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Built site for AMR: 1.8.1.9045@e7af5fc

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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>
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@ -183,48 +183,67 @@
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"K. pneumoniae"</span><span class="op">)</span><span class="op">)</span></span></span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Function `as.mo()` is uncertain about "K. pneumoniae" (assuming</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> Klebsiella pneumoniae). Run `mo_uncertainties()` to review this.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo fullname kingdom phylum</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 B_KLBSL_PNMN Klebsiella pneumoniae Bacteria Proteobacteria</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> class order family genus species</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Gammaproteobacteria Enterobacterales Enterobacteriaceae Klebsiella pneumoniae</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> subspecies rank ref species_id source prevalence</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 species Trevisan, 1887 777151 LPSN 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> snomed</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1098101000112102, 446870005, 1098201000112108, 409801009, 56415008, 714315002</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo fullname kingdom phylum class order family genus species subsp…¹</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&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> B_KLBSL_PNMN Klebsiel… Bacter… Prote… Gamm… Ente… Enter… Kleb… pneumo… <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 6 more variables: rank &lt;chr&gt;, ref &lt;chr&gt;, species_id &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># source &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;, and abbreviated variable</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># name ¹​subspecies</span></span>
<span class="r-in"><span><span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="st">"B_KLBSL_PNMN"</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo fullname kingdom phylum</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 B_KLBSL_PNMN Klebsiella pneumoniae Bacteria Proteobacteria</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> class order family genus species</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 Gammaproteobacteria Enterobacterales Enterobacteriaceae Klebsiella pneumoniae</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> subspecies rank ref species_id source prevalence</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 species Trevisan, 1887 777151 LPSN 1</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> snomed</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1098101000112102, 446870005, 1098201000112108, 409801009, 56415008, 714315002</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 1 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo fullname kingdom phylum class order family genus species subsp…¹</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&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> B_KLBSL_PNMN Klebsiel… Bacter… Prote… Gamm… Ente… Enter… Kleb… pneumo… <span style="color: #949494;">""</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># … with 6 more variables: rank &lt;chr&gt;, ref &lt;chr&gt;, species_id &lt;dbl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># source &lt;chr&gt;, prevalence &lt;dbl&gt;, snomed &lt;list&gt;, and abbreviated variable</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># name ¹​subspecies</span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<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>
<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">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span> </span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-in"><span> </span></span>
<span class="r-in"><span> <span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span>date <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span>from <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/as.Date.html" class="external-link">as.Date</a></span><span class="op">(</span><span class="st">"2018-01-01"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/as.Date.html" class="external-link">as.Date</a></span><span class="op">(</span><span class="st">"2018-01-07"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> by <span class="op">=</span> <span class="fl">1</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> bacteria <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><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">"S. aureus"</span>, <span class="st">"MRSA"</span>, <span class="st">"MSSA"</span>, <span class="st">"STAAUR"</span>,</span></span>
<span class="r-in"><span> <span class="st">"E. coli"</span>, <span class="st">"E. coli"</span>, <span class="st">"E. coli"</span><span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">df</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="va">df_joined</span> <span class="op">&lt;-</span> <span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="va">df</span>, <span class="st">"bacteria"</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">df_joined</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> Joining, by = "mo"</span>
<span class="r-in"><span><span class="va">df</span> <span class="op">&lt;-</span> <span class="fu"><a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> date <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/seq.html" class="external-link">seq</a></span><span class="op">(</span></span></span>
<span class="r-in"><span> from <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/as.Date.html" class="external-link">as.Date</a></span><span class="op">(</span><span class="st">"2018-01-01"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> to <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/as.Date.html" class="external-link">as.Date</a></span><span class="op">(</span><span class="st">"2018-01-07"</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> by <span class="op">=</span> <span class="fl">1</span></span></span>
<span class="r-in"><span> <span class="op">)</span>,</span></span>
<span class="r-in"><span> bacteria <span class="op">=</span> <span class="fu"><a href="as.mo.html">as.mo</a></span><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></span>
<span class="r-in"><span> <span class="st">"S. aureus"</span>, <span class="st">"MRSA"</span>, <span class="st">"MSSA"</span>, <span class="st">"STAAUR"</span>,</span></span>
<span class="r-in"><span> <span class="st">"E. coli"</span>, <span class="st">"E. coli"</span>, <span class="st">"E. coli"</span></span></span>
<span class="r-in"><span> <span class="op">)</span><span class="op">)</span>,</span></span>
<span class="r-in"><span> stringsAsFactors <span class="op">=</span> <span class="cn">FALSE</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 Function `as.mo()` is uncertain about "E. coli" (assuming Escherichia</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> coli) and "S. aureus" (assuming Staphylococcus aureus). Run</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> `mo_uncertainties()` to review these uncertainties.</span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">df</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "date" "bacteria"</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df_joined</span> <span class="op">&lt;-</span> <span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="va">df</span>, <span class="st">"bacteria"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</span><span class="va">df_joined</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "date" "bacteria" "fullname" "kingdom" "phylum" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] "class" "order" "family" "genus" "species" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] "subspecies" "rank" "ref" "species_id" "source" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "prevalence" "snomed" </span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># \donttest{</span></span></span>
<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>
<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">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu">left_join_microorganisms</span><span class="op">(</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/colnames.html" class="external-link">colnames</a></span><span class="op">(</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> Joining, by = "mo"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] "date" "patient" "age" "gender" "ward" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [6] "mo" "PEN" "OXA" "FLC" "AMX" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [11] "AMC" "AMP" "TZP" "CZO" "FEP" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [16] "CXM" "FOX" "CTX" "CAZ" "CRO" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [21] "GEN" "TOB" "AMK" "KAN" "TMP" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [26] "SXT" "NIT" "FOS" "LNZ" "CIP" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [31] "MFX" "VAN" "TEC" "TCY" "TGC" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [36] "DOX" "ERY" "CLI" "AZM" "IPM" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [41] "MEM" "MTR" "CHL" "COL" "MUP" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [46] "RIF" "fullname" "kingdom" "phylum" "class" </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [51] "order" "family" "genus" "species" "subspecies"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [56] "rank" "ref" "species_id" "source" "prevalence"</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [61] "snomed" </span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>
</div>