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yh202109 committed Jul 23, 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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<?xml version="1.0" ?>
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2 changes: 1 addition & 1 deletion _sources/std_cdisc.ipynb.txt
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"- MRCT: multi-regional clinical trials\n",
"- COA: clinical outcome assessment. This is an archived version. COA is part of QRS supplement supporting FDA COA qualification program [^6].\n",
"- QRS: questionnaires, ratings and scales. This is an archived version. QRS SDTM CT is currently included in SDTM CT. \n",
"- QS-FT: questionnaire and functional test. This is an archived version. This set was merged into COA at 2014 [^7]."
"- QS-FT: questionnaire and functional test. This is an archived version. This set was merged into COA [^7]."
]
},
{
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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="7.6.0" timestamp="1721700723725" lines-valid="1531" lines-covered="642" line-rate="0.4193" branches-covered="0" branches-valid="0" branch-rate="0" complexity="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="8.486" timestamp="2024-07-23T02:11:45.474505+00:00" hostname="fv-az695-456"><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="0.198" /><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="0.017" /><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="0.763" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_get_outline_list" time="0.877" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_show_outline_tree" time="0.840" /></testsuite></testsuites>
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4 changes: 2 additions & 2 deletions _static/reports/junit/report.html
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8 changes: 4 additions & 4 deletions example_cdtg.html
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Expand Up @@ -135,13 +135,13 @@ <h1>U/Graph/Categorical Plots Using catPlotter<a class="headerlink" href="#u-gra
<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.
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: 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: 30.0% 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: 10.0% 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/c515e85b2a74c98c57a5a003e681461f0a2c0318df882016d80adb6b240e0ee7.png" src="_images/c515e85b2a74c98c57a5a003e681461f0a2c0318df882016d80adb6b240e0ee7.png" />
<img alt="_images/5ad8c73467329533d3526b4003dc62662d49910fbd74188d39b6e9d01a58afcb.png" src="_images/5ad8c73467329533d3526b4003dc62662d49910fbd74188d39b6e9d01a58afcb.png" />
</div>
</div>
<p>To create a line plot:</p>
Expand All @@ -153,7 +153,7 @@ <h1>U/Graph/Categorical Plots Using catPlotter<a class="headerlink" href="#u-gra
</div>
</div>
<div class="cell_output docutils container">
<img alt="_images/3541a4cedf1df7108d7b05a128e5abafe7f3765136e49480987ca4bb185f0d35.png" src="_images/3541a4cedf1df7108d7b05a128e5abafe7f3765136e49480987ca4bb185f0d35.png" />
<img alt="_images/359a2bd3e7e0e0fc0afbdec6b322b00df6209ebbb3e12b68f0de4eeaadc091ba.png" src="_images/359a2bd3e7e0e0fc0afbdec6b322b00df6209ebbb3e12b68f0de4eeaadc091ba.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 1 469
1 STD1 TRT1 SUBJ01 VISIT1 2 1538
0 STD1 TRT1 SUBJ01 VISIT1 1 654
1 STD1 TRT1 SUBJ01 VISIT1 2 1234
</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 1 0
1 STD1 TRT1 SUBJ02 VISIT1 0 1
0 STD1 TRT1 SUBJ01 VISIT1 0 1
1 STD1 TRT1 SUBJ01 VISIT2 0 1

N(1000&lt;=V&lt;=2000) N(all)
0 3 4
1 4 5
0 1 2
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 10 6 20
1 STD1 TRT1 VISIT2 3 7 5 15
2 STD1 TRT1 VISIT3 5 2 4 11
3 STD1 TRT1 VISIT4 1 4 1 6
4 STD1 TRT2 VISIT1 4 13 3 20
5 STD1 TRT2 VISIT2 7 8 2 17
6 STD1 TRT2 VISIT3 2 7 2 11
7 STD1 TRT2 VISIT4 1 2 2 5
8 STD2 TRT1 VISIT1 3 12 5 20
9 STD2 TRT1 VISIT2 6 4 6 16
10 STD2 TRT1 VISIT3 3 3 3 9
11 STD2 TRT1 VISIT4 1 2 1 4
12 STD2 TRT2 VISIT1 10 3 7 20
13 STD2 TRT2 VISIT2 5 7 4 16
14 STD2 TRT2 VISIT3 5 2 1 8
15 STD2 TRT2 VISIT4 2 2 2 6
0 STD1 TRT1 VISIT1 11 9 0 20
1 STD1 TRT1 VISIT2 2 9 5 16
2 STD1 TRT1 VISIT3 4 6 2 12
3 STD1 TRT1 VISIT4 0 2 3 5
4 STD1 TRT2 VISIT1 3 15 2 20
5 STD1 TRT2 VISIT2 4 8 2 14
6 STD1 TRT2 VISIT3 0 7 1 8
7 STD1 TRT2 VISIT4 0 3 0 3
8 STD2 TRT1 VISIT1 2 13 5 20
9 STD2 TRT1 VISIT2 4 8 4 16
10 STD2 TRT1 VISIT3 2 8 4 14
11 STD2 TRT1 VISIT4 0 7 2 9
12 STD2 TRT2 VISIT1 7 10 3 20
13 STD2 TRT2 VISIT2 3 7 7 17
14 STD2 TRT2 VISIT3 6 6 1 13
15 STD2 TRT2 VISIT4 1 5 1 7
</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 37 30 75
1 STD1 TRT1 VISIT2 6 25 25 56
2 STD1 TRT1 VISIT3 10 7 20 37
3 STD1 TRT1 VISIT4 2 14 5 21
4 STD1 TRT2 VISIT1 8 43 15 66
5 STD1 TRT2 VISIT2 14 26 10 50
6 STD1 TRT2 VISIT3 4 24 10 38
7 STD1 TRT2 VISIT4 2 8 10 20
8 STD2 TRT1 VISIT1 6 43 25 74
9 STD2 TRT1 VISIT2 12 16 30 58
10 STD2 TRT1 VISIT3 6 10 15 31
11 STD2 TRT1 VISIT4 2 7 5 14
12 STD2 TRT2 VISIT1 20 10 35 65
13 STD2 TRT2 VISIT2 10 25 20 55
14 STD2 TRT2 VISIT3 10 8 5 23
15 STD2 TRT2 VISIT4 4 6 10 20
0 STD1 TRT1 VISIT1 22 34 0 56
1 STD1 TRT1 VISIT2 4 33 25 62
2 STD1 TRT1 VISIT3 8 21 10 39
3 STD1 TRT1 VISIT4 0 8 15 23
4 STD1 TRT2 VISIT1 6 51 10 67
5 STD1 TRT2 VISIT2 8 30 10 48
6 STD1 TRT2 VISIT3 0 25 5 30
7 STD1 TRT2 VISIT4 0 10 0 10
8 STD2 TRT1 VISIT1 4 45 25 74
9 STD2 TRT1 VISIT2 8 28 20 56
10 STD2 TRT1 VISIT3 4 30 20 54
11 STD2 TRT1 VISIT4 0 25 10 35
12 STD2 TRT2 VISIT1 14 36 15 65
13 STD2 TRT2 VISIT2 6 25 35 66
14 STD2 TRT2 VISIT3 12 19 5 36
15 STD2 TRT2 VISIT4 2 18 5 25
</pre></div>
</div>
</div>
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