115115 < button type ="button " class ="quarto-btn-toggle btn " data-bs-toggle ="collapse " role ="button " data-bs-target =".quarto-sidebar-collapse-item " aria-controls ="quarto-sidebar " aria-expanded ="false " aria-label ="Toggle sidebar navigation " onclick ="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); } ">
116116 < i class ="bi bi-layout-text-sidebar-reverse "> </ i >
117117 </ button >
118- < nav class ="quarto-page-breadcrumbs " aria-label ="breadcrumb "> < ol class ="breadcrumb "> < li class ="breadcrumb-item "> < a href ="./explore .html "> Working with the OMOP CDM</ a > </ li > < li class ="breadcrumb-item "> < a href ="./adding_features.html "> < span class ="chapter-number "> 8</ span > < span class ="chapter-title "> Identifying patient characteristics</ span > </ a > </ li > </ ol > </ nav >
118+ < nav class ="quarto-page-breadcrumbs " aria-label ="breadcrumb "> < ol class ="breadcrumb "> < li class ="breadcrumb-item "> < a href ="./omop .html "> Working with the OMOP CDM from R </ a > </ li > < li class ="breadcrumb-item "> < a href ="./adding_features.html "> < span class ="chapter-number "> 8</ span > < span class ="chapter-title "> Identifying patient characteristics</ span > </ a > </ li > </ ol > </ nav >
119119 < a class ="flex-grow-1 " role ="navigation " data-bs-toggle ="collapse " data-bs-target =".quarto-sidebar-collapse-item " aria-controls ="quarto-sidebar " aria-expanded ="false " aria-label ="Toggle sidebar navigation " onclick ="if (window.quartoToggleHeadroom) { window.quartoToggleHeadroom(); } ">
120120 </ a >
121121 < button type ="button " class ="btn quarto-search-button " aria-label ="Search " onclick ="window.quartoOpenSearch(); ">
176176 < li class ="sidebar-item ">
177177 < div class ="sidebar-item-container ">
178178 < a href ="./dbplyr_packages.html " class ="sidebar-item-text sidebar-link ">
179- < span class ="menu-text "> < span class ="chapter-number "> 4</ span > < span class ="chapter-title "> Building data pipelines</ span > </ span > </ a >
179+ < span class ="menu-text "> < span class ="chapter-number "> 4</ span > < span class ="chapter-title "> Building analytic pipelines for a data model </ span > </ span > </ a >
180180 </ div >
181181</ li >
182182 </ ul >
183183 </ li >
184184 < li class ="sidebar-item sidebar-item-section ">
185185 < div class ="sidebar-item-container ">
186- < a href ="./explore .html " class ="sidebar-item-text sidebar-link ">
187- < span class ="menu-text "> Working with the OMOP CDM</ span > </ a >
186+ < a href ="./omop .html " class ="sidebar-item-text sidebar-link ">
187+ < span class ="menu-text "> Working with the OMOP CDM from R </ span > </ a >
188188 < a class ="sidebar-item-toggle text-start " data-bs-toggle ="collapse " data-bs-target ="#quarto-sidebar-section-2 " role ="navigation " aria-expanded ="true " aria-label ="Toggle section ">
189189 < i class ="bi bi-chevron-right ms-2 "> </ i >
190190 </ a >
@@ -255,7 +255,7 @@ <h2 id="toc-title">Table of contents</h2>
255255<!-- main -->
256256< main class ="content " id ="quarto-document-content ">
257257
258- < header id ="title-block-header " class ="quarto-title-block default "> < nav class ="quarto-page-breadcrumbs quarto-title-breadcrumbs d-none d-lg-block " aria-label ="breadcrumb "> < ol class ="breadcrumb "> < li class ="breadcrumb-item "> < a href ="./explore .html "> Working with the OMOP CDM</ a > </ li > < li class ="breadcrumb-item "> < a href ="./adding_features.html "> < span class ="chapter-number "> 8</ span > < span class ="chapter-title "> Identifying patient characteristics</ span > </ a > </ li > </ ol > </ nav >
258+ < header id ="title-block-header " class ="quarto-title-block default "> < nav class ="quarto-page-breadcrumbs quarto-title-breadcrumbs d-none d-lg-block " aria-label ="breadcrumb "> < ol class ="breadcrumb "> < li class ="breadcrumb-item "> < a href ="./omop .html "> Working with the OMOP CDM from R </ a > </ li > < li class ="breadcrumb-item "> < a href ="./adding_features.html "> < span class ="chapter-number "> 8</ span > < span class ="chapter-title "> Identifying patient characteristics</ span > </ a > </ li > </ ol > </ nav >
259259< div class ="quarto-title ">
260260< h1 class ="title "> < span class ="chapter-number "> 8</ span > < span class ="chapter-title "> Identifying patient characteristics</ span > </ h1 >
261261</ div >
@@ -309,7 +309,7 @@ <h2 data-number="8.1" class="anchored" data-anchor-id="adding-specific-demograph
309309< div class ="cell-output cell-output-stdout ">
310310< pre > < code > Rows: ??
311311Columns: 18
312- Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpmeklJq\file668448b62f55 .duckdb]
312+ Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpItzU3r\file5580112859cc .duckdb]
313313$ condition_occurrence_id <int> 1, 3, 8, 9, 12, 18, 19, 20, 21, 23, 24, …
314314$ person_id <int> 2, 7, 16, 16, 25, 42, 42, 42, 44, 47, 47…
315315$ condition_concept_id <int> 381316, 381316, 381316, 313217, 381316, …
@@ -341,7 +341,7 @@ <h2 data-number="8.1" class="anchored" data-anchor-id="adding-specific-demograph
341341< pre > < code > <SQL>
342342SELECT
343343 condition_occurrence_id,
344- og_002_1736509005 .person_id AS person_id,
344+ og_002_1736606688 .person_id AS person_id,
345345 condition_concept_id,
346346 condition_start_date,
347347 condition_start_datetime,
@@ -358,7 +358,7 @@ <h2 data-number="8.1" class="anchored" data-anchor-id="adding-specific-demograph
358358 condition_status_source_value,
359359 age,
360360 RHS.sex AS sex
361- FROM og_002_1736509005
361+ FROM og_002_1736606688
362362LEFT JOIN (
363363 SELECT
364364 person_id,
@@ -376,13 +376,13 @@ <h2 data-number="8.1" class="anchored" data-anchor-id="adding-specific-demograph
376376 day_of_birth
377377 FROM (
378378 SELECT DISTINCT person_id
379- FROM og_002_1736509005
379+ FROM og_002_1736606688
380380 ) LHS
381381 INNER JOIN main.person
382382 ON (LHS.person_id = person.person_id)
383383 ) q01
384384) RHS
385- ON (og_002_1736509005 .person_id = RHS.person_id)</ code > </ pre >
385+ ON (og_002_1736606688 .person_id = RHS.person_id)</ code > </ pre >
386386</ div >
387387</ div >
388388< p > We now have two variables added containing values for age and sex.</ p >
@@ -392,7 +392,7 @@ <h2 data-number="8.1" class="anchored" data-anchor-id="adding-specific-demograph
392392< div class ="cell-output cell-output-stdout ">
393393< pre > < code > Rows: ??
394394Columns: 18
395- Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpmeklJq\file668448b62f55 .duckdb]
395+ Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpItzU3r\file5580112859cc .duckdb]
396396$ condition_occurrence_id <int> 1, 3, 8, 9, 12, 18, 19, 20, 21, 23, 24, …
397397$ person_id <int> 2, 7, 16, 16, 25, 42, 42, 42, 44, 47, 47…
398398$ condition_concept_id <int> 381316, 381316, 381316, 313217, 381316, …
@@ -456,7 +456,7 @@ <h2 data-number="8.2" class="anchored" data-anchor-id="adding-multiple-demograph
456456< div class ="cell-output cell-output-stdout ">
457457< pre > < code > Rows: ??
458458Columns: 27
459- Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpmeklJq\file668448b62f55 .duckdb]
459+ Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpItzU3r\file5580112859cc .duckdb]
460460$ drug_exposure_id <int> 245761, 245762, 245763, 245765, 245766, 2…
461461$ person_id <int> 7764, 7764, 7764, 7764, 7764, 7764, 7764,…
462462$ drug_concept_id <int> 40213227, 40213201, 40213198, 40213154, 4…
@@ -498,8 +498,8 @@ <h2 data-number="8.2" class="anchored" data-anchor-id="adding-multiple-demograph
498498< pre > < code > # A tibble: 2 × 4
499499 sex mean_age mean_prior_observation mean_future_observation
500500 <chr> <dbl> <dbl> <dbl>
501- 1 Female 39.4 2096 . 1661 .
502- 2 Male 43.0 2455 . 1768 .</ code > </ pre >
501+ 1 Male 43.0 2455 . 1768 .
502+ 2 Female 39.4 2096 . 1661 .</ code > </ pre >
503503</ div >
504504</ div >
505505< div class ="callout callout-style-default callout-tip callout-titled ">
@@ -522,8 +522,8 @@ <h2 data-number="8.2" class="anchored" data-anchor-id="adding-multiple-demograph
522522< span id ="cb18-4 "> < a href ="#cb18-4 " aria-hidden ="true " tabindex ="-1 "> </ a > dplyr< span class ="sc "> ::</ span > < span class ="fu "> show_query</ span > ()</ span > </ code > < button title ="Copy to Clipboard " class ="code-copy-button "> < i class ="bi "> </ i > </ button > </ pre > </ div >
523523< div class ="cell-output cell-output-stdout ">
524524< pre > < code > <SQL>
525- SELECT og_004_1736509007 .*
526- FROM og_004_1736509007
525+ SELECT og_004_1736606693 .*
526+ FROM og_004_1736606693
527527WHERE (sex = 'Male')</ code > </ pre >
528528</ div >
529529</ div >
@@ -623,7 +623,7 @@ <h2 data-number="8.3" class="anchored" data-anchor-id="creating-categories"><spa
623623< div class ="cell-output cell-output-stdout ">
624624< pre > < code > Rows: ??
625625Columns: 20
626- Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpmeklJq\file668448b62f55 .duckdb]
626+ Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpItzU3r\file5580112859cc .duckdb]
627627$ condition_occurrence_id <int> 1, 3, 8, 9, 12, 18, 19, 20, 21, 23, 24, …
628628$ person_id <int> 2, 7, 16, 16, 25, 42, 42, 42, 44, 47, 47…
629629$ condition_concept_id <int> 381316, 381316, 381316, 313217, 381316, …
@@ -660,7 +660,7 @@ <h2 data-number="8.4" class="anchored" data-anchor-id="adding-custom-variables">
660660< div class ="cell-output cell-output-stdout ">
661661< pre > < code > Rows: ??
662662Columns: 6
663- Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpmeklJq\file668448b62f55 .duckdb]
663+ Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpItzU3r\file5580112859cc .duckdb]
664664$ observation_period_id <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 1…
665665$ person_id <int> 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 1…
666666$ observation_period_start_date <date> 2014-05-09, 1977-04-11, 2014-04-19, 201…
@@ -688,7 +688,7 @@ <h2 data-number="8.4" class="anchored" data-anchor-id="adding-custom-variables">
688688< div class ="cell-output cell-output-stdout ">
689689< pre > < code > Rows: ??
690690Columns: 2
691- Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpmeklJq\file668448b62f55 .duckdb]
691+ Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpItzU3r\file5580112859cc .duckdb]
692692$ person_id <int> 2, 7, 16, 18, 25, 36, 42, 44, 47, 51, 52,…
693693$ condition_occurrence_records <dbl> 1, 1, 2, 2, 1, 4, 3, 2, 5, 1, 3, 2, 1, 4,…</ code > </ pre >
694694</ div >
@@ -716,7 +716,7 @@ <h2 data-number="8.4" class="anchored" data-anchor-id="adding-custom-variables">
716716 FROM main.person
717717 LEFT JOIN (
718718 SELECT person_id, COUNT(*) AS condition_occurrence_records
719- FROM og_002_1736509005
719+ FROM og_002_1736606688
720720 GROUP BY person_id
721721 ) RHS
722722 ON (person.person_id = RHS.person_id)
@@ -743,7 +743,7 @@ <h2 data-number="8.4" class="anchored" data-anchor-id="adding-custom-variables">
743743< span id ="cb33-2 "> < a href ="#cb33-2 " aria-hidden ="true " tabindex ="-1 "> </ a > < span class ="fu "> tally</ span > ()</ span > </ code > < button title ="Copy to Clipboard " class ="code-copy-button "> < i class ="bi "> </ i > </ button > </ pre > </ div >
744744< div class ="cell-output cell-output-stdout ">
745745< pre > < code > # Source: SQL [?? x 1]
746- # Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpmeklJq\file668448b62f55 .duckdb]
746+ # Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpItzU3r\file5580112859cc .duckdb]
747747 n
748748 <dbl>
7497491 9967</ code > </ pre >
@@ -752,7 +752,7 @@ <h2 data-number="8.4" class="anchored" data-anchor-id="adding-custom-variables">
752752< span id ="cb35-2 "> < a href ="#cb35-2 " aria-hidden ="true " tabindex ="-1 "> </ a > < span class ="fu "> tally</ span > ()</ span > </ code > < button title ="Copy to Clipboard " class ="code-copy-button "> < i class ="bi "> </ i > </ button > </ pre > </ div >
753753< div class ="cell-output cell-output-stdout ">
754754< pre > < code > # Source: SQL [?? x 1]
755- # Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpmeklJq\file668448b62f55 .duckdb]
755+ # Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpItzU3r\file5580112859cc .duckdb]
756756 n
757757 <dbl>
7587581 337509</ code > </ pre >
@@ -765,7 +765,7 @@ <h2 data-number="8.4" class="anchored" data-anchor-id="adding-custom-variables">
765765< span id ="cb37-6 "> < a href ="#cb37-6 " aria-hidden ="true " tabindex ="-1 "> </ a > < span class ="fu "> tally</ span > ()</ span > </ code > < button title ="Copy to Clipboard " class ="code-copy-button "> < i class ="bi "> </ i > </ button > </ pre > </ div >
766766< div class ="cell-output cell-output-stdout ">
767767< pre > < code > # Source: SQL [?? x 1]
768- # Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpmeklJq\file668448b62f55 .duckdb]
768+ # Database: DuckDB v1.1.3 [eburn@Windows 10 x64:R 4.4.0/C:\Users\eburn\AppData\Local\Temp\RtmpItzU3r\file5580112859cc .duckdb]
769769 n
770770 <dbl>
7717711 410683</ code > </ pre >
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