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yh202109 committed Jun 29, 2024
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6 changes: 3 additions & 3 deletions _downloads/214d05cd65dcc9387b037da1ce5a5c33/report.html
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2 changes: 1 addition & 1 deletion _downloads/9911a4d807ac9f1a695f0aa2cf687076/coverage.xml
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<?xml version="1.0" ?>
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<sources>
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3 changes: 1 addition & 2 deletions _sources/statlab_corr_tau.rst.txt
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Expand Up @@ -29,7 +29,7 @@ StatLab/Corr/Kendall's tau
Background
*************

Kendall's tau (:math:`\tau`) is a statistic used for measuring rank correlation [1]_ [2]_.
Kendall's tau (:math:`\tau`) is a statistic used for measuring rank correlation [1]_ [2]_ .

*************
Notation
Expand Down Expand Up @@ -72,7 +72,6 @@ The coefficient :math:`\tau` (tau-a) can be calculated as
:eq:`eq_tau1` can also be expressed as

.. math::
:label: eq_tau2
\tau = \frac{2}{n(n-1)} \left( \sum_{i=1}^n \sum_{j < n} Z_{ij} \right),
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2 changes: 1 addition & 1 deletion _static/reports/coverage/coverage.xml
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<?xml version="1.0" ?>
<coverage version="7.5.4" timestamp="1719628526665" lines-valid="1248" lines-covered="431" line-rate="0.3454" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
<coverage version="7.5.4" timestamp="1719628686445" lines-valid="1248" lines-covered="431" line-rate="0.3454" branches-covered="0" branches-valid="0" branch-rate="0" complexity="0">
<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.5.4 -->
<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
<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="27" time="6.789" timestamp="2024-06-29T02:35:15.118736" hostname="fv-az1773-436"><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_emt.TestEmt" name="test_expected_file_lists" time="0.004" /><testcase classname="tests.test_emt.TestEmt" name="test_find_files" time="0.005" /><testcase classname="tests.test_emt.TestEmt" name="test_find_hlgt" time="0.004" /><testcase classname="tests.test_emt.TestEmt" name="test_find_hlt" time="0.004" /><testcase classname="tests.test_emt.TestEmt" name="test_find_llt" time="0.008" /><testcase classname="tests.test_emt.TestEmt" name="test_find_pt" time="0.004" /><testcase classname="tests.test_emt.TestEmt" name="test_find_pt_given_soc" time="0.006" /><testcase classname="tests.test_emt.TestEmt" name="test_find_pt_given_soc_primary_only" time="0.006" /><testcase classname="tests.test_emt.TestEmt" name="test_find_soc" time="0.004" /><testcase classname="tests.test_emt.TestEmt" name="test_list_files" time="0.026" /><testcase classname="tests.test_kappa.TestKappaCalculator" name="test_bootstrap_cohen_ci" time="0.228" /><testcase classname="tests.test_kappa.TestKappaCalculator" name="test_cohen" time="0.068" /><testcase classname="tests.test_kappa.TestKappaCalculator" name="test_fleiss_kappa" time="0.067" /><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" /></testsuite></testsuites>
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6 changes: 3 additions & 3 deletions _static/reports/junit/report.html
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10 changes: 4 additions & 6 deletions example_cdtg.html
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Expand Up @@ -116,15 +116,13 @@ <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: 33.3% 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: 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)
/home/runner/.cache/pypoetry/virtualenvs/mtbp3-STzYEG9e-py3.10/lib/python3.10/site-packages/seaborn/categorical.py:3399: UserWarning: 15.0% 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: 10.0% of the points cannot be placed; you may want to decrease the size of the markers or use stripplot.
/home/runner/.cache/pypoetry/virtualenvs/mtbp3-STzYEG9e-py3.10/lib/python3.10/site-packages/seaborn/categorical.py:3399: UserWarning: 30.0% 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/017b98779412920991b08967db3f401c6fce0b2dca7528b961d46b6cce21f01e.png" src="_images/017b98779412920991b08967db3f401c6fce0b2dca7528b961d46b6cce21f01e.png" />
<img alt="_images/5cfdf2c765a5912ca22fcef44910e0f4d08cbd4132e26ee712ca94ce7bacacfe.png" src="_images/5cfdf2c765a5912ca22fcef44910e0f4d08cbd4132e26ee712ca94ce7bacacfe.png" />
</div>
</div>
<p>To create a line plot:</p>
Expand All @@ -136,7 +134,7 @@ <h1>U/Graph/Categorical Plots Using catPlotter<a class="headerlink" href="#u-gra
</div>
</div>
<div class="cell_output docutils container">
<img alt="_images/66d3a199d0e1956d2355e15cabcaa1638a131588a0085b5c72fe7fbb902a11ef.png" src="_images/66d3a199d0e1956d2355e15cabcaa1638a131588a0085b5c72fe7fbb902a11ef.png" />
<img alt="_images/796ddd9fb78a1f2e2648ea53148edaf0ba038f9c72240580807443955afde5a9.png" src="_images/796ddd9fb78a1f2e2648ea53148edaf0ba038f9c72240580807443955afde5a9.png" />
</div>
</div>
</section>
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74 changes: 37 additions & 37 deletions example_clinical.html
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Expand Up @@ -114,8 +114,8 @@ <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 1 725
1 STD1 TRT1 SUBJ01 VISIT1 2 1499
0 STD1 TRT1 SUBJ01 VISIT1 1 1061
1 STD1 TRT1 SUBJ01 VISIT1 2 1813
</pre></div>
</div>
</div>
Expand All @@ -133,11 +133,11 @@ <h2>Example 1<a class="headerlink" href="#example-1" title="Link to this heading
<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 1
1 STD1 TRT1 SUBJ02 VISIT1 1 2
1 STD1 TRT1 SUBJ01 VISIT2 0 1

N(1000&lt;=V&lt;=2000) N(all)
0 3 4
1 0 3
0 4 5
1 3 4
</pre></div>
</div>
</div>
Expand All @@ -152,22 +152,22 @@ <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 10 8 2 20
1 STD1 TRT1 VISIT2 5 7 3 15
2 STD1 TRT1 VISIT3 3 1 3 7
3 STD1 TRT1 VISIT4 1 1 0 2
4 STD1 TRT2 VISIT1 5 9 6 20
5 STD1 TRT2 VISIT2 1 9 1 11
6 STD1 TRT2 VISIT3 2 5 1 8
7 STD1 TRT2 VISIT4 0 1 1 2
8 STD2 TRT1 VISIT1 7 7 6 20
9 STD2 TRT1 VISIT2 2 7 4 13
10 STD2 TRT1 VISIT3 2 7 2 11
11 STD2 TRT1 VISIT4 3 2 0 5
12 STD2 TRT2 VISIT1 6 7 7 20
13 STD2 TRT2 VISIT2 4 7 4 15
14 STD2 TRT2 VISIT3 3 4 1 8
15 STD2 TRT2 VISIT4 2 0 0 2
0 STD1 TRT1 VISIT1 3 11 6 20
1 STD1 TRT1 VISIT2 3 10 4 17
2 STD1 TRT1 VISIT3 2 9 1 12
3 STD1 TRT1 VISIT4 0 6 1 7
4 STD1 TRT2 VISIT1 6 9 5 20
5 STD1 TRT2 VISIT2 3 6 6 15
6 STD1 TRT2 VISIT3 2 4 2 8
7 STD1 TRT2 VISIT4 2 3 1 6
8 STD2 TRT1 VISIT1 4 9 7 20
9 STD2 TRT1 VISIT2 2 7 5 14
10 STD2 TRT1 VISIT3 1 5 4 10
11 STD2 TRT1 VISIT4 1 1 2 4
12 STD2 TRT2 VISIT1 5 12 3 20
13 STD2 TRT2 VISIT2 5 6 5 16
14 STD2 TRT2 VISIT3 2 7 3 12
15 STD2 TRT2 VISIT4 1 4 3 8
</pre></div>
</div>
</div>
Expand All @@ -181,22 +181,22 @@ <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 20 26 10 56
1 STD1 TRT1 VISIT2 10 25 15 50
2 STD1 TRT1 VISIT3 6 4 15 25
3 STD1 TRT1 VISIT4 2 3 0 5
4 STD1 TRT2 VISIT1 10 33 30 73
5 STD1 TRT2 VISIT2 2 32 5 39
6 STD1 TRT2 VISIT3 4 16 5 25
7 STD1 TRT2 VISIT4 0 4 5 9
8 STD2 TRT1 VISIT1 14 26 30 70
9 STD2 TRT1 VISIT2 4 28 20 52
10 STD2 TRT1 VISIT3 4 24 10 38
11 STD2 TRT1 VISIT4 6 7 0 13
12 STD2 TRT2 VISIT1 12 25 35 72
13 STD2 TRT2 VISIT2 8 27 20 55
14 STD2 TRT2 VISIT3 6 14 5 25
15 STD2 TRT2 VISIT4 4 0 0 4
0 STD1 TRT1 VISIT1 6 39 30 75
1 STD1 TRT1 VISIT2 6 34 20 60
2 STD1 TRT1 VISIT3 4 31 5 40
3 STD1 TRT1 VISIT4 0 22 5 27
4 STD1 TRT2 VISIT1 12 31 25 68
5 STD1 TRT2 VISIT2 6 20 30 56
6 STD1 TRT2 VISIT3 4 14 10 28
7 STD1 TRT2 VISIT4 4 9 5 18
8 STD2 TRT1 VISIT1 8 31 35 74
9 STD2 TRT1 VISIT2 4 24 25 53
10 STD2 TRT1 VISIT3 2 17 20 39
11 STD2 TRT1 VISIT4 2 4 10 16
12 STD2 TRT2 VISIT1 10 43 15 68
13 STD2 TRT2 VISIT2 10 19 25 54
14 STD2 TRT2 VISIT3 4 25 15 44
15 STD2 TRT2 VISIT4 2 13 15 30
</pre></div>
</div>
</div>
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6 changes: 3 additions & 3 deletions example_ectd.html
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Expand Up @@ -375,6 +375,9 @@ <h2>The Comprehensive Table of Contents Headings and Hierarchy (CTOC) by FDA<a c
└── 3.3 Literature references
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
</div>
<p>To view CTOC of Module 4:</p>
Expand Down Expand Up @@ -691,9 +694,6 @@ <h2>The Comprehensive Table of Contents Headings and Hierarchy (CTOC) by FDA<a c
└── 5.4 Literature references
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
</div>
<p>To search a word within the hierarchy:</p>
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6 changes: 0 additions & 6 deletions example_ectd2.html
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Expand Up @@ -566,9 +566,6 @@ <h2>The Comprehensive Table of Contents Headings and Hierarchy (CTOC) by FDA<a c
└── 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>
<p>To view CTOC of Module 5:</p>
Expand Down Expand Up @@ -753,9 +750,6 @@ <h2>The Comprehensive Table of Contents Headings and Hierarchy (CTOC) by FDA<a c
└── 5.4 Literature references
</pre></div>
</div>
<div class="output stream highlight-myst-ansi notranslate"><div class="highlight"><pre><span></span>
</pre></div>
</div>
</div>
</div>
<p>To search a word within the hierarchy:</p>
Expand Down
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