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@ -17,7 +17,7 @@ my_data_with_all_these_columns %>%
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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="">3.0.0.9010</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.0.9011</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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@ -284,10 +284,10 @@ my_data_with_all_these_columns %&gt;%
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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 use the selectors separately to retrieve all possible antimicrobials:</span></span></span>
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<span class="r-in"><span><span class="fu">carbapenems</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> <span style="color: #0000BB;">ℹ in </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;">: Imipenem/EDTA (</span><span style="color: #0000BB; background-color: #EEEEEE;">IPE</span><span style="color: #0000BB;">) and meropenem/nacubactam</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (</span><span style="color: #0000BB; background-color: #EEEEEE;">MNC</span><span style="color: #0000BB;">) are not included since </span><span style="color: #0000BB; background-color: #EEEEEE;">only_treatable = TRUE</span><span style="color: #0000BB;">.</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ This 'ab' vector was retrieved using </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;">, which should</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> normally be used inside a </span><span style="color: #0000BB; background-color: #EEEEEE;">dplyr</span><span style="color: #0000BB;"> verb or </span><span style="color: #0000BB; background-color: #EEEEEE;">data.frame</span><span style="color: #0000BB;"> call, e.g.:</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ in </span><span style="color: #0000BB; background-color: #EEEEEE;">`carbapenems()`</span><span style="color: #0000BB;">: Imipenem/EDTA (</span><span style="color: #0000BB; background-color: #EEEEEE;">`IPE`</span><span style="color: #0000BB;">) and meropenem/nacubactam</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (</span><span style="color: #0000BB; background-color: #EEEEEE;">`MNC`</span><span style="color: #0000BB;">) are not included since </span><span style="color: #0000BB; background-color: #EEEEEE;">`only_treatable = TRUE`</span><span style="color: #0000BB;">.</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ This 'ab' vector was retrieved using </span><span style="color: #0000BB; background-color: #EEEEEE;">`carbapenems()`</span><span style="color: #0000BB;">, which should</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> normally be used inside a </span><span style="color: #0000BB; background-color: #EEEEEE;">`dplyr`</span><span style="color: #0000BB;"> verb or </span><span style="color: #0000BB; background-color: #EEEEEE;">`data.frame`</span><span style="color: #0000BB;"> call, e.g.:</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> • your_data %>% select(carbapenems())</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> • your_data %>% select(column_a, column_b, carbapenems())</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> • your_data %>% filter(any(carbapenems() == "R"))</span></span>
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@ -392,7 +392,7 @@ my_data_with_all_these_columns %&gt;%
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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 'IPM' (imipenem) and 'MEM' (meropenem)</span></span></span>
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<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">carbapenems</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> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`carbapenems()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 2</span></span>
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<span class="r-out co"><span class="r-pr">#></span> IPM MEM </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #949494; font-style: italic;"><sir></span></span>
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@ -410,7 +410,7 @@ my_data_with_all_these_columns %&gt;%
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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">example_isolates</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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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`aminoglycosides()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 5</span></span>
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<span class="r-out co"><span class="r-pr">#></span> mo GEN TOB AMK KAN </span>
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@ -429,7 +429,7 @@ my_data_with_all_these_columns %&gt;%
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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 antimicrobials with DDDs for oral treatment</span></span></span>
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<span class="r-in"><span><span class="va">example_isolates</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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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">administrable_per_os()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">' (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">'</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`administrable_per_os()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">' (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">'</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">' (amoxicillin/clavulanic acid),</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">' (cefuroxime), '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin), '</span><span style="color: #0000BB; font-weight: bold;">TMP</span><span style="color: #0000BB;">'</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (trimethoprim), '</span><span style="color: #0000BB; font-weight: bold;">NIT</span><span style="color: #0000BB;">' (nitrofurantoin), '</span><span style="color: #0000BB; font-weight: bold;">FOS</span><span style="color: #0000BB;">' (fosfomycin), '</span><span style="color: #0000BB; font-weight: bold;">LNZ</span><span style="color: #0000BB;">'</span></span>
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@ -457,7 +457,7 @@ my_data_with_all_these_columns %&gt;%
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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">example_isolates</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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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`carbapenems()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 55 × 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;"><sir></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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@ -479,7 +479,7 @@ my_data_with_all_these_columns %&gt;%
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …</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">example_isolates</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> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`carbapenems()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 55 × 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;"><sir></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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@ -503,7 +503,7 @@ my_data_with_all_these_columns %&gt;%
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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">example_isolates</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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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`carbapenems()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Filtering any of columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' to contain value "S", "I" or "R"</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 962 × 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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@ -526,7 +526,7 @@ my_data_with_all_these_columns %&gt;%
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TCY <sir>, TGC <sir>, DOX <sir>, ERY <sir>, CLI <sir>, AZM <sir>,</span></span>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># IPM <sir>, MEM <sir>, MTR <sir>, CHL <sir>, COL <sir>, MUP <sir>, …</span></span>
|
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<span class="r-in"><span><span class="va">example_isolates</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> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`carbapenems()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
|
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<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Filtering all of columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' to contain value "S", "I" or "R"</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 756 × 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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@ -551,8 +551,8 @@ my_data_with_all_these_columns %&gt;%
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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 antimicrobial selectors using c()</span></span></span>
|
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<span class="r-in"><span><span class="va">example_isolates</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>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`carbapenems()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`aminoglycosides()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 26 × 46</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
|
||||
@ -577,8 +577,8 @@ my_data_with_all_these_columns %&gt;%
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># filter + select in one go: get penicillins in carbapenem-resistant strains</span></span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</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>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">penicillins()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`carbapenems()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`penicillins()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), and '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (piperacillin/tazobactam)</span></span>
|
||||
@ -603,11 +603,11 @@ my_data_with_all_these_columns %&gt;%
|
||||
<span class="r-in"><span><span class="co"># drugs are both omitted since benzylpenicillin is not administrable per os</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># and erythromycin is not a penicillin:</span></span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</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>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">penicillins()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`penicillins()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), and '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (piperacillin/tazobactam)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">administrable_per_os()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">' (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`administrable_per_os()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">' (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">' (amoxicillin/clavulanic acid),</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), '</span><span style="color: #0000BB; font-weight: bold;">CXM</span><span style="color: #0000BB;">' (cefuroxime), '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin), '</span><span style="color: #0000BB; font-weight: bold;">TMP</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (trimethoprim), '</span><span style="color: #0000BB; font-weight: bold;">NIT</span><span style="color: #0000BB;">' (nitrofurantoin), '</span><span style="color: #0000BB; font-weight: bold;">FOS</span><span style="color: #0000BB;">' (fosfomycin), '</span><span style="color: #0000BB; font-weight: bold;">LNZ</span><span style="color: #0000BB;">'</span></span>
|
||||
@ -635,7 +635,7 @@ my_data_with_all_these_columns %&gt;%
|
||||
<span class="r-in"><span><span class="co"># very flexible. For instance, to select antimicrobials with an oral DDD</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># of at least 1 gram:</span></span></span>
|
||||
<span class="r-in"><span><span class="va">example_isolates</span><span class="op">[</span>, <span class="fu">amr_selector</span><span class="op">(</span><span class="va">oral_ddd</span> <span class="op">></span> <span class="fl">1</span> <span class="op">&</span> <span class="va">oral_units</span> <span class="op">==</span> <span class="st">"g"</span><span class="op">)</span><span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">amr_selector(oral_ddd > 1 & oral_units == "g")</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`amr_selector(oral_ddd > 1 & oral_units == "g")`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin), '</span><span style="color: #0000BB; font-weight: bold;">FOS</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (fosfomycin), '</span><span style="color: #0000BB; font-weight: bold;">LNZ</span><span style="color: #0000BB;">' (linezolid), '</span><span style="color: #0000BB; font-weight: bold;">VAN</span><span style="color: #0000BB;">' (vancomycin), '</span><span style="color: #0000BB; font-weight: bold;">ERY</span><span style="color: #0000BB;">' (erythromycin),</span></span>
|
||||
@ -679,17 +679,17 @@ my_data_with_all_these_columns %&gt;%
|
||||
<span class="r-msg co"><span class="r-pr">#></span> The following objects are masked from ‘package:AMR’:</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> %like%, like</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`carbapenems()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>It should never be needed to print an antimicrobial selector class. Are you</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> using data.table? Then add the argument <span style="background-color: #EEEEEE;">with = FALSE</span>, see our examples at</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="background-color: #EEEEEE;">?amr_selector</span>.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> using data.table? Then add the argument <span style="background-color: #EEEEEE;">`with = FALSE`</span>, see our examples at</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span style="background-color: #EEEEEE;">`?amr_selector`</span>.</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Class 'amr_selector'</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] IPM MEM</span>
|
||||
<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://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="co"># so `with = FALSE` is required</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">dt</span><span class="op">[</span>, <span class="fu">carbapenems</span><span class="op">(</span><span class="op">)</span>, with <span class="op">=</span> <span class="cn">FALSE</span><span class="op">]</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`carbapenems()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> IPM MEM</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <sir> <sir></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: <NA> <NA></span>
|
||||
@ -708,7 +708,7 @@ my_data_with_all_these_columns %&gt;%
|
||||
<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://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">dt</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>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`aminoglycosides()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> mo GEN TOB AMK KAN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <mo> <sir> <sir> <sir> <sir></span>
|
||||
@ -726,8 +726,8 @@ my_data_with_all_these_columns %&gt;%
|
||||
<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://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">dt</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></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">aminoglycosides()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`carbapenems()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`aminoglycosides()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">GEN</span><span style="color: #0000BB;">' (gentamicin), '</span><span style="color: #0000BB; font-weight: bold;">TOB</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (tobramycin), '</span><span style="color: #0000BB; font-weight: bold;">AMK</span><span style="color: #0000BB;">' (amikacin), and '</span><span style="color: #0000BB; font-weight: bold;">KAN</span><span style="color: #0000BB;">' (kanamycin)</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> IPM MEM GEN TOB AMK KAN</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <sir> <sir> <sir> <sir> <sir> <sir></span>
|
||||
@ -747,7 +747,7 @@ my_data_with_all_these_columns %&gt;%
|
||||
<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://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">dt</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">"S"</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`carbapenems()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <Date> <char> <num> <char> <char> <mo> <sir> <sir> <sir></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> 1: 2002-01-19 738003 71 M Clinical B_ESCHR_COLI R <NA> <NA></span>
|
||||
@ -816,8 +816,8 @@ my_data_with_all_these_columns %&gt;%
|
||||
<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://r-datatable.com" class="external-link">"data.table"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
|
||||
<span class="r-in"><span> <span class="va">dt</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">"S"</span><span class="op">)</span>, <span class="fu">penicillins</span><span class="op">(</span><span class="op">)</span>, with <span class="op">=</span> <span class="cn">FALSE</span><span class="op">]</span></span></span>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">carbapenems()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">penicillins()</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`carbapenems()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">IPM</span><span style="color: #0000BB;">' (imipenem) and '</span><span style="color: #0000BB; font-weight: bold;">MEM</span><span style="color: #0000BB;">' (meropenem)</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ For </span><span style="color: #0000BB; background-color: #EEEEEE;">`penicillins()`</span><span style="color: #0000BB;"> using columns '</span><span style="color: #0000BB; font-weight: bold;">PEN</span><span style="color: #0000BB;">' (benzylpenicillin), '</span><span style="color: #0000BB; font-weight: bold;">OXA</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (oxacillin), '</span><span style="color: #0000BB; font-weight: bold;">FLC</span><span style="color: #0000BB;">' (flucloxacillin), '</span><span style="color: #0000BB; font-weight: bold;">AMX</span><span style="color: #0000BB;">' (amoxicillin), '</span><span style="color: #0000BB; font-weight: bold;">AMC</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (amoxicillin/clavulanic acid), '</span><span style="color: #0000BB; font-weight: bold;">AMP</span><span style="color: #0000BB;">' (ampicillin), and '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">'</span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;"> (piperacillin/tazobactam)</span></span>
|
||||
|
||||
Reference in New Issue
Block a user