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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="">2.1.1</small>
<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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@@ -225,16 +225,30 @@
<span class="r-msg co"><span class="r-pr">#&gt;</span> ℹ Reset 17 previously matched input values.</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu"><a href="as.mo.html">as.mo</a></span><span class="op">(</span><span class="st">"E. coli"</span><span class="op">)</span></span></span>
<span class="r-err co"><span class="r-pr">#&gt;</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">#&gt;</span> Class 'mo'</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] B_ESCHR_COLI</span>
<span class="r-in"><span><span class="fu"><a href="as.mo.html">mo_uncertainties</a></span><span class="op">(</span><span class="op">)</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> No uncertainties to show. Only uncertainties of the last call to as.mo()</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> or any mo_*() function are stored.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Matching scores are based on the resemblance between the input and the full</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> taxonomic name, and the pathogenicity in humans. See ?mo_matching_score.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> --------------------------------------------------------------------------------</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> "E. coli" -&gt; Escherichia coli (B_ESCHR_COLI, 0.688)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Also matched: Enterobacter cowanii (0.600), Eubacterium combesii</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> (0.600), Eggerthia catenaformis (0.591), Eubacterium callanderi</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> (0.591), Enterocloster citroniae (0.587), Eubacterium cylindroides</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> (0.583), Enterococcus casseliflavus (0.577), Enterobacter cloacae</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> cloacae (0.571), Enterobacter cloacae complex (0.571), and Ehrlichia</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> canis (0.567)</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> Only the first 10 other matches of each record are shown. Run</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> print(mo_uncertainties(), n = ...) to view more entries, or save</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo_uncertainties() to an object.</span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">mo_matching_score</span><span class="op">(</span></span></span>
<span class="r-in"><span> x <span class="op">=</span> <span class="st">"E. coli"</span>,</span></span>
<span class="r-in"><span> n <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">"Escherichia coli"</span>, <span class="st">"Entamoeba coli"</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">#&gt;</span> <span class="error">Error in .Call(Cchmatch, x, table, as.integer(nomatch[1L])):</span> NULL value passed as symbol address</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 0.6875000 0.3809524</span>
</code></pre></div>
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