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@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9022</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9023</small>
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<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
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@ -212,32 +212,32 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
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<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># these examples all return "ERY", the ID of erythromycin:</span></span></span>
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<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"J01FA01"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
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<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"J 01 FA 01"</span><span class="op">)</span></span></span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> in like(): argument `x` must not be NULL</span>
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<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Erythromycin"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
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<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"eryt"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
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<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">" eryt 123"</span><span class="op">)</span></span></span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error:</span> in like(): argument `x` must not be NULL</span>
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<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"ERYT"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
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<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"ERY"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
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<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"eritromicine"</span><span class="op">)</span> <span class="co"># spelled wrong, yet works</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
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<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Erythrocin"</span><span class="op">)</span> <span class="co"># trade name</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
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<span class="r-in"><span><span class="fu">as.ab</span><span class="op">(</span><span class="st">"Romycin"</span><span class="op">)</span> <span class="co"># trade name</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> Class <ab></span>
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<span class="r-out co"><span class="r-pr">#></span> Class 'ab'</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] ERY</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># spelling from different languages and dyslexia are no problem</span></span></span>
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@ -256,33 +256,34 @@ This package contains <strong>all ~550 antibiotic, antimycotic and antiviral dru
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<span class="r-out co"><span class="r-pr">#></span> [1] "Erythromycin"</span>
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<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_name</a></span><span class="op">(</span><span class="st">"eryt"</span><span class="op">)</span> <span class="co"># "Erythromycin"</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Erythromycin"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span> <span class="co"># you can quickly rename <rsi> columns using dplyr >= 1.0.0:</span></span></span>
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<span class="r-in"><span> <span class="co"># you can quickly rename 'rsi' columns using set_ab_names() with dplyr:</span></span></span>
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<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/rename.html" class="external-link">rename_with</a></span><span class="op">(</span><span class="va">as.ab</span>, <span class="fu">where</span><span class="op">(</span><span class="va">is.rsi</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="fu">where</span><span class="op">(</span><span class="va">is.rsi</span><span class="op">)</span>, property <span class="op">=</span> <span class="st">"atc"</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
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<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, and 36 more variables: AMC <rsi>, AMP <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TZP <rsi>, CZO <rsi>, FEP <rsi>, CXM <rsi>, FOX <rsi>, CTX <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CAZ <rsi>, CRO <rsi>, GEN <rsi>, TOB <rsi>, AMK <rsi>, KAN <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TMP <rsi>, SXT <rsi>, NIT <rsi>, FOS <rsi>, LNZ <rsi>, CIP <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MFX <rsi>, VAN <rsi>, TEC <rsi>, TCY <rsi>, TGC <rsi>, DOX <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ERY <rsi>, CLI <rsi>, AZM <rsi>, IPM <rsi>, MEM <rsi>, MTR <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CHL <rsi>, COL <rsi>, MUP <rsi>, RIF <rsi></span></span>
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<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo J01CE01 J01CF04 J01CF05</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> <span style="color: #949494; font-style: italic;"><rsi></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 1,990 more rows, and 37 more variables: J01CA04 <rsi>, J01CR02 <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01CA01 <rsi>, J01CR05 <rsi>, J01DB04 <rsi>, J01DE01 <rsi>, J01DC02 <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01DC01 <rsi>, J01DD01 <rsi>, J01DD02 <rsi>, J01DD04 <rsi>, J01GB03 <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01GB01 <rsi>, J01GB06 <rsi>, J01GB04 <rsi>, J01EA01 <rsi>, J01EE01 <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01XE01 <rsi>, J01XX01 <rsi>, J01XX08 <rsi>, J01MA02 <rsi>, J01MA14 <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01XA01 <rsi>, J01XA02 <rsi>, J01AA07 <rsi>, J01AA12 <rsi>, J01AA02 <rsi>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01FA01 <rsi>, J01FF01 <rsi>, J01FA10 <rsi>, J01DH51 <rsi>, …</span></span>
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<span class="r-in"><span><span class="co"># }</span></span></span>
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</code></pre></div>
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</div>
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