Skip to content

Commit

Permalink
Deploying to gh-pages from @ 266396c 🚀
Browse files Browse the repository at this point in the history
  • Loading branch information
@yh202109
yh202109 committed Jun 29, 2024
1 parent 634dcc8 commit 58cef38
Show file tree
Hide file tree
Showing 17 changed files with 197 additions and 193 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="1719692398041" 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="1719699874496" 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 removed _images/30fed8f727ae3c0934095c213e673c06bd657ae68262e21359917c6fa1b5c6d9.png
View file
Binary file not shown.
Binary file added _images/5abfef0c928d0252b573a574020f1f13c69733a95a615baf1ab0699df59ee36c.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 added _images/7ea14b408722d1b71cc3cfae8c65a5d8a8f42b1c5a82844239abbf13925082fa.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/b8a9eb2f0fc1f7e3ab3504ac4d7279678a5096a98e1e5edf0b2af8cc45badd5d.png
View file
Binary file not shown.
7 changes: 5 additions & 2 deletions _sources/statlab_corr_tau.rst.txt
View file
Original file line number Diff line number Diff line change
Expand Up @@ -59,8 +59,8 @@ Let :math:`(Y_{i1}, Y_{i2})` be a pair of random variables corresponding to the
- :math:`Y_{n2}`

Let :math:`Z_{ij1} \equiv sign(Y_{i1}-Y_{j1})`, :math:`Z_{ij2} \equiv sign(Y_{i2}-Y_{j2})`,
:math:`c = \sum_{i=1}^n \sum_{j < n} I(Z_{ij1}Z_{ij2}=1)`,
:math:`d = \sum_{i=1}^n \sum_{j < n} I(Z_{ij1}Z_{ij2}=-1)`
:math:`c = \sum_{i=1}^n \sum_{j < i} I(Z_{ij1}Z_{ij2}=1)`,
:math:`d = \sum_{i=1}^n \sum_{j < i} I(Z_{ij1}Z_{ij2}=-1)`
and :math:`t = \frac{n(n-1)}{2}`.
The coefficient :math:`\tau` (tau-a) can be calculated as

Expand All @@ -85,6 +85,9 @@ Under independent sample assumption, we know that
:math:`Var(Z_{ij1})=Var(Z_{ij2})=1-\frac{1}{n}`.
From :eq:`eq_tau2`, we can see that :math:`\tau` is a rank correlation coefficient.

If there are no ties, the maximum value of :eq:`eq_tau1` becomes less then 1.
Consider the scenario that there are :math:`n_{t1}` ties in :math:`\{Y_{i1}\}`,
and there are :math:`n_{t2}` ties in :math:`\{Y_{i2}\}`.


*************
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="1719692398041" 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="1719699874496" 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="10.258" timestamp="2024-06-29T20:19:43.109920" hostname="fv-az1499-971"><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="0.229" /><testcase classname="tests.test_kappa.TestKappaCalculator" name="test_cohen" time="0.069" /><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>
<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="27" time="6.139" timestamp="2024-06-29T22:24:23.740902" hostname="fv-az841-20"><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="0.025" /><testcase classname="tests.test_kappa.TestKappaCalculator" name="test_bootstrap_cohen_ci" time="0.227" /><testcase classname="tests.test_kappa.TestKappaCalculator" name="test_cohen" time="0.067" /><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.

10 changes: 4 additions & 6 deletions example_cdtg.html
View file
Original file line number Diff line number Diff line change
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: 27.8% 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: 33.3% 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: 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)
/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.
/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)
</pre></div>
</div>
<img alt="_images/30fed8f727ae3c0934095c213e673c06bd657ae68262e21359917c6fa1b5c6d9.png" src="_images/30fed8f727ae3c0934095c213e673c06bd657ae68262e21359917c6fa1b5c6d9.png" />
<img alt="_images/5abfef0c928d0252b573a574020f1f13c69733a95a615baf1ab0699df59ee36c.png" src="_images/5abfef0c928d0252b573a574020f1f13c69733a95a615baf1ab0699df59ee36c.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/b8a9eb2f0fc1f7e3ab3504ac4d7279678a5096a98e1e5edf0b2af8cc45badd5d.png" src="_images/b8a9eb2f0fc1f7e3ab3504ac4d7279678a5096a98e1e5edf0b2af8cc45badd5d.png" />
<img alt="_images/7ea14b408722d1b71cc3cfae8c65a5d8a8f42b1c5a82844239abbf13925082fa.png" src="_images/7ea14b408722d1b71cc3cfae8c65a5d8a8f42b1c5a82844239abbf13925082fa.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 1 437
1 STD1 TRT1 SUBJ01 VISIT1 2 1978
0 STD1 TRT1 SUBJ01 VISIT1 1 1861
1 STD1 TRT1 SUBJ01 VISIT1 2 1433
</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 0
1 STD1 TRT1 SUBJ01 VISIT2 0 1
0 STD1 TRT1 SUBJ01 VISIT1 0 1
1 STD1 TRT1 SUBJ02 VISIT1 1 0

N(1000&lt;=V&lt;=2000) N(all)
0 2 3
1 2 3
0 3 4
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 3 13 4 20
1 STD1 TRT1 VISIT2 3 9 5 17
2 STD1 TRT1 VISIT3 4 5 2 11
3 STD1 TRT1 VISIT4 2 2 1 5
4 STD1 TRT2 VISIT1 3 10 7 20
5 STD1 TRT2 VISIT2 4 3 7 14
6 STD1 TRT2 VISIT3 1 5 3 9
7 STD1 TRT2 VISIT4 2 1 1 4
8 STD2 TRT1 VISIT1 6 10 4 20
9 STD2 TRT1 VISIT2 0 10 5 15
10 STD2 TRT1 VISIT3 3 4 4 11
11 STD2 TRT1 VISIT4 2 2 0 4
12 STD2 TRT2 VISIT1 7 7 6 20
13 STD2 TRT2 VISIT2 4 8 3 15
14 STD2 TRT2 VISIT3 2 8 5 15
15 STD2 TRT2 VISIT4 3 4 3 10
0 STD1 TRT1 VISIT1 4 13 3 20
1 STD1 TRT1 VISIT2 2 8 6 16
2 STD1 TRT1 VISIT3 3 6 3 12
3 STD1 TRT1 VISIT4 1 2 0 3
4 STD1 TRT2 VISIT1 5 11 4 20
5 STD1 TRT2 VISIT2 1 7 7 15
6 STD1 TRT2 VISIT3 2 2 4 8
7 STD1 TRT2 VISIT4 0 2 3 5
8 STD2 TRT1 VISIT1 6 7 7 20
9 STD2 TRT1 VISIT2 2 8 4 14
10 STD2 TRT1 VISIT3 0 5 6 11
11 STD2 TRT1 VISIT4 3 4 1 8
12 STD2 TRT2 VISIT1 3 12 5 20
13 STD2 TRT2 VISIT2 1 11 2 14
14 STD2 TRT2 VISIT3 3 6 0 9
15 STD2 TRT2 VISIT4 2 1 1 4
</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 6 44 20 70
1 STD1 TRT1 VISIT2 6 31 25 62
2 STD1 TRT1 VISIT3 8 16 10 34
3 STD1 TRT1 VISIT4 4 7 5 16
4 STD1 TRT2 VISIT1 6 35 35 76
5 STD1 TRT2 VISIT2 8 9 35 52
6 STD1 TRT2 VISIT3 2 19 15 36
7 STD1 TRT2 VISIT4 4 4 5 13
8 STD2 TRT1 VISIT1 12 35 20 67
9 STD2 TRT1 VISIT2 0 36 25 61
10 STD2 TRT1 VISIT3 6 15 20 41
11 STD2 TRT1 VISIT4 4 8 0 12
12 STD2 TRT2 VISIT1 14 23 30 67
13 STD2 TRT2 VISIT2 8 28 15 51
14 STD2 TRT2 VISIT3 4 28 25 57
15 STD2 TRT2 VISIT4 6 13 15 34
0 STD1 TRT1 VISIT1 8 46 15 69
1 STD1 TRT1 VISIT2 4 27 30 61
2 STD1 TRT1 VISIT3 6 21 15 42
3 STD1 TRT1 VISIT4 2 6 0 8
4 STD1 TRT2 VISIT1 10 40 20 70
5 STD1 TRT2 VISIT2 2 24 35 61
6 STD1 TRT2 VISIT3 4 6 20 30
7 STD1 TRT2 VISIT4 0 7 15 22
8 STD2 TRT1 VISIT1 12 26 35 73
9 STD2 TRT1 VISIT2 4 29 20 53
10 STD2 TRT1 VISIT3 0 16 30 46
11 STD2 TRT1 VISIT4 6 13 5 24
12 STD2 TRT2 VISIT1 6 36 25 67
13 STD2 TRT2 VISIT2 2 38 10 50
14 STD2 TRT2 VISIT3 6 20 0 26
15 STD2 TRT2 VISIT4 4 4 5 13
</pre></div>
</div>
</div>
Expand Down
6 changes: 3 additions & 3 deletions example_ectd.html
View file
Original file line number Diff line number Diff line change
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>
Expand Down
Loading

0 comments on commit 58cef38

Please sign in to comment.