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Built site for AMR: 1.8.2.9118@c51fb24
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@@ -14,7 +14,7 @@
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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="">1.8.2.9115</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9118</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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@@ -338,18 +338,18 @@
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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> ℹ 502 combinations had less than minimum = 30 results and were ignored</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 10 × 7</span></span>
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<span class="r-out co"><span class="r-pr">#></span> `Pathogen (N min-max)` AMK GEN IPM KAN MEM TOB</span>
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<span class="r-out co"><span class="r-pr">#></span> `Pathogen (N min-max)` S S1 S2 S3 S4 S5</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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> CoNS (43-309) 0 86 52 0 52 22</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> E. coli (0-462) 100 98 100 <span style="color: #BB0000;">NA</span> 100 97</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> E. faecalis (0-39) 0 0 100 0 <span style="color: #BB0000;">NA</span> 0</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> K. pneumoniae (0-58) <span style="color: #BB0000;">NA</span> 90 100 <span style="color: #BB0000;">NA</span> 100 90</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> P. aeruginosa (17-30) <span style="color: #BB0000;">NA</span> 100 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 100</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> P. mirabilis (0-34) <span style="color: #BB0000;">NA</span> 94 94 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 94</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> S. aureus (2-233) <span style="color: #BB0000;">NA</span> 99 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 98</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> S. epidermidis (8-163) 0 79 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 51</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> S. hominis (3-80) <span style="color: #BB0000;">NA</span> 92 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 85</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> S. pneumoniae (11-117) 0 0 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 0</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> CoNS (43-309) 86 22 0 0 52 52</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> E. coli (0-462) 98 97 100 <span style="color: #BB0000;">NA</span> 100 100</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> E. faecalis (0-39) 0 0 0 0 100 <span style="color: #BB0000;">NA</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> K. pneumoniae (0-58) 90 90 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 100 100</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> P. aeruginosa (17-30) 100 100 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> P. mirabilis (0-34) 94 94 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 94 <span style="color: #BB0000;">NA</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> S. aureus (2-233) 99 98 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> S. epidermidis (8-163) 79 51 0 0 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> S. hominis (3-80) 92 85 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> S. pneumoniae (11-117) 0 0 0 0 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</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="antibiotic_class_selectors.html">aminoglycosides</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
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@@ -358,11 +358,29 @@
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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 4 combinations had less than minimum = 30 results and were ignored</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 5</span></span>
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<span class="r-out co"><span class="r-pr">#></span> `Pathogen (N min-max)` 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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Gram-negative (35-686) 96 96 0 98</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> Gram-positive (436-1170) 34 63 0 0</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S".</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S1".</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S2".</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S3".</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S1".</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S2".</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S3".</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>there are records with missing times, which will be dropped.</span>
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||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>multiple rows match for ab=NA: first taken</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 2</span></span>
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<span class="r-out co"><span class="r-pr">#></span> `Pathogen (N min-max)` `NA`</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;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Gram-negative (35-686) 96</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> Gram-positive (436-1170) 63</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="antibiotic_class_selectors.html">carbapenems</a></span><span class="op">(</span><span class="op">)</span>,</span></span>
|
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@@ -370,14 +388,32 @@
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<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"name"</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> ℹ 172 combinations had less than minimum = 30 results and were ignored</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 5 × 3</span></span>
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<span class="r-out co"><span class="r-pr">#></span> `Pathogen (N min-max)` Imipenem Meropenem</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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Coagulase-negative Staphylococcus (CoNS) (48-48) 52 52</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> Enterococcus faecalis (0-38) 100 <span style="color: #BB0000;">NA</span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Escherichia coli (418-422) 100 100</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae (51-53) 100 100</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> Proteus mirabilis (27-32) 94 <span style="color: #BB0000;">NA</span></span>
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<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S1".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S1".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S1".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>there are records with missing times, which will be dropped.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>multiple rows match for ab=NA: first taken</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 5 × 2</span></span>
|
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<span class="r-out co"><span class="r-pr">#></span> `Pathogen (N min-max)` `NA`</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;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Coagulase-negative Staphylococcus (CoNS) (48-48) 52</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> Enterococcus faecalis (0-38) 100</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> Escherichia coli (418-422) 100</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> Klebsiella pneumoniae (51-53) 100</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">5</span> Proteus mirabilis (27-32) 94</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># Combined antibiogram -------------------------------------------------</span></span></span>
|
||||
@@ -388,10 +424,10 @@
|
||||
<span class="r-in"><span> mo_transform <span class="op">=</span> <span class="st">"gramstain"</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ 3 combinations had less than minimum = 30 results and were ignored</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 4</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> `Pathogen (N min-max)` TZP `TZP + GEN` `TZP + TOB`</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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Gram-negative (641-693) 88 99 98</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> Gram-positive (345-1044) 86 98 95</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> `Pathogen (N min-max)` S S1 S2</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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Gram-negative (641-693) 88 98 99</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> Gram-positive (345-1044) 86 95 98</span>
|
||||
<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="https://rdrr.io/r/base/c.html" class="external-link">c</a></span><span class="op">(</span><span class="st">"TZP"</span>, <span class="st">"TZP+TOB"</span><span class="op">)</span>,</span></span>
|
||||
@@ -399,12 +435,21 @@
|
||||
<span class="r-in"><span> ab_transform <span class="op">=</span> <span class="st">"name"</span>,</span></span>
|
||||
<span class="r-in"><span> sep <span class="op">=</span> <span class="st">" & "</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ 2 combinations had less than minimum = 30 results and were ignored</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 3</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> `Pathogen (N min-max)` `Piperacillin/tazobactam` Piperacillin/tazobactam & …¹</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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Gram-negative (641-693) 88 98</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> Gram-positive (345-550) 86 95</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># … with abbreviated variable name ¹`Piperacillin/tazobactam & Tobramycin`</span></span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S1".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S1".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>there are records with missing times, which will be dropped.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>multiple rows match for ab=NA: first taken</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 2</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> `Pathogen (N min-max)` `NA`</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;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> Gram-negative (641-693) 88</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> Gram-positive (345-550) 86</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>
|
||||
@@ -418,22 +463,22 @@
|
||||
<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> ℹ 1581 combinations had less than minimum = 30 results and were ignored</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 14 × 8</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> `Syndromic Group` `Pathogen (N min-max)` AMK GEN IPM KAN MEM TOB</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> `Syndromic Group` `Pathogen (N min-max)` S S1 S2 S3 S4 S5</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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical CoNS (23-205) <span style="color: #BB0000;">NA</span> 89 57 <span style="color: #BB0000;">NA</span> 57 26</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ICU CoNS (10-73) <span style="color: #BB0000;">NA</span> 79 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Outpatient CoNS (3-31) <span style="color: #BB0000;">NA</span> 84 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical E. coli (0-299) 100 98 100 <span style="color: #BB0000;">NA</span> 100 98</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> ICU E. coli (0-137) 100 99 100 <span style="color: #BB0000;">NA</span> 100 96</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical K. pneumoniae (0-51) <span style="color: #BB0000;">NA</span> 92 100 <span style="color: #BB0000;">NA</span> 100 92</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical P. mirabilis (0-30) <span style="color: #BB0000;">NA</span> 100 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 100</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Clinical S. aureus (2-150) <span style="color: #BB0000;">NA</span> 99 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 97</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> ICU S. aureus (0-66) <span style="color: #BB0000;">NA</span> 100 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical S. epidermidis (4-79) <span style="color: #BB0000;">NA</span> 82 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 55</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> ICU S. epidermidis (4-75) <span style="color: #BB0000;">NA</span> 72 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 41</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Clinical S. hominis (1-45) <span style="color: #BB0000;">NA</span> 96 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 94</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> Clinical S. pneumoniae (5-78) 0 0 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">14</span> ICU S. pneumoniae (5-30) 0 0 <span style="color: #BB0000;">NA</span> 0 <span style="color: #BB0000;">NA</span> 0</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Clinical CoNS (23-205) 89 26 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 57 57</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> ICU CoNS (10-73) 79 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Outpatient CoNS (3-31) 84 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Clinical E. coli (0-299) 98 98 100 <span style="color: #BB0000;">NA</span> 100 100</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> ICU E. coli (0-137) 99 96 100 <span style="color: #BB0000;">NA</span> 100 100</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Clinical K. pneumoniae (0-51) 92 92 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> 100 100</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Clinical P. mirabilis (0-30) 100 100 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Clinical S. aureus (2-150) 99 97 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> ICU S. aureus (0-66) 100 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Clinical S. epidermidis (4-79) 82 55 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> ICU S. epidermidis (4-75) 72 41 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Clinical S. hominis (1-45) 96 94 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> Clinical S. pneumoniae (5-78) 0 0 0 0 <span style="color: #BB0000;">NA</span> <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. pneumoniae (5-30) 0 0 0 0 <span style="color: #BB0000;">NA</span> <span style="color: #BB0000;">NA</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>
|
||||
@@ -450,11 +495,27 @@
|
||||
<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 2 combinations had less than minimum = 30 results and were ignored</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 5</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> `Grupo sindrómico` `Patógeno (N min-max)` 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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> No UCI E. coli (0-325) 100 98 98</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> UCI E. coli (0-137) 100 99 96</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S1".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S2".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S1".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>in as.ab(): these values could not be coerced to a valid antimicrobial</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> ID: "S2".</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>there are records with missing times, which will be dropped.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>multiple rows match for ab=NA: first taken</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>there are records with missing times, which will be dropped.</span>
|
||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>multiple rows match for ab=NA: first taken</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 2 × 3</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> `Grupo sindrómico` `Patógeno (N min-max)` `NA`</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;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> No UCI E. coli (0-325) 98</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> UCI E. coli (0-137) 99</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># Weighted-incidence syndromic combination antibiogram (WISCA) ---------</span></span></span>
|
||||
@@ -469,12 +530,12 @@
|
||||
<span class="r-in"><span> <span class="st">"WISCA Group 1"</span>, <span class="st">"WISCA Group 2"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ 8 combinations had less than minimum = 10 results and were ignored</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 4 × 6</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> `Syndromic Group` `Pathogen (N min-max)` AMC `AMC + CIP` TZP `TZP + TOB`</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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> WISCA Group 1 Gram-negative (261-285) 76 95 89 99</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> WISCA Group 2 Gram-negative (380-442) 76 98 88 98</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> WISCA Group 1 Gram-positive (123-406) 76 89 81 95</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> WISCA Group 2 Gram-positive (222-732) 76 89 88 95</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> `Syndromic Group` `Pathogen (N min-max)` S S1 S2 S3</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;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">1</span> WISCA Group 1 Gram-negative (261-285) 76 95 89 99</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">2</span> WISCA Group 2 Gram-negative (380-442) 76 98 88 98</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">3</span> WISCA Group 1 Gram-positive (123-406) 76 89 81 95</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">4</span> WISCA Group 2 Gram-positive (222-732) 76 89 88 95</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># Generate plots with ggplot2 or base R --------------------------------</span></span></span>
|
||||
|
||||
Reference in New Issue
Block a user