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@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9135</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9136</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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@ -338,16 +338,16 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2,000 × 46</span></span>
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<span class="r-out co"><span class="r-pr">#></span> date patient age gender ward mo PEN OXA FLC AMX </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><date></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><mo></span> <span style="color: #949494; font-style: italic;"><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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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical B_ESCHR_COLI R NA NA NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical B_STPHY_AURS R NA S R </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU B_STPHY_EPDR R NA R NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU B_STPHY_EPDR R NA S NA </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2002-01-02 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2002-01-03 A77334 65 F Clinical <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2002-01-07 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2002-01-13 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2002-01-14 462729 78 M Clinical <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>AURS <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #080808; background-color: #FFAFAF;"> R </span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2002-01-16 067927 45 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2002-01-17 858515 79 F ICU <span style="color: #949494;">B_</span>STPHY<span style="color: #949494;">_</span>EPDR <span style="color: #080808; background-color: #FFAFAF;"> R </span> <span style="color: #B2B2B2;"> NA</span> <span style="color: #080808; background-color: #5FD7AF;"> S </span> <span style="color: #B2B2B2;"> NA</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 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 36 more variables: AMC <sir>, AMP <sir>, TZP <sir>, CZO <sir>, FEP <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CXM <sir>, FOX <sir>, CTX <sir>, CAZ <sir>, CRO <sir>, GEN <sir>,</span></span>
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@ -362,9 +362,9 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
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<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
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<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="antimicrobial_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antimicrobial_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
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<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</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> <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-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;"># An Antibiogram (non-WISCA): 10 × 7</span></span>
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<span class="r-out co"><span class="r-pr">#></span> Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem Tobramycin</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</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;"><chr></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;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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@ -378,30 +378,30 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> S. epidermidis 0% (0/44) 79% (128/… <span style="color: #BB0000;">NA</span> 0% (0/44) <span style="color: #BB0000;">NA</span> 51% (45/8…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> S. hominis <span style="color: #BB0000;">NA</span> 92% (74/8… <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 85% (53/6…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> S. pneumoniae 0% (0/117) 0% (0/117) <span style="color: #BB0000;">NA</span> 0% (0/11… <span style="color: #BB0000;">NA</span> 0% (0/117)</span>
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<span class="r-out co"><span class="r-pr">#></span> # Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span>
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<span class="r-out co"><span class="r-pr">#></span> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
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<span class="r-in"><span> antibiotics <span class="op">=</span> <span class="fu"><a href="antimicrobial_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
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<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"atc"</span>,</span></span>
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<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span></span></span>
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<span class="r-in"><span><span class="op">)</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
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<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</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;"># An Antibiogram (non-WISCA): 2 × 5</span></span>
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<span class="r-out co"><span class="r-pr">#></span> Pathogen J01GB01 J01GB03 J01GB04 J01GB06 </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</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;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Gram-negative 96% (658/686) 96% (659/684) 0% (0/35) 98% (251/256)</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> Gram-positive 34% (228/665) 63% (740/1170) 0% (0/436) 0% (0/436) </span>
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<span class="r-out co"><span class="r-pr">#></span> # Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
|
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<span class="r-in"><span></span></span>
|
||||
<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="antimicrobial_class_selectors.html">carbapenems</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> 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">#></span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</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> <span style="color: #949494;"># An Antibiogram (non-WISCA): 5 × 3</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Pathogen Imipenem Meropenem </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</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;"><chr></span> </span>
|
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@ -410,8 +410,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Escherichia coli 100% (422/422) 100% (418/418)</span>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae 100% (51/51) 100% (53/53) </span>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> Proteus mirabilis 94% (30/32) <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> # Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
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<span class="r-in"><span><span class="co"># Combined antibiogram -------------------------------------------------</span></span></span>
|
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@ -429,8 +429,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ abbreviated names: ¹`Piperacillin/tazobactam`,</span></span>
|
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ²`Piperacillin/tazobactam + Gentamicin`,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ³`Piperacillin/tazobactam + Tobramycin`</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> # Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># names of antibiotics do not need to resemble columns exactly:</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">antibiogram</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
|
||||
@ -444,8 +444,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</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;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Gram-negative 91% (621/684) 99% (684/694) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> Gram-positive 77% (560/724) 93% (784/847) </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> # Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># Syndromic antibiogram ------------------------------------------------</span></span></span>
|
||||
@ -455,9 +455,9 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
|
||||
<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="antimicrobial_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>, <span class="fu"><a href="antimicrobial_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">#></span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For carbapenems() using columns 'IPM' (imipenem) and 'MEM' (meropenem)</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-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> <span style="color: #949494;"># An Antibiogram (non-WISCA): 14 × 8</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> `Syndromic Group` Pathogen Amikacin Gentamicin Imipenem Kanamycin Meropenem</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</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;"><chr></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;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
@ -476,12 +476,12 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> Clinical S. pneumo… 0% (0/7… 0% (0/78) <span style="color: #BB0000;">NA</span> 0% (0/78) <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">14</span> ICU S. pneumo… 0% (0/3… 0% (0/30) <span style="color: #BB0000;">NA</span> 0% (0/30) <span style="color: #BB0000;">NA</span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 1 more variable: Tobramycin <chr></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> # Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># now define a data set with only E. coli</span></span></span>
|
||||
<span class="r-in"><span><span class="va">ex1</span> <span class="op"><-</span> <span class="va">example_isolates</span><span class="op">[</span><span class="fu"><a href="https://rdrr.io/r/base/which.html" class="external-link">which</a></span><span class="op">(</span><span class="fu"><a href="mo_property.html">mo_genus</a></span><span class="op">(</span><span class="op">)</span> <span class="op">==</span> <span class="st">"Escherichia"</span><span class="op">)</span>, <span class="op">]</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_genus()</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> <span style="color: #0000BB;">ℹ Using column '</span><span style="color: #0000BB; font-weight: bold;">mo</span><span style="color: #0000BB;">' as input for </span><span style="color: #0000BB; background-color: #EEEEEE;">mo_genus()</span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># with a custom language, though this will be determined automatically</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># (i.e., this table will be in Spanish on Spanish systems)</span></span></span>
|
||||
@ -493,15 +493,15 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
|
||||
<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">#></span> ℹ For aminoglycosides() using columns 'GEN' (gentamicin), 'TOB'</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> (tobramycin), 'AMK' (amikacin), and 'KAN' (kanamycin)</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;"># An Antibiogram (non-WISCA): 2 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> `Grupo sindrómico` Patógeno Amikacina Gentamicina Tobramicina </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</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;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> No UCI E. coli 100% (119/119) 98% (316/323) 98% (318/325)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> UCI E. coli 100% (52/52) 99% (135/137) 96% (132/137)</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> # Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># WISCA antibiogram ----------------------------------------------------</span></span></span>
|
||||
@ -520,8 +520,8 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ abbreviated names: ¹`Piperacillin/tazobactam`,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ²`Piperacillin/tazobactam + Gentamicin`,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ³`Piperacillin/tazobactam + Tobramycin`</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> # Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> # or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># Use `plot()` or `ggplot2::autoplot()` to create a plot of this antibiogram,</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># or use it directly in R Markdown or https://quarto.org, see ?antibiogram</span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># Print the output for R Markdown / Quarto -----------------------------</span></span></span>
|
||||
@ -531,7 +531,7 @@ $$p_i = \frac{x_i}{\sum_{j=1}^K x_j}$$</p>
|
||||
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
|
||||
<span class="r-in"><span> wisca <span class="op">=</span> <span class="cn">TRUE</span></span></span>
|
||||
<span class="r-in"><span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ For ureidopenicillins() using column 'TZP' (piperacillin/tazobactam)</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;">ureidopenicillins()</span><span style="color: #0000BB;"> using column '</span><span style="color: #0000BB; font-weight: bold;">TZP</span><span style="color: #0000BB;">' (piperacillin/tazobactam)</span></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>
|
||||
|
||||
Reference in New Issue
Block a user