Skip to content

Commit

Permalink
Deploying to gh-pages from @ 0cc223e 🚀
Browse files Browse the repository at this point in the history
  • Loading branch information
@yh202109
yh202109 committed Jun 29, 2024
1 parent 26b518b commit 4bf63af
Show file tree
Hide file tree
Showing 18 changed files with 221 additions and 194 deletions.
6 changes: 3 additions & 3 deletions _downloads/214d05cd65dcc9387b037da1ce5a5c33/report.html
View file

Large diffs are not rendered by default.

2 changes: 1 addition & 1 deletion _downloads/9911a4d807ac9f1a695f0aa2cf687076/coverage.xml
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<?xml version="1.0" ?>
<coverage version="7.5.4" timestamp="1719626635270" 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="1719627600371" 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>
Expand Down
Binary file added _images/2857e7a4ad740e223eb0dfbfd55bb77bcd59700583c26af511150657a4f624db.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Binary file removed _images/9dfdc59992135147ce6e3ff66ff5e4b8b5f87e47835b7907cbf1c3e2c7d716f9.png
View file
Binary file not shown.
Binary file removed _images/ab5b74ed8c081c821a08f247d57b0606fb1dce2d77e3e4bc0d4a0e9512332480.png
View file
Binary file not shown.
Binary file added _images/d59278a11a9caa9f1772f600e75e55115919bedc6e431287bdcbabce4b816b58.png
View file
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
22 changes: 19 additions & 3 deletions _sources/statlab_corr_tau.rst.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ Kendall's tau (:math:`\tau`) is a statistic used for measuring rank correlation
Notation
*************

Let :math:`Y_{i1}` and :math:`Y_{i2}` be a pair of random variables corresponding to the :math:`i` th sample where :math:`i = 1, \ldots, n`.
Let :math:`(Y_{i1}, Y_{i2})` be a pair of random variables corresponding to the :math:`i` th sample where :math:`i = 1, \ldots, n`.

.. list-table:: Observed Value
:widths: 10 10 10
Expand Down Expand Up @@ -63,9 +63,25 @@ The coefficient :math:`\tau` (tau-a) can be calculated as
.. math::
:label: eq_tau1
\tau =& \frac{2}{n(n-1)} \left( \sum_{i=1}^n \sum_{j < n} sign(Y_{i1}-Y_{j1})sign(Y_{i2}-Y_{j2}) \right) \\
=& \frac{2}{n(n-1)} \left( 2\sum_{i=1}^n \sum_{j < n} I(sign(Y_{i1}-Y_{j1})sign(Y_{i2}-Y_{j2})=1)-\frac{n(n-1)}{2} \right).
\tau = \frac{2}{n(n-1)} \left( \sum_{i=1}^n \sum_{j < n} sign(Y_{i1}-Y_{j1})sign(Y_{i2}-Y_{j2}) \right),
Let :math:`c = \sum_{i=1}^n \sum_{j < n} I(sign(Y_{i1}-Y_{j1})sign(Y_{i2}-Y_{j2})=1)`,
:math:`d = \sum_{i=1}^n \sum_{j < n} I(sign(Y_{i1}-Y_{j1})sign(Y_{i2}-Y_{j2})=-1)`
and :math:`t = \frac{n(n-1)}{2}`.
:eq:`eq_tau1` can be expressed as

.. math::
:label: eq_tau2
\tau = \frac{ c - d }{t}.
If there were no ties, :eq:`eq_tau2` can be expressed as

.. math::
\tau = \frac{ 2c - t }{t}.
The maximum value of :eq:`eq_tau1` is 1 at :math:`c=t`, and the minimum is -1 at :math:`d=t`


*************
Expand Down
2 changes: 1 addition & 1 deletion _static/reports/coverage/coverage.xml
View file
Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
<?xml version="1.0" ?>
<coverage version="7.5.4" timestamp="1719626635270" 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="1719627600371" 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>
Expand Down
2 changes: 1 addition & 1 deletion _static/reports/junit/junit.xml
View file
Original file line number Diff line number Diff line change
@@ -1 +1 @@
<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="27" time="5.679" timestamp="2024-06-29T02:03:45.026784" hostname="fv-az1016-248"><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="0.011" /><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="0.007" /><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="0.226" /><testcase classname="tests.test_kappa.TestKappaCalculator" name="test_cohen" time="0.067" /><testcase classname="tests.test_kappa.TestKappaCalculator" name="test_fleiss_kappa" time="0.065" /><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="0.000" /><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" /></testsuite></testsuites>
<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="27" time="8.064" timestamp="2024-06-29T02:19:47.707964" hostname="fv-az695-574"><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_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="0.007" /><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="0.227" /><testcase classname="tests.test_kappa.TestKappaCalculator" name="test_cohen" time="0.069" /><testcase classname="tests.test_kappa.TestKappaCalculator" name="test_fleiss_kappa" time="0.066" /><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>
6 changes: 3 additions & 3 deletions _static/reports/junit/report.html
View file

Large diffs are not rendered by default.

12 changes: 10 additions & 2 deletions example_cdtg.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -116,7 +116,15 @@ <h1>U/Graph/Categorical Plots Using catPlotter<a class="headerlink" href="#u-gra
</div>
</div>
<div class="cell_output docutils container">
<img alt="_images/ab5b74ed8c081c821a08f247d57b0606fb1dce2d77e3e4bc0d4a0e9512332480.png" src="_images/ab5b74ed8c081c821a08f247d57b0606fb1dce2d77e3e4bc0d4a0e9512332480.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)
/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)
/home/runner/.cache/pypoetry/virtualenvs/mtbp3-STzYEG9e-py3.10/lib/python3.10/site-packages/seaborn/categorical.py:3399: UserWarning: 35.0% 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/d59278a11a9caa9f1772f600e75e55115919bedc6e431287bdcbabce4b816b58.png" src="_images/d59278a11a9caa9f1772f600e75e55115919bedc6e431287bdcbabce4b816b58.png" />
</div>
</div>
<p>To create a line plot:</p>
Expand All @@ -128,7 +136,7 @@ <h1>U/Graph/Categorical Plots Using catPlotter<a class="headerlink" href="#u-gra
</div>
</div>
<div class="cell_output docutils container">
<img alt="_images/9dfdc59992135147ce6e3ff66ff5e4b8b5f87e47835b7907cbf1c3e2c7d716f9.png" src="_images/9dfdc59992135147ce6e3ff66ff5e4b8b5f87e47835b7907cbf1c3e2c7d716f9.png" />
<img alt="_images/2857e7a4ad740e223eb0dfbfd55bb77bcd59700583c26af511150657a4f624db.png" src="_images/2857e7a4ad740e223eb0dfbfd55bb77bcd59700583c26af511150657a4f624db.png" />
</div>
</div>
</section>
Expand Down
76 changes: 38 additions & 38 deletions example_clinical.html
View file
Original file line number Diff line number Diff line change
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 1 367
1 STD1 TRT1 SUBJ01 VISIT1 2 862
0 STD1 TRT1 SUBJ01 VISIT1 1 1203
1 STD1 TRT1 SUBJ01 VISIT1 2 1074
</pre></div>
</div>
</div>
Expand All @@ -132,12 +132,12 @@ <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 1 3
1 STD1 TRT1 SUBJ01 VISIT2 1 0
0 STD1 TRT1 SUBJ01 VISIT1 0 1
1 STD1 TRT1 SUBJ01 VISIT2 0 1

N(1000&lt;=V&lt;=2000) N(all)
0 1 5
1 3 4
0 2 3
1 1 2
</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 4 10 6 20
1 STD1 TRT1 VISIT2 3 9 2 14
2 STD1 TRT1 VISIT3 1 5 1 7
3 STD1 TRT1 VISIT4 2 0 0 2
4 STD1 TRT2 VISIT1 3 15 2 20
5 STD1 TRT2 VISIT2 3 8 4 15
6 STD1 TRT2 VISIT3 1 5 4 10
7 STD1 TRT2 VISIT4 0 2 2 4
8 STD2 TRT1 VISIT1 6 10 4 20
9 STD2 TRT1 VISIT2 4 8 1 13
10 STD2 TRT1 VISIT3 3 1 2 6
11 STD2 TRT1 VISIT4 0 1 2 3
12 STD2 TRT2 VISIT1 6 11 3 20
13 STD2 TRT2 VISIT2 4 9 3 16
14 STD2 TRT2 VISIT3 2 6 2 10
15 STD2 TRT2 VISIT4 0 7 0 7
0 STD1 TRT1 VISIT1 3 10 7 20
1 STD1 TRT1 VISIT2 4 7 3 14
2 STD1 TRT1 VISIT3 3 4 4 11
3 STD1 TRT1 VISIT4 2 2 2 6
4 STD1 TRT2 VISIT1 7 8 5 20
5 STD1 TRT2 VISIT2 6 9 2 17
6 STD1 TRT2 VISIT3 3 7 2 12
7 STD1 TRT2 VISIT4 2 3 3 8
8 STD2 TRT1 VISIT1 7 7 6 20
9 STD2 TRT1 VISIT2 1 7 7 15
10 STD2 TRT1 VISIT3 5 3 2 10
11 STD2 TRT1 VISIT4 2 2 2 6
12 STD2 TRT2 VISIT1 5 9 6 20
13 STD2 TRT2 VISIT2 2 9 5 16
14 STD2 TRT2 VISIT3 2 2 7 11
15 STD2 TRT2 VISIT4 2 2 1 5
</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 8 36 30 74
1 STD1 TRT1 VISIT2 6 32 10 48
2 STD1 TRT1 VISIT3 2 18 5 25
3 STD1 TRT1 VISIT4 4 0 0 4
4 STD1 TRT2 VISIT1 6 53 10 69
5 STD1 TRT2 VISIT2 6 31 20 57
6 STD1 TRT2 VISIT3 2 15 20 37
7 STD1 TRT2 VISIT4 0 6 10 16
8 STD2 TRT1 VISIT1 12 35 20 67
9 STD2 TRT1 VISIT2 8 27 5 40
10 STD2 TRT1 VISIT3 6 4 10 20
11 STD2 TRT1 VISIT4 0 3 10 13
12 STD2 TRT2 VISIT1 12 39 15 66
13 STD2 TRT2 VISIT2 8 32 15 55
14 STD2 TRT2 VISIT3 4 20 10 34
15 STD2 TRT2 VISIT4 0 24 0 24
0 STD1 TRT1 VISIT1 6 31 35 72
1 STD1 TRT1 VISIT2 8 24 15 47
2 STD1 TRT1 VISIT3 6 13 20 39
3 STD1 TRT1 VISIT4 4 7 10 21
4 STD1 TRT2 VISIT1 14 27 25 66
5 STD1 TRT2 VISIT2 12 32 10 54
6 STD1 TRT2 VISIT3 6 24 10 40
7 STD1 TRT2 VISIT4 4 11 15 30
8 STD2 TRT1 VISIT1 14 25 30 69
9 STD2 TRT1 VISIT2 2 25 35 62
10 STD2 TRT1 VISIT3 10 10 10 30
11 STD2 TRT1 VISIT4 4 7 10 21
12 STD2 TRT2 VISIT1 10 31 30 71
13 STD2 TRT2 VISIT2 4 32 25 61
14 STD2 TRT2 VISIT3 4 6 35 45
15 STD2 TRT2 VISIT4 4 8 5 17
</pre></div>
</div>
</div>
Expand Down
3 changes: 0 additions & 3 deletions example_ectd.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -691,9 +691,6 @@ <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
6 changes: 3 additions & 3 deletions example_ectd2.html
View file
Original file line number Diff line number Diff line change
Expand Up @@ -382,6 +382,9 @@ <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 @@ -563,9 +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
Loading

0 comments on commit 4bf63af

Please sign in to comment.