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yh202109 · Jul 21, 2024 · 6a68ff7 · 6a68ff7
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diff --git a/_downloads/214d05cd65dcc9387b037da1ce5a5c33/report.html b/_downloads/214d05cd65dcc9387b037da1ce5a5c33/report.html
diff --git a/_downloads/9911a4d807ac9f1a695f0aa2cf687076/coverage.xml b/_downloads/9911a4d807ac9f1a695f0aa2cf687076/coverage.xml
@@ -1,5 +1,5 @@
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+<coverage version="7.6.0" timestamp="1721586462396" lines-valid="1494" lines-covered="642" line-rate="0.4297" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
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diff --git a/_images/52a37971a191bc5931ba183837c27a7cfee6077a57d62ef18dc8985b47ea226f.png b/_images/52a37971a191bc5931ba183837c27a7cfee6077a57d62ef18dc8985b47ea226f.png
diff --git a/_images/533c386576f281089b9bf96459fc1da2b1d74b711328feaa8ad023239134a57e.png b/_images/533c386576f281089b9bf96459fc1da2b1d74b711328feaa8ad023239134a57e.png
diff --git a/_images/97a420d71e1361b711e9e67a2ed8dbc5ed1ebc55ff669adabdd6cf2c995300f8.png b/_images/97a420d71e1361b711e9e67a2ed8dbc5ed1ebc55ff669adabdd6cf2c995300f8.png
diff --git a/_images/d4bf13e7296f9358479bd81daae4f4d3909203b45c4ed23f891b91dd1c0d5182.png b/_images/d4bf13e7296f9358479bd81daae4f4d3909203b45c4ed23f891b91dd1c0d5182.png
diff --git a/_sources/statlab_kappa2.rst.txt b/_sources/statlab_kappa2.rst.txt
@@ -36,7 +36,7 @@ with categorical rating outcomes [1]_ [2]_.
 Notation 
 *************
 
-Assume there are the same :math:`R+N_0` (:math:`geq 2+N_0`) raters and each of :math:`n` samples were rated by :math:`R` randomly selected raters and were not rated by the rest of :math:`N_0` raters.
+Assume there are the same :math:`R+N_0` (:math:`\geq 2+N_0`) raters and each of :math:`n` samples were rated by :math:`R` randomly selected raters and were not rated by the rest of :math:`N_0` raters.
 For :math:`J` categories rating, let :math:`Y_{r,i} \in \{v_0, v_1,v_2,\ldots, v_J \}` represent rating 
 from rater :math:`r=1,2,\ldots,R+N_0` for sample :math:`i = 1, \ldots, n`.
 Let :math:`N_{ij}` represent the total number of raters gave rating :math:`(v_j)` to sample :math:`i`, where :math:`j \in \{0, 1,\ldots,J\}`.
@@ -287,7 +287,7 @@ To calculate :eq:`eq_kappa2_vn2`,
 we can use the MGF, :math:`\left(\sum_{j}p_je^{t_j}\right)^R`, to derive
 :math:`E\left(N_{ij}^2\right) = Rp_j + R(R-1)p_j^2`, 
 :math:`E\left(N_{ij}^3\right) = Rp_j + 3R(R-1)p_j^2 + R(R-1)(R-2)p_j^3`, and 
-:math:`E\left(N_{ij}^4\right) = ` (Lab Exercise; to be used in :eq:`eq_kappa2_vn3` and :eq:`eq_kappa2_vn5`). 
+:math:`E\left(N_{ij}^4\right) =` (Lab Exercise; to be used in :eq:`eq_kappa2_vn3` and :eq:`eq_kappa2_vn5`). 
 
 The first element of :eq:`eq_kappa2_vn2` can be calculated as [2]_ :sup:`(Eq. 12)`
 
@@ -313,12 +313,7 @@ The second element of :eq:`eq_kappa2_vn2` can be calculated using
   :label: eq_kappa2_vn5
 
   E\left( N_{ij}^2 N_{ik}^2 \right)
-  =& E\left(N_{ik}^2E\left(N_{ij}^2|N_{ik}\right)\right) \\
-  =& \frac{p_j}{1-p_k}E\left(RN_{ik}^2-N_{ik}^3\right) 
-  + \frac{p_j^2}{(1-p_k)^2}E\left((R^2-R)N_{ik}^2 - (2R+1)N_{ik}^3-N_{ik}^4\right)
-  =& \left(\frac{p_j}{1-p_k} + \frac{p_j^2}{(1-p_k)^2}(R^2-R)\right)E(N_{ik}^2) 
-  -\left(\frac{p_j}{1-p_k}E(N_{ik}^3) + \frac{p_j^2}{(1-p_k)^2}(2R+1)\right)E(N_{ik}^3)
-  -\frac{p_j^2}{(1-p_k)^2}E(N_{ik}^4)
+  = R(R-1)p_j(p_k+(R-2)p_k^2) + R(R-1)(R-2)p_j^2(p_k+(R-3)2p_k^2)
 
 Combining :eq:`eq_kappa2_vn3`, :eq:`eq_kappa2_vn4`, and :eq:`eq_kappa2_vn5`, 
 :eq:`eq_kappa2_vn2` can be calculated as [2]_ :sup:`(Eq. 15)`

diff --git a/_static/reports/coverage/coverage.xml b/_static/reports/coverage/coverage.xml
@@ -1,5 +1,5 @@
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+<coverage version="7.6.0" timestamp="1721586462396" lines-valid="1494" lines-covered="642" line-rate="0.4297" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
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diff --git a/_static/reports/junit/junit.xml b/_static/reports/junit/junit.xml
@@ -1 +1 @@
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+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="38" time="10.859" timestamp="2024-07-21T18:27:21.666185+00:00" hostname="fv-az885-740"><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_1df_invalid_input" time="0.002" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_1df_missing_column" time="0.001" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_1df_with_difference" time="0.005" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_1df_without_difference" time="0.002" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_2df_with_existing_column" time="0.010" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_2df_with_non_existing_column" time="0.001" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_2df_with_non_existing_group" time="0.001" /><testcase classname="tests.test_cdt.TestCdt" name="test_diff_2cols_in_2df_with_same_group_and_column" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_find_section_given_words" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_find_section_given_words_invalid_include" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_find_section_given_words_invalid_outfmt" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_load_list" time="0.001" /><testcase classname="tests.test_health_ectd.TestCtocByFDA" name="test_show_ctoc_tree" time="0.200" /><testcase classname="tests.test_health_emt.TestEmt" name="test_expected_file_lists" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_files" time="0.005" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_hlgt" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_hlt" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_llt" time="0.007" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_pt" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_pt_given_soc" time="0.006" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_pt_given_soc_primary_only" time="0.006" /><testcase classname="tests.test_health_emt.TestEmt" name="test_find_soc" time="0.004" /><testcase classname="tests.test_health_emt.TestEmt" name="test_list_files" time="0.025" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_dataframe" time="0.001" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_json" time="0.001" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_list" time="0.001" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_string" time="0.001" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_tree" time="0.013" /><testcase classname="tests.test_lsr.TestLsrTree" name="test_list_files_tree2" time="0.008" /><testcase classname="tests.test_statlab_corr.TestCorrCalculator" name="test_calculate_kendall_tau_with_dataframe" time="0.002" /><testcase classname="tests.test_statlab_corr.TestCorrCalculator" name="test_calculate_kendall_tau_with_list" time="0.002" /><testcase classname="tests.test_statlab_corr.TestCorrCalculator" name="test_plot_y_list" time="0.017" /><testcase classname="tests.test_statlab_kappa.TestKappaCalculator" name="test_bootstrap_cohen_ci" time="0.238" /><testcase classname="tests.test_statlab_kappa.TestKappaCalculator" name="test_cohen" time="0.070" /><testcase classname="tests.test_statlab_kappa.TestKappaCalculator" name="test_fleiss_kappa" time="0.067" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_compare_file_size" time="0.767" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_get_outline_list" time="0.875" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_show_outline_tree" time="0.842" /></testsuite></testsuites>
diff --git a/_static/reports/junit/report.html b/_static/reports/junit/report.html
diff --git a/example_cdtg.html b/example_cdtg.html
@@ -133,15 +133,13 @@ <h1>U/Graph/Categorical Plots Using catPlotter<a class="headerlink" href="#u-gra
 </div>
 </div>
 <div class="cell_output docutils container">
-<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/home/runner/.cache/pypoetry/virtualenvs/mtbp3-STzYEG9e-py3.10/lib/python3.10/site-packages/seaborn/categorical.py:3399: UserWarning: 16.7% of the points cannot be placed; you may want to decrease the size of the markers or use stripplot.
+<div class="output stderr highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>/home/runner/.cache/pypoetry/virtualenvs/mtbp3-STzYEG9e-py3.10/lib/python3.10/site-packages/seaborn/categorical.py:3399: UserWarning: 38.9% of the points cannot be placed; you may want to decrease the size of the markers or use stripplot.
   warnings.warn(msg, UserWarning)
 /home/runner/.cache/pypoetry/virtualenvs/mtbp3-STzYEG9e-py3.10/lib/python3.10/site-packages/seaborn/categorical.py:3399: UserWarning: 40.0% of the points cannot be placed; you may want to decrease the size of the markers or use stripplot.
   warnings.warn(msg, UserWarning)
-/home/runner/.cache/pypoetry/virtualenvs/mtbp3-STzYEG9e-py3.10/lib/python3.10/site-packages/seaborn/categorical.py:3399: UserWarning: 25.0% of the points cannot be placed; you may want to decrease the size of the markers or use stripplot.
-  warnings.warn(msg, UserWarning)
 </pre></div>
 </div>
-<img alt="_images/d4bf13e7296f9358479bd81daae4f4d3909203b45c4ed23f891b91dd1c0d5182.png" src="_images/d4bf13e7296f9358479bd81daae4f4d3909203b45c4ed23f891b91dd1c0d5182.png" />
+<img alt="_images/97a420d71e1361b711e9e67a2ed8dbc5ed1ebc55ff669adabdd6cf2c995300f8.png" src="_images/97a420d71e1361b711e9e67a2ed8dbc5ed1ebc55ff669adabdd6cf2c995300f8.png" />
 </div>
 </div>
 <p>To create a line plot:</p>
@@ -153,7 +151,7 @@ <h1>U/Graph/Categorical Plots Using catPlotter<a class="headerlink" href="#u-gra
 </div>
 </div>
 <div class="cell_output docutils container">
-<img alt="_images/52a37971a191bc5931ba183837c27a7cfee6077a57d62ef18dc8985b47ea226f.png" src="_images/52a37971a191bc5931ba183837c27a7cfee6077a57d62ef18dc8985b47ea226f.png" />
+<img alt="_images/533c386576f281089b9bf96459fc1da2b1d74b711328feaa8ad023239134a57e.png" src="_images/533c386576f281089b9bf96459fc1da2b1d74b711328feaa8ad023239134a57e.png" />
 </div>
 </div>
 </section>