab/kappa.py
+++ b/mtbp3/statlab/kappa.py
@@ -324,17 +324,6 @@ def create_bubble_plot(self, out_path="", axis_label=[], max_size_ratio=0, hist=
 
 if __name__ == "__main__":
 
-    fruits = ['Apple', 'Orange', 'Pear']
-    r1 = random.choices(fruits, k=100)
-    r2 = random.choices(fruits, k=100)
-
-    kappa = KappaCalculator([r1,r2], stringna='NA')
-    print("Cohen's kappa (mtbp3.statlab): "+str(kappa.cohen_kappa))
-    print("Number of raters per sample: "+str(kappa.n_rater))
-    print("Number of rating categories: "+str(kappa.n_category))
-    print("Number of sample: "+str(kappa.y_count.shape[0]))
-    p1 = '/Users/yh2020/dt2/proj/mtbp3/docs/_static/fig/'
-    kappa.create_bubble_plot(out_path=p1+'statlab_kappa_fig1.svg')
-    kappa.create_bubble_plot(hist=True, out_path=p1+'statlab_kappa_fig2.svg')
-    kappa.create_bubble_plot(hist=True, reverse_y=False, out_path=p1+'statlab_kappa_fig3.svg')
+    pass
+