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Changed the analysis for the percentage of valid investigations
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Was using proc genmod. At Doug's recommendation I changed it to proc surveyfreq with a cluster statement. The results were essentially identical.
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@mbcann01
mbcann01 committed Apr 3, 2019
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247 changes: 154 additions & 93 deletions sas/.ipynb_checkpoints/analysis_main_effects-checkpoint.ipynb
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"<IPython.core.display.HTML object>"
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},
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{
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"<p><span class=\"c systemtitle\">The SAS System</span> </p>\r\n",
"</div>\r\n",
"<div class=\"proc_title_group\">\r\n",
"<p class=\"c proctitle\">The GENMOD Procedure</p>\r\n",
"<p class=\"c proctitle\">The SURVEYFREQ Procedure</p>\r\n",
"</div>\r\n",
"<div style=\"padding-bottom: 8px; padding-top: 1px\">\r\n",
"<table class=\"table\" style=\"border-spacing: 0\" aria-label=\"Analysis Of GEE Parameter Estimates - Empirical Std Errors\">\r\n",
"<caption aria-label=\"Analysis Of GEE Parameter Estimates - Empirical Std Errors\"></caption>\r\n",
"<colgroup><col/><col/><col/><col/><col/><col/><col/></colgroup>\r\n",
"<table class=\"table\" style=\"border-spacing: 0\" aria-label=\"Data Summary\">\r\n",
"<caption aria-label=\"Data Summary\"></caption>\r\n",
"<colgroup><col/><col/></colgroup>\r\n",
"<thead>\r\n",
"<tr>\r\n",
"<th class=\"c b header\" colspan=\"7\" scope=\"colgroup\">Analysis Of GEE Parameter Estimates</th>\r\n",
"</tr>\r\n",
"<tr>\r\n",
"<th class=\"c b header\" colspan=\"7\" scope=\"colgroup\">Empirical Standard Error Estimates</th>\r\n",
"</tr>\r\n",
"<tr>\r\n",
"<th class=\"b header\" scope=\"col\">Parameter</th>\r\n",
"<th class=\"r b header\" scope=\"col\">Estimate</th>\r\n",
"<th class=\"r b header\" scope=\"col\">Standard<br/>Error</th>\r\n",
"<th class=\"c b header\" colspan=\"2\" scope=\"colgroup\">95% Confidence Limits</th>\r\n",
"<th class=\"r b header\" scope=\"col\">Z</th>\r\n",
"<th class=\"r b header\" scope=\"col\">Pr&#160;&gt;&#160;|Z|</th>\r\n",
"<th class=\"c b header\" colspan=\"2\" scope=\"colgroup\">Data Summary</th>\r\n",
"</tr>\r\n",
"</thead>\r\n",
"<tbody>\r\n",
"<tr>\r\n",
"<th class=\"rowheader\" scope=\"row\">Intercept</th>\r\n",
"<td class=\"r data\">0.8298</td>\r\n",
"<td class=\"r data\">0.0388</td>\r\n",
"<td class=\"r data\">0.7538</td>\r\n",
"<td class=\"r data\">0.9058</td>\r\n",
"<td class=\"r data\">21.41</td>\r\n",
"<td class=\"r data\">&lt;.0001</td>\r\n",
"<th class=\"rowheader\" scope=\"row\">Number of Clusters</th>\r\n",
"<td class=\"r data\">326</td>\r\n",
"</tr>\r\n",
"<tr>\r\n",
"<th class=\"rowheader\" scope=\"row\">detect</th>\r\n",
"<td class=\"r data\" style=\"white-space: nowrap\">-0.0060</td>\r\n",
"<td class=\"r data\">0.0461</td>\r\n",
"<td class=\"r data\" style=\"white-space: nowrap\">-0.0964</td>\r\n",
"<td class=\"r data\">0.0844</td>\r\n",
"<td class=\"r data\" style=\"white-space: nowrap\">-0.13</td>\r\n",
"<td class=\"r data\">0.8962</td>\r\n",
"<th class=\"rowheader\" scope=\"row\">Number of Observations</th>\r\n",
"<td class=\"r data\">327</td>\r\n",
"</tr>\r\n",
"</tbody>\r\n",
"</table>\r\n",
"</div>\r\n",
"<div id=\"IDX1\" style=\"padding-bottom: 8px; padding-top: 1px\">\r\n",
"<table class=\"table\" style=\"border-spacing: 0\" aria-label=\"ESTIMATE Statement Results\">\r\n",
"<caption aria-label=\"ESTIMATE Statement Results\"></caption>\r\n",
"<colgroup><col/></colgroup><colgroup><col/><col/><col/><col/><col/><col/><col/><col/><col/><col/></colgroup>\r\n",
"<div style=\"padding-bottom: 8px; padding-top: 1px\">\r\n",
"<table class=\"table\" style=\"border-spacing: 0\" aria-label=\"CrossTabulation Table\">\r\n",
"<caption aria-label=\"CrossTabulation Table\"></caption>\r\n",
"<colgroup><col/><col/></colgroup><colgroup><col/><col/><col/><col/><col/><col/><col/><col/><col/></colgroup>\r\n",
"<thead>\r\n",
"<tr>\r\n",
"<th class=\"c b header\" colspan=\"11\" scope=\"colgroup\">Contrast Estimate Results</th>\r\n",
"</tr>\r\n",
"<tr>\r\n",
"<th class=\"b header\" rowspan=\"2\" scope=\"col\">Label</th>\r\n",
"<th class=\"r b header\" rowspan=\"2\" scope=\"col\">Mean Estimate</th>\r\n",
"<th class=\"c b header\" colspan=\"2\" scope=\"colgroup\">Mean</th>\r\n",
"<th class=\"r b header\" rowspan=\"2\" scope=\"col\">L&apos;Beta Estimate</th>\r\n",
"<th class=\"r b header\" rowspan=\"2\" scope=\"col\">Standard<br/>Error</th>\r\n",
"<th class=\"r b header\" rowspan=\"2\" scope=\"col\">Alpha</th>\r\n",
"<th class=\"c b header\" colspan=\"2\" scope=\"colgroup\">L&apos;Beta</th>\r\n",
"<th class=\"r b header\" rowspan=\"2\" scope=\"col\">Chi-Square</th>\r\n",
"<th class=\"r b header\" rowspan=\"2\" scope=\"col\">Pr&#160;&gt;&#160;ChiSq</th>\r\n",
"<th class=\"c b header\" colspan=\"11\" scope=\"colgroup\">Table of detect by any_valid</th>\r\n",
"</tr>\r\n",
"<tr>\r\n",
"<th class=\"c b header\" colspan=\"2\" scope=\"colgroup\">Confidence Limits</th>\r\n",
"<th class=\"c b header\" colspan=\"2\" scope=\"colgroup\">Confidence Limits</th>\r\n",
"<th class=\"b header\" scope=\"col\">detect</th>\r\n",
"<th class=\"b header\" scope=\"col\">any_valid</th>\r\n",
"<th class=\"r b header\" scope=\"col\">Frequency</th>\r\n",
"<th class=\"r b header\" scope=\"col\">Percent</th>\r\n",
"<th class=\"r b header\" scope=\"col\">Std Err of<br/>Percent</th>\r\n",
"<th class=\"c b header\" colspan=\"2\" scope=\"colgroup\">95% Confidence Limits<br/>for Percent</th>\r\n",
"<th class=\"r b header\" scope=\"col\">Row<br/>Percent</th>\r\n",
"<th class=\"r b header\" scope=\"col\">Std Err of<br/>Row Percent</th>\r\n",
"<th class=\"c b header\" colspan=\"2\" scope=\"colgroup\">95% Confidence Limits<br/>for Row Percent</th>\r\n",
"</tr>\r\n",
"</thead>\r\n",
"<tbody>\r\n",
"<tr>\r\n",
"<th class=\"rowheader\" scope=\"row\">Proportion valid when detect = 0</th>\r\n",
"<td class=\"r data\">0.8298</td>\r\n",
"<td class=\"r data\">0.7538</td>\r\n",
"<td class=\"r data\">0.9058</td>\r\n",
"<td class=\"r data\">0.8298</td>\r\n",
"<td class=\"r data\">0.0388</td>\r\n",
"<td class=\"r data\">0.05</td>\r\n",
"<td class=\"r data\">0.7538</td>\r\n",
"<td class=\"r data\">0.9058</td>\r\n",
"<td class=\"r data\">458.25</td>\r\n",
"<td class=\"r data\">&lt;.0001</td>\r\n",
"<th class=\"rowheader\" scope=\"row\">0</th>\r\n",
"<th class=\"rowheader\" scope=\"row\">0</th>\r\n",
"<td class=\"r data\">16</td>\r\n",
"<td class=\"r data\">4.8930</td>\r\n",
"<td class=\"r data\">1.1950</td>\r\n",
"<td class=\"r data\">2.5421</td>\r\n",
"<td class=\"r data\">7.2438</td>\r\n",
"<td class=\"r data\">17.0213</td>\r\n",
"<td class=\"r data\">3.8822</td>\r\n",
"<td class=\"r data\">9.3838</td>\r\n",
"<td class=\"r data\">24.6588</td>\r\n",
"</tr>\r\n",
"<tr>\r\n",
"<th class=\"rowheader\" scope=\"row\">&#160;</th>\r\n",
"<th class=\"rowheader\" scope=\"row\">1</th>\r\n",
"<td class=\"r data\">78</td>\r\n",
"<td class=\"r data\">23.8532</td>\r\n",
"<td class=\"r data\">2.3627</td>\r\n",
"<td class=\"r data\">19.2051</td>\r\n",
"<td class=\"r data\">28.5013</td>\r\n",
"<td class=\"r data\">82.9787</td>\r\n",
"<td class=\"r data\">3.8822</td>\r\n",
"<td class=\"r data\">75.3412</td>\r\n",
"<td class=\"r data\">90.6162</td>\r\n",
"</tr>\r\n",
"<tr>\r\n",
"<th class=\"rowheader\" scope=\"row\">&#160;</th>\r\n",
"<th class=\"rowheader\" scope=\"row\">Total</th>\r\n",
"<td class=\"r data\">94</td>\r\n",
"<td class=\"r data\">28.7462</td>\r\n",
"<td class=\"r data\">2.5097</td>\r\n",
"<td class=\"r data\">23.8089</td>\r\n",
"<td class=\"r data\">33.6835</td>\r\n",
"<td class=\"r data\">100.0000</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"</tr>\r\n",
"<tr>\r\n",
"<th class=\"rowheader\" scope=\"row\">Proportion valid when detect = 1</th>\r\n",
"<td class=\"r data\">0.8238</td>\r\n",
"<td class=\"r data\">0.7748</td>\r\n",
"<td class=\"r data\">0.8728</td>\r\n",
"<td class=\"r data\">0.8238</td>\r\n",
"<td class=\"r data\">0.0250</td>\r\n",
"<td class=\"r data\">0.05</td>\r\n",
"<td class=\"r data\">0.7748</td>\r\n",
"<td class=\"r data\">0.8728</td>\r\n",
"<td class=\"r data\">1086.4</td>\r\n",
"<td class=\"r data\">&lt;.0001</td>\r\n",
"<th class=\"rowheader\" scope=\"row\">1</th>\r\n",
"<th class=\"rowheader\" scope=\"row\">0</th>\r\n",
"<td class=\"r data\">41</td>\r\n",
"<td class=\"r data\">12.5382</td>\r\n",
"<td class=\"r data\">1.8349</td>\r\n",
"<td class=\"r data\">8.9285</td>\r\n",
"<td class=\"r data\">16.1480</td>\r\n",
"<td class=\"r data\">17.5966</td>\r\n",
"<td class=\"r data\">2.5008</td>\r\n",
"<td class=\"r data\">12.6768</td>\r\n",
"<td class=\"r data\">22.5163</td>\r\n",
"</tr>\r\n",
"<tr>\r\n",
"<th class=\"rowheader\" scope=\"row\">&#160;</th>\r\n",
"<th class=\"rowheader\" scope=\"row\">1</th>\r\n",
"<td class=\"r data\">192</td>\r\n",
"<td class=\"r data\">58.7156</td>\r\n",
"<td class=\"r data\">2.7327</td>\r\n",
"<td class=\"r data\">53.3395</td>\r\n",
"<td class=\"r data\">64.0916</td>\r\n",
"<td class=\"r data\">82.4034</td>\r\n",
"<td class=\"r data\">2.5008</td>\r\n",
"<td class=\"r data\">77.4837</td>\r\n",
"<td class=\"r data\">87.3232</td>\r\n",
"</tr>\r\n",
"<tr>\r\n",
"<th class=\"rowheader\" scope=\"row\">&#160;</th>\r\n",
"<th class=\"rowheader\" scope=\"row\">Total</th>\r\n",
"<td class=\"r data\">233</td>\r\n",
"<td class=\"r data\">71.2538</td>\r\n",
"<td class=\"r data\">2.5097</td>\r\n",
"<td class=\"r data\">66.3165</td>\r\n",
"<td class=\"r data\">76.1911</td>\r\n",
"<td class=\"r data\">100.0000</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"</tr>\r\n",
"<tr>\r\n",
"<th class=\"rowheader\" scope=\"row\">Total</th>\r\n",
"<th class=\"rowheader\" scope=\"row\">0</th>\r\n",
"<td class=\"r data\">57</td>\r\n",
"<td class=\"r data\">17.4312</td>\r\n",
"<td class=\"r data\">2.1025</td>\r\n",
"<td class=\"r data\">13.2949</td>\r\n",
"<td class=\"r data\">21.5675</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"</tr>\r\n",
"<tr>\r\n",
"<th class=\"rowheader\" scope=\"row\">&#160;</th>\r\n",
"<th class=\"rowheader\" scope=\"row\">1</th>\r\n",
"<td class=\"r data\">270</td>\r\n",
"<td class=\"r data\">82.5688</td>\r\n",
"<td class=\"r data\">2.1025</td>\r\n",
"<td class=\"r data\">78.4325</td>\r\n",
"<td class=\"r data\">86.7051</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"</tr>\r\n",
"<tr>\r\n",
"<th class=\"rowheader\" scope=\"row\">&#160;</th>\r\n",
"<th class=\"rowheader\" scope=\"row\">Total</th>\r\n",
"<td class=\"r data\">327</td>\r\n",
"<td class=\"r data\">100.0000</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"<td class=\"r data\">&#160;</td>\r\n",
"</tr>\r\n",
"</tbody>\r\n",
"</table>\r\n",
"</div>\r\n",
"</div>\r\n",
"</div>\r\n",
"</body>\r\n",
"</html>\r\n"
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"source": [
"* Percentage valid for EMS in medstar_service area during and not during detect;\n",
"proc genmod data = full_data;\n",
"proc surveyfreq data = full_data;\n",
" where total_allegations_investigated > 0 & ems = 1 & medstar_service_area = 1;\n",
" class case;\n",
" model any_valid = detect / link = id;\n",
" repeated subject = case / type = CS;\n",
" \n",
" estimate \"Proportion valid when detect = 0\" INTERCEPT 1;\n",
" estimate \"Proportion valid when detect = 1\" INTERCEPT 1 detect 1;\n",
" \n",
" ods select GEEEmpPEst Estimates;\n",
" table detect*any_valid / row cl;\n",
" cluster case;\n",
"run;"
]
},
Expand All @@ -2578,7 +2639,7 @@
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"outputs": [
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Expand Down Expand Up @@ -3834,7 +3895,7 @@
"<IPython.core.display.HTML object>"
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Expand All @@ -3859,7 +3920,7 @@
},
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Expand Down Expand Up @@ -5506,7 +5567,7 @@
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Expand Down Expand Up @@ -7142,7 +7203,7 @@
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Expand Down Expand Up @@ -8895,7 +8956,7 @@
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Expand Down Expand Up @@ -8923,7 +8984,7 @@
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Expand Down Expand Up @@ -10583,7 +10644,7 @@
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}
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