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@@ -10,7 +10,7 @@
<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="">1.8.1.9030</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.1.9045</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">
@@ -158,7 +158,7 @@
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
<dl><dt>x</dt>
<dd><p>data with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd>
<dd><p>a data set with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd>
<dt>col_mo</dt>
@@ -229,351 +229,79 @@
<span class="r-in"><span><span class="va">x</span> <span class="op">&lt;-</span> <span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for `col_mo`.</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/utils/head.html" class="external-link">head</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S I R total</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 (unknown species) PEN 14 0 1 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 (unknown species) OXA 0 0 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 (unknown species) FLC 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 (unknown species) AMX 15 0 1 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 (unknown species) AMC 15 0 0 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 (unknown species) AMP 15 0 1 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 6 × 6</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S I R total</span>
<span class="r-out co"><span class="r-pr">#&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;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> (unknown species) PEN 14 0 1 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> (unknown species) OXA 0 0 1 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> (unknown species) FLC 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> (unknown species) AMX 15 0 1 16</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">5</span> (unknown species) AMC 15 0 0 15</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">6</span> (unknown species) AMP 15 0 1 16</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Use 'format()' on this result to get a publishable/printable format.</span>
<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>
<span class="r-out co"><span class="r-pr">#&gt;</span> Group Drug</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Aminoglycosides Amikacin (J01GB06)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 Gentamicin (J01GB03)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 Kanamycin (J01GB04)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 Tobramycin (J01GB01)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 Amphenicols Chloramphenicol (J01BA01)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 Antimycobacterials Rifampicin (J04AB02)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 Beta-lactams/penicillins Amoxicillin (J01CA04)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 Amoxicillin/clavulanic acid (J01CR02)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 Ampicillin (J01CA01)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 Benzylpenicillin (J01CE01)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 11 Flucloxacillin (J01CF05)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 12 Oxacillin (J01CF04)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 13 Piperacillin/tazobactam (J01CR05)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 14 Carbapenems Imipenem (J01DH51)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 15 Meropenem (J01DH02)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 16 Cephalosporins (1st gen.) Cefazolin (J01DB04)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 17 Cephalosporins (2nd gen.) Cefoxitin (J01DC01)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 18 Cefuroxime (J01DC02)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 19 Cephalosporins (3rd gen.) Cefotaxime (J01DD01)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 20 Ceftazidime (J01DD02)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 21 Ceftriaxone (J01DD04)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 22 Cephalosporins (4th gen.) Cefepime (J01DE01)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 23 Glycopeptides Teicoplanin (J01XA02)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24 Vancomycin (J01XA01)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 25 Macrolides/lincosamides Azithromycin (J01FA10)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 26 Clindamycin (J01FF01)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 27 Erythromycin (J01FA01)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 28 Other antibacterials Fosfomycin (J01XX01)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 29 Mupirocin (D06AX09)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 30 Nitrofurantoin (J01XE01)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 31 Oxazolidinones Linezolid (J01XX08)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 32 Polymyxins Colistin (J01XB01)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 33 Quinolones Ciprofloxacin (J01MA02)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 34 Moxifloxacin (J01MA14)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 35 Tetracyclines Doxycycline (J01AA02)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 36 Tetracycline (J01AA07)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 37 Tigecycline (J01AA12)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 38 Trimethoprims Trimethoprim (J01EA01)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 39 Trimethoprim/sulfamethoxazole (J01EE01)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> CoNS E. coli E. faecalis K. pneumoniae</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 100.0% (43/43) 0.0% (0/171) 100.0% (39/39) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 13.6% (42/309) 2.0% (9/460) 100.0% (39/39) 10.3% (6/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 100.0% (43/43) 100.0% (39/39) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 78.2% (43/55) 2.6% (12/462) 100.0% (39/39) 10.3% (6/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 100.0% (467/467) 100.0% (58/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 93.0% (132/142) 50.0% (196/392) 100.0% (58/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 42.6% (132/310) 13.1% (61/467) 10.3% (6/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 93.0% (132/142) 50.0% (196/392) 100.0% (58/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 77.6% (228/294) 100.0% (467/467) 100.0% (58/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 11 42.8% (134/313) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 12 54.8% (34/62) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 13 69.7% (23/33) 5.5% (23/416) 11.3% (6/53)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 14 47.9% (23/48) 0.0% (0/422) 0.0% (0/38) 0.0% (0/51)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 15 47.9% (23/48) 0.0% (0/418) 0.0% (0/53)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 16 47.9% (23/48) 2.4% (2/82) 100.0% (39/39) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 17 47.9% (23/48) 6.9% (26/377) 100.0% (39/39) 2.2% (1/46)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 18 42.6% (133/312) 5.4% (25/465) 100.0% (39/39) 10.3% (6/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 19 47.9% (23/48) 2.4% (11/459) 100.0% (39/39) 5.2% (3/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 20 100.0% (313/313) 2.4% (11/460) 100.0% (39/39) 5.2% (3/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 21 47.9% (23/48) 2.4% (11/459) 100.0% (39/39) 5.2% (3/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 22 47.9% (23/48) 2.8% (9/317) 100.0% (39/39) 5.3% (2/38)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 23 100.0% (467/467) 100.0% (58/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24 0.3% (1/304) 100.0% (467/467) 0.0% (0/39) 100.0% (58/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 25 44.1% (138/313) 100.0% (467/467) 100.0% (39/39) 100.0% (58/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 26 33.5% (59/176) 100.0% (467/467) 100.0% (39/39) 100.0% (58/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 27 44.1% (138/313) 100.0% (467/467) 100.0% (39/39) 100.0% (58/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 28 0.0% (0/61) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 29 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 30 2.8% (13/458) 19.0% (11/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 31 100.0% (467/467) 100.0% (58/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 32 100.0% (313/313) 0.0% (0/240) 100.0% (39/39) 5.9% (2/34)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 33 27.4% (69/252) 12.5% (57/456) 3.6% (2/55)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 34 100.0% (57/57) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 35 22.2% (67/302) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 36 22.5% (59/262) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 37 0.0% (0/195) 0.0% (0/68) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 38 41.4% (126/304) 39.1% (155/396) 100.0% (39/39) 18.4% (9/49)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 39 12.2% (30/246) 31.6% (147/465) 100.0% (39/39) 10.3% (6/58)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> P. aeruginosa P. mirabilis S. aureus S. epidermidis</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 100.0% (44/44)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 0.0% (0/30) 5.9% (2/34) 0.9% (2/233) 21.5% (35/163)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 100.0% (30/30) 100.0% (44/44)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 0.0% (0/30) 5.9% (2/34) 2.3% (2/86) 49.4% (44/89)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 100.0% (30/30) 0.0% (0/46) 3.1% (1/32)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 100.0% (30/30) 100.0% (36/36) 0.0% (0/108) 2.7% (2/73)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 100.0% (30/30) 93.9% (123/131) 98.9% (90/91)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 100.0% (30/30) 2.8% (1/36) 0.4% (1/235) 54.5% (90/165)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 100.0% (30/30) 93.9% (123/131) 98.9% (90/91)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 100.0% (30/30) 100.0% (36/36) 80.9% (123/152) 89.4% (93/104)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 11 0.4% (1/235) 55.7% (97/174)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 12 0.0% (0/99) 50.0% (37/74)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 13 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 14 6.3% (2/32) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 15 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 16 100.0% (30/30) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 17 100.0% (30/30) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 18 100.0% (30/30) 0.0% (0/36) 0.4% (1/235) 56.1% (97/173)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 19 100.0% (30/30) 0.0% (0/36) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 20 3.3% (1/30) 0.0% (0/36) 100.0% (235/235) 100.0% (174/174)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 21 100.0% (30/30) 0.0% (0/36) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 22 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 23 100.0% (30/30) 100.0% (36/36) 0.0% (0/80) 64.1% (25/39)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24 100.0% (30/30) 100.0% (36/36) 0.0% (0/232) 0.0% (0/171)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 25 100.0% (30/30) 100.0% (36/36) 8.9% (21/235) 53.8% (93/173)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 26 100.0% (30/30) 100.0% (36/36) 6.0% (9/151) 37.5% (42/112)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 27 100.0% (30/30) 100.0% (36/36) 8.9% (21/235) 53.8% (93/173)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 28 0.0% (0/80) 21.9% (14/64)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 29 0.0% (0/84) 8.7% (6/69)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 30 100.0% (36/36) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 31 100.0% (30/30) 100.0% (36/36) 0.0% (0/82) 0.0% (0/68)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 32 100.0% (36/36) 100.0% (235/235) 100.0% (174/174)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 33 0.0% (0/30) 5.6% (2/36) 10.5% (20/191) 36.0% (49/136)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 34 2.2% (1/46) 0.0% (0/31)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 35 100.0% (30/30) 100.0% (36/36) 3.0% (7/231) 32.4% (55/170)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 36 100.0% (30/30) 100.0% (36/36) 3.2% (7/217) 32.9% (55/167)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 37 100.0% (30/30) 100.0% (36/36) 0.0% (0/209) 0.0% (0/109)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 38 100.0% (30/30) 36.4% (12/33) 8.4% (13/155) 58.5% (69/118)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 39 100.0% (30/30) 25.0% (9/36) 3.9% (9/231) 17.5% (24/137)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> S. hominis S. pneumoniae</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 100.0% (117/117)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 7.5% (6/80) 100.0% (117/117)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 100.0% (117/117)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 14.5% (9/62) 100.0% (117/117)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 6.5% (2/31) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 0.0% (0/61) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 0.0% (0/112)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 35.0% (28/80) 0.0% (0/112)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 0.0% (0/112)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 0.0% (0/117)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 11 34.6% (28/81) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 12 39.7% (23/58) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 13 0.0% (0/112)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 14 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 15 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 17 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 18 33.3% (27/81) 0.0% (0/61)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 19 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 20 100.0% (81/81) 100.0% (117/117)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 21 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 22 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 23 6.8% (4/59) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24 0.0% (0/81) 0.0% (0/94)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 25 40.7% (33/81) 7.8% (9/116)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 26 29.4% (20/68) 6.5% (4/62)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 27 40.7% (33/81) 7.8% (9/116)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 28 100.0% (59/59) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 29 1.6% (1/61) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 30 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 31 0.0% (0/60) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 32 100.0% (81/81) 100.0% (117/117)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 33 20.0% (14/70) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 34 0.0% (0/32) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 35 55.0% (44/80) 4.5% (5/112)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 36 54.3% (44/81) 4.7% (5/106)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 37 0.0% (0/36) </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 38 57.9% (22/38) 17.9% (17/95)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 39 24.7% (20/81) 7.3% (8/109)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 39 × 12</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&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 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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</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>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 29 more rows, 2 more variables: `S. hominis` &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># `S. pneumoniae` &lt;chr&gt;, and abbreviated variable names ¹​`E. coli`,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ²​`E. faecalis`, ³​`K. pneumoniae`, ⁴​`P. aeruginosa`, ⁵​`P. mirabilis`,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ⁶​`S. aureus`, ⁷​`S. epidermidis`</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># Use FUN to change to transformation of microorganism codes</span></span></span>
<span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>, </span></span>
<span class="r-in"><span> FUN <span class="op">=</span> <span class="va">mo_gramstain</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Using column 'mo' as input for `col_mo`.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S I R total</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Gram-negative PEN 8 0 717 725</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 Gram-negative OXA 6 0 0 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 Gram-negative FLC 6 0 0 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 Gram-negative AMX 226 0 405 631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 Gram-negative AMC 463 89 174 726</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 Gram-negative AMP 226 0 405 631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 Gram-negative TZP 554 11 76 641</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 Gram-negative CZO 94 2 110 206</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 Gram-negative FEP 470 1 14 485</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 Gram-negative CXM 539 22 142 703</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 11 Gram-negative FOX 435 8 135 578</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 12 Gram-negative CTX 578 1 57 636</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 13 Gram-negative CAZ 607 0 27 634</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 14 Gram-negative CRO 578 1 57 636</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 15 Gram-negative GEN 651 8 25 684</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 16 Gram-negative TOB 651 7 28 686</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 17 Gram-negative AMK 251 0 5 256</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 18 Gram-negative KAN 0 0 35 35</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 19 Gram-negative TMP 364 1 223 588</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 20 Gram-negative SXT 506 0 197 703</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 21 Gram-negative NIT 491 51 122 664</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 22 Gram-negative FOS 71 0 7 78</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 23 Gram-negative LNZ 0 0 707 707</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24 Gram-negative CIP 610 11 63 684</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 25 Gram-negative MFX 0 0 63 63</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 26 Gram-negative VAN 0 0 707 707</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 27 Gram-negative TEC 0 0 707 707</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 28 Gram-negative TCY 15 1 110 126</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 29 Gram-negative TGC 87 0 101 188</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 30 Gram-negative DOX 10 0 108 118</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 31 Gram-negative ERY 1 2 696 699</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 32 Gram-negative CLI 18 1 709 728</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 33 Gram-negative AZM 1 2 696 699</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 34 Gram-negative IPM 616 10 5 631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 35 Gram-negative MEM 624 0 2 626</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 36 Gram-negative MTR 21 0 2 23</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 37 Gram-negative CHL 1 0 30 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 38 Gram-negative COL 309 0 78 387</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 39 Gram-negative MUP 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 40 Gram-negative RIF 1 0 695 696</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 41 Gram-positive PEN 395 11 483 889</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 42 Gram-positive OXA 245 0 113 358</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 43 Gram-positive FLC 659 0 278 937</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 44 Gram-positive AMX 302 3 398 703</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 45 Gram-positive AMC 864 2 272 1138</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 46 Gram-positive AMP 302 3 398 703</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 47 Gram-positive TZP 294 2 49 345</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 48 Gram-positive CZO 151 0 89 240</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 49 Gram-positive FEP 150 0 89 239</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 50 Gram-positive CXM 756 0 328 1084</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 51 Gram-positive FOX 151 0 89 240</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 52 Gram-positive CTX 218 0 89 307</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 53 Gram-positive CAZ 0 0 1177 1177</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 54 Gram-positive CRO 218 0 89 307</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 55 Gram-positive GEN 721 19 430 1170</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 56 Gram-positive TOB 228 0 437 665</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 57 Gram-positive AMK 0 0 436 436</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 58 Gram-positive KAN 0 0 436 436</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 59 Gram-positive TMP 553 9 343 905</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 60 Gram-positive SXT 883 6 163 1052</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 61 Gram-positive NIT 73 0 5 78</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 62 Gram-positive FOS 132 0 141 273</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 63 Gram-positive LNZ 312 0 2 314</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 64 Gram-positive CIP 502 58 164 724</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 65 Gram-positive MFX 136 4 8 148</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 66 Gram-positive VAN 1141 0 5 1146</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 67 Gram-positive TEC 237 0 32 269</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 68 Gram-positive TCY 800 22 245 1067</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 69 Gram-positive TGC 610 0 0 610</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 70 Gram-positive DOX 802 7 206 1015</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 71 Gram-positive ERY 797 7 385 1189</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 72 Gram-positive CLI 556 3 220 779</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 73 Gram-positive AZM 797 7 385 1189</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 74 Gram-positive IPM 207 0 50 257</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 75 Gram-positive MEM 156 0 47 203</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 76 Gram-positive MTR 1 0 2 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 77 Gram-positive CHL 120 0 3 123</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 78 Gram-positive COL 0 0 1237 1237</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 79 Gram-positive MUP 251 3 16 270</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 80 Gram-positive RIF 301 2 3 306</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Use 'format()' on this result to get a publishable/printable format.</span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> FUN <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">x</span> <span class="op">==</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> <span class="st">"E. coli"</span>,</span></span>
<span class="r-in"><span> <span class="st">"Others"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-in"><span> FUN <span class="op">=</span> <span class="va">mo_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 Using column 'mo' as input for `col_mo`.</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> coli). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S I R total</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 E. coli PEN 0 0 467 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 E. coli OXA 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 E. coli FLC 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 E. coli AMX 196 0 196 392</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 E. coli AMC 332 74 61 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 E. coli AMP 196 0 196 392</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 E. coli TZP 388 5 23 416</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 E. coli CZO 79 1 2 82</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 E. coli FEP 308 0 9 317</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 E. coli CXM 425 15 25 465</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 11 E. coli FOX 347 4 26 377</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 12 E. coli CTX 448 0 11 459</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 13 E. coli CAZ 449 0 11 460</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 14 E. coli CRO 448 0 11 459</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 15 E. coli GEN 451 0 9 460</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 16 E. coli TOB 450 0 12 462</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 17 E. coli AMK 171 0 0 171</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 18 E. coli KAN 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 19 E. coli TMP 241 0 155 396</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 20 E. coli SXT 318 0 147 465</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 21 E. coli NIT 429 16 13 458</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 22 E. coli FOS 61 0 0 61</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 23 E. coli LNZ 0 0 467 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 24 E. coli CIP 398 1 57 456</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 25 E. coli MFX 0 0 57 57</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 26 E. coli VAN 0 0 467 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 27 E. coli TEC 0 0 467 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 28 E. coli TCY 1 0 2 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 29 E. coli TGC 68 0 0 68</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 30 E. coli DOX 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 31 E. coli ERY 0 0 467 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 32 E. coli CLI 0 0 467 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 33 E. coli AZM 0 0 467 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 34 E. coli IPM 422 0 0 422</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 35 E. coli MEM 418 0 0 418</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 36 E. coli MTR 2 0 0 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 37 E. coli CHL 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 38 E. coli COL 240 0 0 240</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 39 E. coli MUP 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 40 E. coli RIF 0 0 467 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 41 Others PEN 417 11 734 1162</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 42 Others OXA 251 0 114 365</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 43 Others FLC 665 0 278 943</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 44 Others AMX 347 3 608 958</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 45 Others AMC 1010 17 385 1412</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 46 Others AMP 347 3 608 958</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 47 Others TZP 474 8 103 585</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 48 Others CZO 166 1 197 364</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 49 Others FEP 312 1 94 407</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 50 Others CXM 872 7 445 1324</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 51 Others FOX 239 4 198 441</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 52 Others CTX 348 1 135 484</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 53 Others CAZ 158 0 1193 1351</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 54 Others CRO 348 1 135 484</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 55 Others GEN 921 27 447 1395</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 56 Others TOB 429 7 453 889</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 57 Others AMK 80 0 441 521</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 58 Others KAN 0 0 471 471</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 59 Others TMP 677 10 416 1103</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 60 Others SXT 1074 6 214 1294</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 61 Others NIT 136 35 114 285</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 62 Others FOS 142 0 148 290</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 63 Others LNZ 314 0 242 556</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 64 Others CIP 714 68 171 953</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 65 Others MFX 136 4 14 154</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 66 Others VAN 1149 0 245 1394</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 67 Others TEC 237 0 272 509</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 68 Others TCY 819 23 355 1197</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 69 Others TGC 629 0 101 730</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 70 Others DOX 814 7 315 1136</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 71 Others ERY 801 9 617 1427</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 72 Others CLI 586 4 463 1053</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 73 Others AZM 801 9 617 1427</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 74 Others IPM 402 10 55 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 75 Others MEM 362 0 49 411</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 76 Others MTR 27 0 5 32</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 77 Others CHL 121 0 33 154</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 78 Others COL 69 0 1331 1400</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 79 Others MUP 251 3 16 270</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 80 Others RIF 303 2 231 536</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 80 × 6</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S I R total</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;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> Gram-negative PEN 8 0 717 725</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> Gram-negative OXA 6 0 0 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> Gram-negative FLC 6 0 0 6</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> Gram-negative AMX 226 0 405 631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> Gram-negative AMC 463 89 174 726</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> Gram-negative AMP 226 0 405 631</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> Gram-negative TZP 554 11 76 641</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> Gram-negative CZO 94 2 110 206</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> Gram-negative FEP 470 1 14 485</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> Gram-negative CXM 539 22 142 703</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 70 more rows</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Use 'format()' on this result to get a publishable/printable format.</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">bug_drug_combinations</span><span class="op">(</span><span class="va">example_isolates</span>,</span></span>
<span class="r-in"><span> FUN <span class="op">=</span> <span class="kw">function</span><span class="op">(</span><span class="va">x</span><span class="op">)</span> <span class="op">{</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/ifelse.html" class="external-link">ifelse</a></span><span class="op">(</span><span class="va">x</span> <span class="op">==</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"Escherichia coli"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> <span class="st">"E. coli"</span>,</span></span>
<span class="r-in"><span> <span class="st">"Others"</span></span></span>
<span class="r-in"><span> <span class="op">)</span></span></span>
<span class="r-in"><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 Using column 'mo' as input for `col_mo`.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 80 × 6</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab S I R total</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;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> E. coli PEN 0 0 467 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> E. coli OXA 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> E. coli FLC 0 0 0 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> E. coli AMX 196 0 196 392</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> E. coli AMC 332 74 61 467</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> E. coli AMP 196 0 196 392</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> E. coli TZP 388 5 23 416</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> E. coli CZO 79 1 2 82</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> E. coli FEP 308 0 9 317</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> E. coli CXM 425 15 25 465</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 70 more rows</span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Use 'format()' on this result to get a publishable/printable format.</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>