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@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9004</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.0.0.9005</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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@ -247,13 +247,13 @@
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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: #949494;"># … with 1,990 more rows, and 36 more variables: AMC <sir>, AMP <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TZP <sir>, CZO <sir>, FEP <sir>, CXM <sir>, FOX <sir>, CTX <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CAZ <sir>, CRO <sir>, GEN <sir>, TOB <sir>, AMK <sir>, KAN <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TMP <sir>, SXT <sir>, NIT <sir>, FOS <sir>, LNZ <sir>, CIP <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># MFX <sir>, VAN <sir>, TEC <sir>, TCY <sir>, TGC <sir>, DOX <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ERY <sir>, CLI <sir>, AZM <sir>, IPM <sir>, MEM <sir>, MTR <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># CHL <sir>, COL <sir>, MUP <sir>, RIF <sir></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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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># TOB <sir>, AMK <sir>, KAN <sir>, TMP <sir>, SXT <sir>, NIT <sir>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># FOS <sir>, LNZ <sir>, CIP <sir>, MFX <sir>, VAN <sir>, TEC <sir>,</span></span>
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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></span>
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<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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<span class="r-in"><span><span class="va">x</span> <span class="op"><-</span> <span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
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@ -270,22 +270,21 @@
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<span class="r-msg co"><span class="r-pr">#></span> Use 'format()' on this result to get a publishable/printable format.</span>
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<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/format.html" class="external-link">format</a></span><span class="op">(</span><span class="va">x</span>, translate_ab <span class="op">=</span> <span class="st">"name (atc)"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 39 × 12</span></span>
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<span class="r-out co"><span class="r-pr">#></span> Group Drug CoNS E. co…¹ E. fa…² K. pn…³ P. ae…⁴ P. mi…⁵ S. au…⁶ S. ep…⁷</span>
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<span class="r-out co"><span class="r-pr">#></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 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> <span style="color: #949494;">"</span>Aminogl… Amik… <span style="color: #949494;">"</span>100… <span style="color: #949494;">"</span> 0.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">""</span> Gent… <span style="color: #949494;">"</span> 13… <span style="color: #949494;">"</span> 2.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span> 10.3… <span style="color: #949494;">"</span> 0.0… <span style="color: #949494;">"</span> 5.9… <span style="color: #949494;">"</span> 0.9… <span style="color: #949494;">"</span> 21.5…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">""</span> Kana… <span style="color: #949494;">"</span>100… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">""</span> Tobr… <span style="color: #949494;">"</span> 78… <span style="color: #949494;">"</span> 2.6… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span> 10.3… <span style="color: #949494;">"</span> 0.0… <span style="color: #949494;">"</span> 5.9… <span style="color: #949494;">"</span> 2.3… <span style="color: #949494;">"</span> 49.4…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">"</span>Ampheni… Chlo… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 0.0… <span style="color: #949494;">"</span> 3.1…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">"</span>Antimyc… Rifa… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span> 0.0… <span style="color: #949494;">"</span> 2.7…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">"</span>Beta-la… Amox… <span style="color: #949494;">"</span> 93… <span style="color: #949494;">"</span> 50.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 93.9… <span style="color: #949494;">"</span> 98.9…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">""</span> Amox… <span style="color: #949494;">"</span> 42… <span style="color: #949494;">"</span> 13.1… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 10.3… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span> 2.8… <span style="color: #949494;">"</span> 0.4… <span style="color: #949494;">"</span> 54.5…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">""</span> Ampi… <span style="color: #949494;">"</span> 93… <span style="color: #949494;">"</span> 50.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 93.9… <span style="color: #949494;">"</span> 98.9…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">""</span> Benz… <span style="color: #949494;">"</span> 77… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span>100.0… <span style="color: #949494;">"</span> 80.9… <span style="color: #949494;">"</span> 89.4…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 29 more rows, 2 more variables: `S. hominis` <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `S. pneumoniae` <chr>, and abbreviated variable names ¹`E. coli`,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ²`E. faecalis`, ³`K. pneumoniae`, ⁴`P. aeruginosa`, ⁵`P. mirabilis`,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ⁶`S. aureus`, ⁷`S. epidermidis`</span></span>
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<span class="r-out co"><span class="r-pr">#></span> Group Drug CoNS `E. coli` `E. faecalis` `K. pneumoniae` `P. aeruginosa`</span>
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<span class="r-out co"><span class="r-pr">#></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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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">"</span>Aminogl… Amik… <span style="color: #949494;">"</span>100… <span style="color: #949494;">"</span> 0.0% … <span style="color: #949494;">"</span>100.0% (39/… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">""</span> Gent… <span style="color: #949494;">"</span> 13… <span style="color: #949494;">"</span> 2.0% … <span style="color: #949494;">"</span>100.0% (39/… <span style="color: #949494;">"</span> 10.3% (6/58)<span style="color: #949494;">"</span> <span style="color: #949494;">"</span> 0.0% (0/30)<span style="color: #949494;">"</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">""</span> Kana… <span style="color: #949494;">"</span>100… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0% (39/… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0% (30/30…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">""</span> Tobr… <span style="color: #949494;">"</span> 78… <span style="color: #949494;">"</span> 2.6% … <span style="color: #949494;">"</span>100.0% (39/… <span style="color: #949494;">"</span> 10.3% (6/58)<span style="color: #949494;">"</span> <span style="color: #949494;">"</span> 0.0% (0/30)<span style="color: #949494;">"</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">"</span>Ampheni… Chlo… <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0% (30/30…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">"</span>Antimyc… Rifa… <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0% … <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0% (58/58… <span style="color: #949494;">"</span>100.0% (30/30…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">"</span>Beta-la… Amox… <span style="color: #949494;">"</span> 93… <span style="color: #949494;">"</span> 50.0% … <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0% (58/58… <span style="color: #949494;">"</span>100.0% (30/30…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">""</span> Amox… <span style="color: #949494;">"</span> 42… <span style="color: #949494;">"</span> 13.1% … <span style="color: #949494;">""</span> <span style="color: #949494;">"</span> 10.3% (6/58)<span style="color: #949494;">"</span> <span style="color: #949494;">"</span>100.0% (30/30…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">""</span> Ampi… <span style="color: #949494;">"</span> 93… <span style="color: #949494;">"</span> 50.0% … <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0% (58/58… <span style="color: #949494;">"</span>100.0% (30/30…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">""</span> Benz… <span style="color: #949494;">"</span> 77… <span style="color: #949494;">"</span>100.0% … <span style="color: #949494;">""</span> <span style="color: #949494;">"</span>100.0% (58/58… <span style="color: #949494;">"</span>100.0% (30/30…</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 29 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 5 more variables: `P. mirabilis` <chr>, `S. aureus` <chr>,</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># `S. epidermidis` <chr>, `S. hominis` <chr>, `S. pneumoniae` <chr></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># Use FUN to change to transformation of microorganism codes</span></span></span>
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<span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
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@ -304,7 +303,7 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Gram-negative CIP 610 11 63 684</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Gram-negative CLI 18 1 709 728</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Gram-negative COL 309 0 78 387</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 70 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 70 more rows</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> Use 'format()' on this result to get a publishable/printable format.</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
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@ -328,7 +327,7 @@
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> E. coli CIP 398 1 57 456</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> E. coli CLI 0 0 467 467</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> E. coli COL 240 0 0 240</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with 70 more rows</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 70 more rows</span></span>
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<span class="r-msg co"><span class="r-pr">#></span> Use 'format()' on this result to get a publishable/printable format.</span>
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<span class="r-in"><span><span class="co"># }</span></span></span>
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</code></pre></div>
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