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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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4 changes: 2 additions & 2 deletions _sources/std_cdisc.ipynb.txt
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Expand Up @@ -130,7 +130,7 @@
"source": [
"### Get CT Packages\n",
"\n",
"CDISC Controlled Terminology (CT) is maintained and distributed as part of the National Cancer Institute (NCI) Thesaurus.\n",
"CDISC Controlled Terminology (CT) is maintained and distributed as part of the National Cancer Institute (NCI) Thesaurus [^5].\n",
"\n",
"\n",
"To get a list of newest CT packages available:\n",
Expand Down Expand Up @@ -162,7 +162,7 @@
"- 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 This is an archived version.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 This is an archived version.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 This is an archived version.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 [^r7]."
"- QS-FT: questionnaire and functional test. This is an archived version. This set was merged into COA at 2014 [^7]."
]
},
{
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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="10.870" timestamp="2024-07-23T02:06:54.898382+00:00" hostname="fv-az1040-398"><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="0.199" /><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="0.027" /><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="0.230" /><testcase classname="tests.test_statlab_kappa.TestKappaCalculator" name="test_cohen" time="0.071" /><testcase classname="tests.test_statlab_kappa.TestKappaCalculator" name="test_fleiss_kappa" time="0.067" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_compare_file_size" time="0.766" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_get_outline_list" time="0.892" /><testcase classname="tests.test_stdiso_pdfsummary.TestPdfSummary" name="test_show_outline_tree" time="0.841" /></testsuite></testsuites>
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4 changes: 2 additions & 2 deletions _static/reports/junit/report.html
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10 changes: 6 additions & 4 deletions example_cdtg.html
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Expand Up @@ -133,13 +133,15 @@ <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: 16.7% 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: 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: 15.0% 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)
/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/ff50a7ea2dfc05a5261cf3269b44c96a1b62a6f9f4c7ab0b870e0cbafc48c6b2.png" src="_images/ff50a7ea2dfc05a5261cf3269b44c96a1b62a6f9f4c7ab0b870e0cbafc48c6b2.png" />
<img alt="_images/c515e85b2a74c98c57a5a003e681461f0a2c0318df882016d80adb6b240e0ee7.png" src="_images/c515e85b2a74c98c57a5a003e681461f0a2c0318df882016d80adb6b240e0ee7.png" />
</div>
</div>
<p>To create a line plot:</p>
Expand All @@ -151,7 +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/43f3120150079b85ddb5e84af3b2c4c179b0bde8113d885a91a321bed57c3a6d.png" src="_images/43f3120150079b85ddb5e84af3b2c4c179b0bde8113d885a91a321bed57c3a6d.png" />
<img alt="_images/3541a4cedf1df7108d7b05a128e5abafe7f3765136e49480987ca4bb185f0d35.png" src="_images/3541a4cedf1df7108d7b05a128e5abafe7f3765136e49480987ca4bb185f0d35.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 1 684
1 STD1 TRT1 SUBJ01 VISIT1 2 745
0 STD1 TRT1 SUBJ01 VISIT1 1 469
1 STD1 TRT1 SUBJ01 VISIT1 2 1538
</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 2
1 STD1 TRT1 SUBJ01 VISIT2 1 2
0 STD1 TRT1 SUBJ01 VISIT1 1 0
1 STD1 TRT1 SUBJ02 VISIT1 0 1

N(1000&lt;=V&lt;=2000) N(all)
0 0 2
1 2 5
0 3 4
1 4 5
</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 7 7 6 20
1 STD1 TRT1 VISIT2 3 6 4 13
2 STD1 TRT1 VISIT3 2 3 4 9
3 STD1 TRT1 VISIT4 2 0 1 3
4 STD1 TRT2 VISIT1 2 11 7 20
5 STD1 TRT2 VISIT2 5 7 4 16
6 STD1 TRT2 VISIT3 2 4 3 9
7 STD1 TRT2 VISIT4 0 3 1 4
8 STD2 TRT1 VISIT1 4 11 5 20
9 STD2 TRT1 VISIT2 5 11 1 17
10 STD2 TRT1 VISIT3 5 4 2 11
11 STD2 TRT1 VISIT4 3 2 2 7
12 STD2 TRT2 VISIT1 5 11 4 20
13 STD2 TRT2 VISIT2 3 3 10 16
14 STD2 TRT2 VISIT3 1 3 2 6
15 STD2 TRT2 VISIT4 2 0 0 2
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
</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 14 25 30 69
1 STD1 TRT1 VISIT2 6 22 20 48
2 STD1 TRT1 VISIT3 4 11 20 35
3 STD1 TRT1 VISIT4 4 0 5 9
4 STD1 TRT2 VISIT1 4 38 35 77
5 STD1 TRT2 VISIT2 10 25 20 55
6 STD1 TRT2 VISIT3 4 14 15 33
7 STD1 TRT2 VISIT4 0 10 5 15
8 STD2 TRT1 VISIT1 8 36 25 69
9 STD2 TRT1 VISIT2 10 41 5 56
10 STD2 TRT1 VISIT3 10 16 10 36
11 STD2 TRT1 VISIT4 6 8 10 24
12 STD2 TRT2 VISIT1 10 40 20 70
13 STD2 TRT2 VISIT2 6 11 50 67
14 STD2 TRT2 VISIT3 2 12 10 24
15 STD2 TRT2 VISIT4 4 0 0 4
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
</pre></div>
</div>
</div>
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