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reference/antibiogram.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9112</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9116</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
@ -311,9 +311,35 @@
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> antibiotics <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"><a href="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antibiotic_class_selectors.html">carbapenems</a></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">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ The function aminoglycosides() should be used inside a dplyr verb or</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> data.frame call, e.g.:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% select(aminoglycosides())</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% select(column_a, column_b, aminoglycosides())</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% filter(any(aminoglycosides() == "R"))</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data[, aminoglycosides()]</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data[, c("column_a", "column_b", aminoglycosides())]</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Now returning a vector of all possible antimicrobials that</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> aminoglycosides() can select.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ The function carbapenems() should be used inside a dplyr verb or</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> data.frame call, e.g.:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% select(carbapenems())</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% select(column_a, column_b, carbapenems())</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% filter(any(carbapenems() == "R"))</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data[, carbapenems()]</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data[, c("column_a", "column_b", carbapenems())]</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Now returning a vector of all possible antimicrobials that carbapenems()</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> can select.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>The following antibiotics were not available and ignored:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> biapenem, dibekacin, doripenem, ertapenem, framycetin, gentamicin-high,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> habekacin, hygromycin, imipenem/EDTA, imipenem/relebactam, isepamicin,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> kanamycin-high, kanamycin/cephalexin, meropenem/nacubactam,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> meropenem/vaborbactam, micronomicin, neomycin, netilmicin, panipenem,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> pentisomicin, plazomicin, propikacin, razupenem, ribostamycin, ritipenem,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ritipenem acoxil, sisomicin, streptoduocin, streptomycin,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> streptomycin-high, tebipenem, and tobramycin-high</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 10 × 7</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem Tobramycin</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
@ -335,8 +361,22 @@
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"atc"</span>,</span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ The function aminoglycosides() should be used inside a dplyr verb or</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> data.frame call, e.g.:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% select(aminoglycosides())</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% select(column_a, column_b, aminoglycosides())</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% filter(any(aminoglycosides() == "R"))</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data[, aminoglycosides()]</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data[, c("column_a", "column_b", aminoglycosides())]</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Now returning a vector of all possible antimicrobials that</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> aminoglycosides() can select.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>The following antibiotics were not available and ignored:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> dibekacin, framycetin, gentamicin-high, habekacin, hygromycin, isepamicin,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> streptoduocin, streptomycin, streptomycin-high, and tobramycin-high</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen J01GB01 J01GB03 J01GB04 J01GB06 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
@ -350,7 +390,20 @@
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"name"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ The function carbapenems() should be used inside a dplyr verb or</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> data.frame call, e.g.:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% select(carbapenems())</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% select(column_a, column_b, carbapenems())</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% filter(any(carbapenems() == "R"))</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data[, carbapenems()]</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data[, c("column_a", "column_b", carbapenems())]</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Now returning a vector of all possible antimicrobials that carbapenems()</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> can select.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>The following antibiotics were not available and ignored: biapenem,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> doripenem, ertapenem, imipenem/EDTA, imipenem/relebactam,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> meropenem/nacubactam, meropenem/vaborbactam, panipenem, razupenem,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ritipenem, ritipenem acoxil, and tebipenem</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 5 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Pathogen Imipenem Meropenem </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
@ -404,9 +457,35 @@
<span class="r-in"><span> antibiotics <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"><a href="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> syndromic_group <span class="op">=</span> <span class="st">"ward"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ The function aminoglycosides() should be used inside a dplyr verb or</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> data.frame call, e.g.:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% select(aminoglycosides())</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% select(column_a, column_b, aminoglycosides())</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% filter(any(aminoglycosides() == "R"))</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data[, aminoglycosides()]</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data[, c("column_a", "column_b", aminoglycosides())]</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Now returning a vector of all possible antimicrobials that</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> aminoglycosides() can select.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ The function carbapenems() should be used inside a dplyr verb or</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> data.frame call, e.g.:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% select(carbapenems())</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% select(column_a, column_b, carbapenems())</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% filter(any(carbapenems() == "R"))</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data[, carbapenems()]</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data[, c("column_a", "column_b", carbapenems())]</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Now returning a vector of all possible antimicrobials that carbapenems()</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> can select.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>The following antibiotics were not available and ignored:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> biapenem, dibekacin, doripenem, ertapenem, framycetin, gentamicin-high,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> habekacin, hygromycin, imipenem/EDTA, imipenem/relebactam, isepamicin,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> kanamycin-high, kanamycin/cephalexin, meropenem/nacubactam,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> meropenem/vaborbactam, micronomicin, neomycin, netilmicin, panipenem,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> pentisomicin, plazomicin, propikacin, razupenem, ribostamycin, ritipenem,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> ritipenem acoxil, sisomicin, streptoduocin, streptomycin,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> streptomycin-high, tebipenem, and tobramycin-high</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 14 × 8</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Syndromic Group` Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
@ -442,8 +521,22 @@
<span class="r-in"><span> <span class="op">)</span>,</span></span>
<span class="r-in"><span> language <span class="op">=</span> <span class="st">"es"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ The function aminoglycosides() should be used inside a dplyr verb or</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> data.frame call, e.g.:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% select(aminoglycosides())</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% select(column_a, column_b, aminoglycosides())</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% filter(any(aminoglycosides() == "R"))</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data[, aminoglycosides()]</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data[, c("column_a", "column_b", aminoglycosides())]</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Now returning a vector of all possible antimicrobials that</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> aminoglycosides() can select.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>The following antibiotics were not available and ignored:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> amikacin/fosfomycin, apramycin, arbekacin, astromicin, bekanamycin,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> dibekacin, framycetin, gentamicin-high, habekacin, hygromycin, isepamicin,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> kanamycin-high, kanamycin/cephalexin, micronomicin, neomycin, netilmicin,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> pentisomicin, plazomicin, propikacin, ribostamycin, sisomicin,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> streptoduocin, streptomycin, streptomycin-high, and tobramycin-high</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># An Antibiogram: 2 × 5</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> `Grupo sindrómico` Patógeno Amikacina Gentamicina Tobramicina </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
@ -486,7 +579,18 @@
<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="antibiotic_class_selectors.html">ureidopenicillins</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span></span></span>
<span class="r-in"><span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ For ureidopenicillins() using column 'TZP' (piperacillin/tazobactam)</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ The function ureidopenicillins() should be used inside a dplyr verb</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> or data.frame call, e.g.:</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% select(ureidopenicillins())</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% select(column_a, column_b, ureidopenicillins())</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data %&gt;% filter(any(ureidopenicillins() == "R"))</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data[, ureidopenicillins()]</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> • your_data[, c("column_a", "column_b", ureidopenicillins())]</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Now returning a vector of all possible antimicrobials that</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ureidopenicillins() can select.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>The following antibiotics were not available and ignored: azlocillin,</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> mezlocillin, and piperacillin</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># in an Rmd file, you would just need to return `ureido` in a chunk,</span></span></span>
<span class="r-in"><span><span class="co"># but to be explicit here:</span></span></span>