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https://github.com/msberends/AMR.git
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Built site for AMR: 1.8.2.9007@b753b84
This commit is contained in:
github-actions
@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9006</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9007</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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@ -533,13 +533,13 @@
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
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<span class="r-in"><span><span class="co"># Becker classification, see ?as.mo ----------------------------------------</span></span></span>
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<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"Staph. epi"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Staphylococcus edaphicus"</span>
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<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"Staph. epi"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"Staph. epidermidis"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Staphylococcus epidermidis"</span>
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<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"Staph. epidermidis"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Coagulase-negative Staphylococcus (CoNS)"</span>
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<span class="r-in"><span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"Staph. epi"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "S. edaphicus"</span>
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<span class="r-in"><span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"Staph. epi"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"Staph. epidermidis"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "S. epidermidis"</span>
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<span class="r-in"><span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"Staph. epidermidis"</span>, Becker <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "CoNS"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># Lancefield classification, see ?as.mo ------------------------------------</span></span></span>
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@ -570,8 +570,10 @@
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<span class="r-out co"><span class="r-pr">#></span> [1] "Bacteria"</span>
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<span class="r-in"><span><span class="fu">mo_type</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Bacteria"</span>
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<span class="r-in"><span><span class="fu">mo_type</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span>, language <span class="op">=</span> <span class="st">"nl"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Bacteriën"</span>
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<span class="r-in"><span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span>, language <span class="op">=</span> <span class="st">"zh"</span><span class="op">)</span> <span class="co"># Chinese, no effect</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Bacteria"</span>
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<span class="r-in"><span><span class="fu">mo_type</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span>, language <span class="op">=</span> <span class="st">"zh"</span><span class="op">)</span> <span class="co"># Chinese, translated</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "细菌"</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"S. pyogenes"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span>, language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span></span></span>
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<span class="r-out co"><span class="r-pr">#></span> [1] "Streptococcus Gruppe A"</span>
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@ -588,55 +590,55 @@
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_gram_positive</span><span class="op">(</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
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<span class="r-in"><span> <span class="fu"><a href="count.html">count</a></span><span class="op">(</span><span class="fu">mo_genus</span><span class="op">(</span><span class="op">)</span>, count <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="count.html">count</a></span><span class="op">(</span><span class="fu">mo_genus</span><span class="op">(</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `mo_is_gram_positive()`</span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `mo_genus()`</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 12 × 3</span></span>
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<span class="r-out co"><span class="r-pr">#></span> `mo_genus()` count n</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><int></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Aerococcus TRUE 2</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Enterococcus TRUE 83</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Fusibacter TRUE 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Gemella TRUE 3</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Globicatella TRUE 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Granulicatella TRUE 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Lactobacillus TRUE 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Leuconostoc TRUE 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Listeria TRUE 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Paenibacillus TRUE 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> Staphylococcus TRUE 840</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Streptococcus TRUE 275</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 12 × 2</span></span>
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<span class="r-out co"><span class="r-pr">#></span> `mo_genus()` n</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Staphylococcus 840</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Streptococcus 275</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Enterococcus 83</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Gemella 3</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Aerococcus 2</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Fusibacter 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Globicatella 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Granulicatella 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Lactobacillus 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Leuconostoc 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> Listeria 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Paenibacillus 1</span>
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<span class="r-in"><span><span class="kw">if</span> <span class="op">(</span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">require</a></span><span class="op">(</span><span class="st"><a href="https://dplyr.tidyverse.org" class="external-link">"dplyr"</a></span><span class="op">)</span><span class="op">)</span> <span class="op">{</span></span></span>
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<span class="r-in"><span> <span class="va">example_isolates</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/filter.html" class="external-link">filter</a></span><span class="op">(</span><span class="fu">mo_is_intrinsic_resistant</span><span class="op">(</span>ab <span class="op">=</span> <span class="st">"vanco"</span><span class="op">)</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> </span></span>
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<span class="r-in"><span> <span class="fu"><a href="count.html">count</a></span><span class="op">(</span><span class="fu">mo_genus</span><span class="op">(</span><span class="op">)</span>, count <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-in"><span> <span class="fu"><a href="count.html">count</a></span><span class="op">(</span><span class="fu">mo_genus</span><span class="op">(</span><span class="op">)</span>, sort <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
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<span class="r-in"><span><span class="op">}</span></span></span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `mo_is_intrinsic_resistant()`</span>
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<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for `mo_genus()`</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 20 × 3</span></span>
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<span class="r-out co"><span class="r-pr">#></span> `mo_genus()` count n</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><lgl></span> <span style="color: #949494; font-style: italic;"><int></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Acinetobacter TRUE 6</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Campylobacter TRUE 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Citrobacter TRUE 11</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Enterobacter TRUE 23</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Enterococcus TRUE 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Escherichia TRUE 467</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Haemophilus TRUE 8</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Hafnia TRUE 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Klebsiella TRUE 77</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Lactobacillus TRUE 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> Leuconostoc TRUE 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Morganella TRUE 6</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> Neisseria TRUE 2</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">14</span> Pantoea TRUE 4</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">15</span> Proteus TRUE 39</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">16</span> Pseudescherichia TRUE 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">17</span> Pseudomonas TRUE 30</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">18</span> Salmonella TRUE 3</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">19</span> Serratia TRUE 25</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">20</span> Stenotrophomonas TRUE 2</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 20 × 2</span></span>
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<span class="r-out co"><span class="r-pr">#></span> `mo_genus()` n</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><int></span></span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Escherichia 467</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Klebsiella 77</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Proteus 39</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Pseudomonas 30</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Serratia 25</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Enterobacter 23</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Citrobacter 11</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Haemophilus 8</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Acinetobacter 6</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Morganella 6</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> Pantoea 4</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Salmonella 3</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> Neisseria 2</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">14</span> Stenotrophomonas 2</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">15</span> Campylobacter 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">16</span> Enterococcus 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">17</span> Hafnia 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">18</span> Lactobacillus 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">19</span> Leuconostoc 1</span>
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<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">20</span> Pseudescherichia 1</span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span></span></span>
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<span class="r-in"><span><span class="co"># get a list with the complete taxonomy (from kingdom to subspecies)</span></span></span>
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