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Built site for AMR: 1.8.1.9026@e05d036
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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="">1.8.1.9021</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9026</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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@ -82,11 +82,6 @@
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Get properties of an antibiotic
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</a>
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<a class="dropdown-item" href="../articles/benchmarks.html">
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<span class="fa fa-shipping-fast"></span>
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Other: benchmarks
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</a>
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</div>
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</li>
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<li class="active nav-item">
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@ -315,7 +310,6 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> NA 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</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</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"># select columns 'mo', 'AMK', 'GEN', 'KAN' and 'TOB'</span></span></span>
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<span class="r-in"><span><span class="va">df</span><span class="op">[</span>, <span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"mo"</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">]</span></span></span>
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@ -335,7 +329,6 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> B_STPHY_EPDR NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> B_STPHY_EPDR NA 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</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</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"># select only antibiotic columns with DDDs for oral treatment</span></span></span>
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<span class="r-in"><span><span class="va">df</span><span class="op">[</span>, <span class="fu">administrable_per_os</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
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@ -356,7 +349,6 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> NA NA R R S </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> NA NA S R 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</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</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"># filter using any() or all()</span></span></span>
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<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span></span>
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@ -376,7 +368,6 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> A B_PROTS_MRBL NA S S S S S S R R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 45 more rows, 3 more variables: MEM <rsi>, TEC <rsi>, VAN <rsi>, and</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># abbreviated variable name ¹hospital_id</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
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<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/subset.html" class="external-link">subset</a></span><span class="op">(</span><span class="va">df</span>, <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 55 × 14</span></span>
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@ -394,7 +385,6 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> A B_PROTS_MRBL NA S S S S S S R R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 45 more rows, 3 more variables: MEM <rsi>, TEC <rsi>, VAN <rsi>, and</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># abbreviated variable name ¹hospital_id</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</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"># filter on any or all results in the carbapenem columns (i.e., IPM, MEM):</span></span></span>
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<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
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@ -415,7 +405,6 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> C B_ESCHR_COLI R R NA R S S NA NA S </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 952 more rows, 3 more variables: MEM <rsi>, TEC <rsi>, VAN <rsi>, and</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># abbreviated variable name ¹hospital_id</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</span></span>
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<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span><span class="op">)</span>, <span class="op">]</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ For `carbapenems()` using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Filtering all of columns 'IPM' and 'MEM' to contain value "R", "S" or "I"</span>
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@ -434,7 +423,6 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> B B_ESCHR_COLI NA S S S S S S NA S </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 746 more rows, 3 more variables: MEM <rsi>, TEC <rsi>, VAN <rsi>, and</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># abbreviated variable name ¹hospital_id</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</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"># filter with multiple antibiotic selectors using c()</span></span></span>
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<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/all.html" class="external-link">all</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, <span class="fu">aminoglycosides</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="op">]</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> D B_STPHY_CONS R R R R R R R R R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 16 more rows, 3 more variables: MEM <rsi>, TEC <rsi>, VAN <rsi>, and</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># abbreviated variable name ¹hospital_id</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows, and `colnames()` to see all variable names</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"># filter + select in one go: get penicillins in carbapenems-resistant strains</span></span></span>
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<span class="r-in"><span><span class="va">df</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"R"</span><span class="op">)</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span><span class="op">]</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> NA S S </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> NA S S </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 45 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</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 combine selectors with '&' to be more specific. For example,</span></span></span>
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<span class="r-in"><span><span class="co"># penicillins() would select benzylpenicillin ('peni G') and</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> NA 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</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</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"># ab_selector() applies a filter in the `antibiotics` data set and is thus very</span></span></span>
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<span class="r-in"><span><span class="co"># flexible. For instance, to select antibiotic columns with an oral DDD of at</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> NA NA S </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> NA 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</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ Use `print(n = ...)` to see more rows</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"># dplyr -------------------------------------------------------------------</span></span></span>
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<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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