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yh202109 committed Jul 21, 2024
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4 changes: 2 additions & 2 deletions _downloads/214d05cd65dcc9387b037da1ce5a5c33/report.html
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2 changes: 1 addition & 1 deletion _downloads/9911a4d807ac9f1a695f0aa2cf687076/coverage.xml
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3 changes: 2 additions & 1 deletion _sources/statlab_kappa2.rst.txt
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Expand Up @@ -312,7 +312,8 @@ The second element of :eq:`eq_kappa2_vn2` can be calculated, using
:label: eq_kappa2_vn5
E\left( \sum_j\sum_{k \neq j} N_{ij}^2 N_{ik}^2 \right)
=& R(R-1) + R(R-1)(2R-5)(\sum_j p_j^2) - 2R(R-1)(R-2)(\sum_j p_j^3) - R(R-1)(R-2)(R-3) \sum_j p_j^4 + R(R-1)(R-2)(R-3) (\sum_{j} p_j^2)^2
= R(R-1) + R(R-1)(2R-5)(\sum_j p_j^2)
- 2R(R-1)(R-2)(\sum_j p_j^3) - R(R-1)(R-2)(R-3) \sum_j p_j^4 + R(R-1)(R-2)(R-3) (\sum_{j} p_j^2)^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)`
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2 changes: 1 addition & 1 deletion _static/reports/coverage/coverage.xml
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<?xml version="1.0" ?>
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<sources>
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2 changes: 1 addition & 1 deletion _static/reports/junit/junit.xml
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<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="38" time="8.681" timestamp="2024-07-21T23:52:50.919342+00:00" hostname="fv-az1117-277"><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="0.009" /><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="0.196" /><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="0.000" /><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="0.016" /><testcase classname="tests.test_statlab_kappa.TestKappaCalculator" name="test_bootstrap_cohen_ci" time="0.226" /><testcase classname="tests.test_statlab_kappa.TestKappaCalculator" name="test_cohen" time="0.067" /><testcase classname="tests.test_statlab_kappa.TestKappaCalculator" name="test_fleiss_kappa" time="0.065" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_compare_file_size" time="0.757" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_get_outline_list" time="0.930" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_show_outline_tree" time="0.959" /></testsuite></testsuites>
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4 changes: 2 additions & 2 deletions _static/reports/junit/report.html
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8 changes: 6 additions & 2 deletions example_cdtg.html
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Expand Up @@ -133,7 +133,11 @@ <h1>U/Graph/Categorical Plots Using catPlotter<a class="headerlink" href="#u-gra
</div>
</div>
<div class="cell_output docutils container">
<img alt="_images/1ff8a44423a7ab6e1f637ef0f22e7eb5d21cf1f16d9733c46fa776aba8941598.png" src="_images/1ff8a44423a7ab6e1f637ef0f22e7eb5d21cf1f16d9733c46fa776aba8941598.png" />
<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: 11.1% 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/087869a24ab142fdad17e2d94e18409e83740b769a9b7a8a4fe2e0bd68611598.png" src="_images/087869a24ab142fdad17e2d94e18409e83740b769a9b7a8a4fe2e0bd68611598.png" />
</div>
</div>
<p>To create a line plot:</p>
Expand All @@ -145,7 +149,7 @@ <h1>U/Graph/Categorical Plots Using catPlotter<a class="headerlink" href="#u-gra
</div>
</div>
<div class="cell_output docutils container">
<img alt="_images/b9c3389ce39ca8d59b3ccd9a0450634aeb3dcc7189c20724cec73c62993a421c.png" src="_images/b9c3389ce39ca8d59b3ccd9a0450634aeb3dcc7189c20724cec73c62993a421c.png" />
<img alt="_images/d6ca436f8f61256419623900fbc99f3f0bb9b36f1b3b1034451d39207f76df54.png" src="_images/d6ca436f8f61256419623900fbc99f3f0bb9b36f1b3b1034451d39207f76df54.png" />
</div>
</div>
</section>
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76 changes: 38 additions & 38 deletions example_clinical.html
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Expand Up @@ -131,8 +131,8 @@ <h2>Example 1<a class="headerlink" href="#example-1" title="Link to this heading
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> study treatment subject visit meal calorie
0 STD1 TRT1 SUBJ01 VISIT1 1 1702
1 STD1 TRT1 SUBJ01 VISIT1 2 1523
0 STD1 TRT1 SUBJ01 VISIT1 1 967
1 STD1 TRT1 SUBJ01 VISIT1 2 703
</pre></div>
</div>
</div>
Expand All @@ -149,12 +149,12 @@ <h2>Example 1<a class="headerlink" href="#example-1" title="Link to this heading
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> study treatment subject visit N(0&lt;=X&lt;500) N(500&lt;=X&lt;1000) \
0 STD1 TRT1 SUBJ01 VISIT1 0 0
1 STD1 TRT1 SUBJ01 VISIT2 0 2
0 STD1 TRT1 SUBJ01 VISIT1 0 2
1 STD1 TRT1 SUBJ02 VISIT1 1 0

N(1000&lt;=V&lt;=2000) N(all)
0 2 2
1 3 5
0 1 3
1 3 4
</pre></div>
</div>
</div>
Expand All @@ -169,22 +169,22 @@ <h2>Example 1<a class="headerlink" href="#example-1" title="Link to this heading
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> study treatment visit N(0&lt;=X&lt;3) N(3&lt;=X&lt;5) N(5&lt;=V&lt;=7) N(all)
0 STD1 TRT1 VISIT1 4 9 7 20
1 STD1 TRT1 VISIT2 1 13 6 20
2 STD1 TRT1 VISIT3 3 6 6 15
3 STD1 TRT1 VISIT4 3 3 0 6
4 STD1 TRT2 VISIT1 7 7 6 20
5 STD1 TRT2 VISIT2 3 9 5 17
6 STD1 TRT2 VISIT3 1 5 5 11
7 STD1 TRT2 VISIT4 1 1 1 3
8 STD2 TRT1 VISIT1 3 11 6 20
9 STD2 TRT1 VISIT2 3 6 7 16
10 STD2 TRT1 VISIT3 4 8 1 13
11 STD2 TRT1 VISIT4 0 3 3 6
12 STD2 TRT2 VISIT1 6 10 4 20
13 STD2 TRT2 VISIT2 5 7 2 14
14 STD2 TRT2 VISIT3 2 4 5 11
15 STD2 TRT2 VISIT4 2 2 2 6
0 STD1 TRT1 VISIT1 4 10 6 20
1 STD1 TRT1 VISIT2 4 9 3 16
2 STD1 TRT1 VISIT3 2 6 4 12
3 STD1 TRT1 VISIT4 2 1 5 8
4 STD1 TRT2 VISIT1 4 11 5 20
5 STD1 TRT2 VISIT2 3 7 6 16
6 STD1 TRT2 VISIT3 0 9 4 13
7 STD1 TRT2 VISIT4 1 3 0 4
8 STD2 TRT1 VISIT1 6 8 6 20
9 STD2 TRT1 VISIT2 5 8 4 17
10 STD2 TRT1 VISIT3 4 5 3 12
11 STD2 TRT1 VISIT4 1 4 0 5
12 STD2 TRT2 VISIT1 8 9 3 20
13 STD2 TRT2 VISIT2 4 2 9 15
14 STD2 TRT2 VISIT3 1 5 3 9
15 STD2 TRT2 VISIT4 1 0 0 1
</pre></div>
</div>
</div>
Expand All @@ -198,22 +198,22 @@ <h2>Example 1<a class="headerlink" href="#example-1" title="Link to this heading
</div>
<div class="cell_output docutils container">
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span> study treatment visit Sum(0&lt;=X&lt;3) Sum(3&lt;=X&lt;5) Sum(5&lt;=V&lt;=7) Sum(all)
0 STD1 TRT1 VISIT1 8 33 35 76
1 STD1 TRT1 VISIT2 2 47 30 79
2 STD1 TRT1 VISIT3 6 21 30 57
3 STD1 TRT1 VISIT4 6 10 0 16
4 STD1 TRT2 VISIT1 14 24 30 68
5 STD1 TRT2 VISIT2 6 32 25 63
6 STD1 TRT2 VISIT3 2 17 25 44
7 STD1 TRT2 VISIT4 2 3 5 10
8 STD2 TRT1 VISIT1 6 41 30 77
9 STD2 TRT1 VISIT2 6 20 35 61
10 STD2 TRT1 VISIT3 8 27 5 40
11 STD2 TRT1 VISIT4 0 12 15 27
12 STD2 TRT2 VISIT1 12 35 20 67
13 STD2 TRT2 VISIT2 10 25 10 45
14 STD2 TRT2 VISIT3 4 15 25 44
15 STD2 TRT2 VISIT4 4 7 10 21
0 STD1 TRT1 VISIT1 8 35 30 73
1 STD1 TRT1 VISIT2 8 32 15 55
2 STD1 TRT1 VISIT3 4 22 20 46
3 STD1 TRT1 VISIT4 4 3 25 32
4 STD1 TRT2 VISIT1 8 39 25 72
5 STD1 TRT2 VISIT2 6 22 30 58
6 STD1 TRT2 VISIT3 0 32 20 52
7 STD1 TRT2 VISIT4 2 11 0 13
8 STD2 TRT1 VISIT1 12 30 30 72
9 STD2 TRT1 VISIT2 10 28 20 58
10 STD2 TRT1 VISIT3 8 18 15 41
11 STD2 TRT1 VISIT4 2 16 0 18
12 STD2 TRT2 VISIT1 16 33 15 64
13 STD2 TRT2 VISIT2 8 7 45 60
14 STD2 TRT2 VISIT3 2 16 15 33
15 STD2 TRT2 VISIT4 2 0 0 2
</pre></div>
</div>
</div>
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3 changes: 0 additions & 3 deletions example_ectd.html
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Expand Up @@ -561,9 +561,6 @@ <h2>Module 4<a class="headerlink" href="#module-4" title="Link to this heading">
└── 4.3 Literature references
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
</div>
</section>
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