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@ -7,7 +7,7 @@
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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="">2.1.1.9266</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9267</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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@ -164,13 +164,13 @@
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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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<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"ceftriaxon"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04" "QJ01DD04"</span>
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<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"cephtriaxone"</span><span class="op">)</span> <span class="co"># small spelling error</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04" "QJ01DD04"</span>
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<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"cephthriaxone"</span><span class="op">)</span> <span class="co"># or a bit more severe</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04" "QJ01DD04"</span>
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<span class="r-in"><span><span class="fu"><a href="ab_property.html">ab_atc</a></span><span class="op">(</span><span class="st">"seephthriaaksone"</span><span class="op">)</span> <span class="co"># and even this works</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04"</span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "J01DD04" "QJ01DD04"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># use ab_* functions to get a specific properties (see ?ab_property);</span></span></span>
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<span class="r-in"><span><span class="co"># they use as.ab() internally:</span></span></span>
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@ -185,6 +185,7 @@
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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="ab_property.html">set_ab_names</a></span><span class="op">(</span><span class="fu"><a href="https://tidyselect.r-lib.org/reference/where.html" class="external-link">where</a></span><span class="op">(</span><span class="va">is.sir</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-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in <span style="background-color: #EEEEEE;">set_ab_names()</span>: no atc found for column(s): "SXT" and "IPM"</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 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;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span> </span>
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@ -202,7 +203,7 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 37 more variables: J01CA04 <sir>, J01CR02 <sir>, J01CA01 <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01CR05 <sir>, J01DB04 <sir>, J01DE01 <sir>, J01DC02 <sir>, J01DC01 <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01DD01 <sir>, J01DD02 <sir>, J01DD04 <sir>, J01GB03 <sir>, J01GB01 <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01GB06 <sir>, J01GB04 <sir>, J01EA01 <sir>, J01EE01 <sir>, J01XE01 <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01GB06 <sir>, J01GB04 <sir>, J01EA01 <sir>, SXT <sir>, J01XE01 <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01XX01 <sir>, J01XX08 <sir>, J01MA02 <sir>, J01MA14 <sir>, J01XA01 <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># J01XA02 <sir>, J01AA07 <sir>, J01AA12 <sir>, J01AA02 <sir>, …</span></span>
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<span class="r-in"><span><span class="co"># }</span></span></span>
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