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@ -10,7 +10,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9001</small>
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@ -509,145 +509,151 @@
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<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="co"># taxonomic tree -----------------------------------------------------------</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="fu">mo_kingdom</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
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<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</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_phylum</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
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||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
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||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Pseudomonadota"</span>
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<span class="r-in"><span><span class="fu">mo_class</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
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||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gammaproteobacteria"</span>
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||||
<span class="r-in"><span><span class="fu">mo_order</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacterales"</span>
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||||
<span class="r-in"><span><span class="fu">mo_family</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacteriaceae"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_genus</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Klebsiella"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_species</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "pneumoniae"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_subspecies</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] ""</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># full names and short names -----------------------------------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">mo_name</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Klebsiella pneumoniae"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Klebsiella pneumoniae"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "K. pneumoniae"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># other properties ---------------------------------------------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">mo_pathogenicity</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] Pathogenic</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Levels: Pathogenic < Potentially pathogenic < Non-pathogenic < Unknown</span>
|
||||
<span class="r-in"><span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gram-negative"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_snomed</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [[1]]</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "1098101000112102" "446870005" "1098201000112108" "409801009" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [5] "56415008" "714315002" "713926009" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<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>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Bacteria"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_rank</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "species"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_url</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Klebsiella pneumoniae </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> "https://lpsn.dsmz.de/species/klebsiella-pneumoniae" </span>
|
||||
<span class="r-in"><span><span class="fu">mo_is_yeast</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">"Candida"</span>, <span class="st">"Trichophyton"</span>, <span class="st">"Klebsiella"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] TRUE FALSE FALSE</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># scientific reference -----------------------------------------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">mo_ref</span><span class="op">(</span><span class="st">"Klebsiella aerogenes"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Tindall et al., 2017"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_authors</span><span class="op">(</span><span class="st">"Klebsiella aerogenes"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Tindall et al."</span>
|
||||
<span class="r-in"><span><span class="fu">mo_year</span><span class="op">(</span><span class="st">"Klebsiella aerogenes"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] 2017</span>
|
||||
<span class="r-in"><span><span class="fu">mo_lpsn</span><span class="op">(</span><span class="st">"Klebsiella aerogenes"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "777146"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_gbif</span><span class="op">(</span><span class="st">"Klebsiella aerogenes"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "9281703"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_synonyms</span><span class="op">(</span><span class="st">"Klebsiella aerogenes"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> Hormaeche et al., 1960 Bascomb et al., 1971 </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> "Enterobacter aerogenes" "Klebsiella mobilis" </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># abbreviations known in the field -----------------------------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">mo_genus</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Staphylococcus"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_species</span><span class="op">(</span><span class="st">"MRSA"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "aureus"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "S. aureus"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"VISA"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gram-positive"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">mo_genus</span><span class="op">(</span><span class="st">"EHEC"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Escherichia"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_species</span><span class="op">(</span><span class="st">"EIEC"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "coli"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_name</span><span class="op">(</span><span class="st">"UPEC"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Escherichia coli"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># known subspecies ---------------------------------------------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"K. pneu rh"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Klebsiella pneumoniae rhinoscleromatis"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"K. pneu rh"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "K. pneumoniae"</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="co"># Becker classification, see ?as.mo ----------------------------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<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>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Staphylococcus epidermidis"</span>
|
||||
<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>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Coagulase-negative Staphylococcus (CoNS)"</span>
|
||||
<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>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "S. epidermidis"</span>
|
||||
<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>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "CoNS"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># Lancefield classification, see ?as.mo ------------------------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"Strep agalactiae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Streptococcus agalactiae"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_fullname</span><span class="op">(</span><span class="st">"Strep agalactiae"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Streptococcus Group B"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"Strep agalactiae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "S. agalactiae"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_shortname</span><span class="op">(</span><span class="st">"Strep agalactiae"</span>, Lancefield <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "GBS"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># language support --------------------------------------------------------</span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span>, language <span class="op">=</span> <span class="st">"de"</span><span class="op">)</span> <span class="co"># German</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gramnegativ"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_gramstain</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 class="co"># Dutch</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gram-negatief"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span>, language <span class="op">=</span> <span class="st">"es"</span><span class="op">)</span> <span class="co"># Spanish</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gram negativo"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span>, language <span class="op">=</span> <span class="st">"el"</span><span class="op">)</span> <span class="co"># Greek</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Αρνητικό κατά Gram"</span>
|
||||
<span class="r-in"><span><span class="fu">mo_gramstain</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span>, language <span class="op">=</span> <span class="st">"uk"</span><span class="op">)</span> <span class="co"># Ukrainian</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Грамнегативні"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># mo_type is equal to mo_kingdom, but mo_kingdom will remain untranslated</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">mo_kingdom</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Bacteria"</span>
|
||||
<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>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Bacteria"</span>
|
||||
<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>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Bacteria"</span>
|
||||
<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>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "细菌"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<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>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Streptococcus Gruppe A"</span>
|
||||
<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">"uk"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Streptococcus Група A"</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># other --------------------------------------------------------------------</span></span></span>
|
||||
@ -658,28 +664,145 @@
|
||||
<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>
|
||||
<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>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in filter(., mo_is_gram_positive()):</span> <span style="color: #00BBBB;">ℹ</span> In argument: `mo_is_gram_positive()`.</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span style="font-weight: bold;">Caused by error:</span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> in mo_is_gram_positive(): argument x is missing and no column with info</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> about microorganisms could be found.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_is_gram_positive()</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_genus()</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 18 × 2</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> `mo_genus()` n</span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Staphylococcus 840</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Streptococcus 275</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Enterococcus 83</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Corynebacterium 17</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Micrococcus 6</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Gemella 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Aerococcus 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Cutibacterium 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Dermabacter 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Fusibacter 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> Globicatella 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Granulicatella 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> Lactobacillus 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">14</span> Leuconostoc 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">15</span> Listeria 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">16</span> Paenibacillus 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">17</span> Rothia 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">18</span> Schaalia 1</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">%>%</a></span></span></span>
|
||||
<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>
|
||||
<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>
|
||||
<span class="r-in"><span><span class="op">}</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in filter(., mo_is_intrinsic_resistant(ab = "vanco")):</span> <span style="color: #00BBBB;">ℹ</span> In argument: `mo_is_intrinsic_resistant(ab = "vanco")`.</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span style="font-weight: bold;">Caused by error:</span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span style="color: #BBBB00;">!</span> in mo_is_intrinsic_resistant(): argument x is missing and no column with</span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> info about microorganisms could be found.</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_is_intrinsic_resistant()</span>
|
||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Using column 'mo' as input for mo_genus()</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 20 × 2</span></span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> `mo_genus()` n</span>
|
||||
<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>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> Escherichia 467</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> Klebsiella 77</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> Proteus 39</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> Pseudomonas 30</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> Serratia 25</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> Enterobacter 23</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> Citrobacter 11</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> Haemophilus 8</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> Acinetobacter 6</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> Morganella 6</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">11</span> Pantoea 4</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">12</span> Salmonella 3</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">13</span> Neisseria 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">14</span> Stenotrophomonas 2</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">15</span> Campylobacter 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">16</span> Enterococcus 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">17</span> Hafnia 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">18</span> Lactobacillus 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">19</span> Leuconostoc 1</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">20</span> Pseudescherichia 1</span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># get a list with the complete taxonomy (from kingdom to subspecies)</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">mo_taxonomy</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $kingdom</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Bacteria"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $phylum</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Pseudomonadota"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $class</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gammaproteobacteria"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $order</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacterales"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $family</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacteriaceae"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $genus</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Klebsiella"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $species</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "pneumoniae"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $subspecies</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] ""</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-in"><span></span></span>
|
||||
<span class="r-in"><span><span class="co"># get a list with the taxonomy, the authors, Gram-stain,</span></span></span>
|
||||
<span class="r-in"><span><span class="co"># SNOMED codes, and URL to the online database</span></span></span>
|
||||
<span class="r-in"><span><span class="fu">mo_info</span><span class="op">(</span><span class="st">"Klebsiella pneumoniae"</span><span class="op">)</span></span></span>
|
||||
<span class="r-err co"><span class="r-pr">#></span> <span class="error">Error in .Call(Cchin, x, table):</span> NULL value passed as symbol address</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $mo</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "B_KLBSL_PNMN"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $kingdom</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Bacteria"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $phylum</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Pseudomonadota"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $class</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gammaproteobacteria"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $order</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacterales"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $family</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacteriaceae"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $genus</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Klebsiella"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $species</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "pneumoniae"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $subspecies</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] ""</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $status</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "accepted"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $synonyms</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> NULL</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $gramstain</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Gram-negative"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $oxygen_tolerance</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "aerobe"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $url</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "https://lpsn.dsmz.de/species/klebsiella-pneumoniae"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $ref</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "Trevisan, 1887"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $snomed</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "1098101000112102" "446870005" "1098201000112108" "409801009" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [5] "56415008" "714315002" "713926009" </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $lpsn</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "777151"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> $gbif</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> [1] "3221874"</span>
|
||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||
</code></pre></div>
|
||||
</div>
|
||||
|
||||
Reference in New Issue
Block a user