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(v1.3.0.9015) as.mo() speedup for valid taxonomic names
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@@ -39,7 +39,7 @@
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</button>
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<span class="navbar-brand">
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<a class="navbar-link" href="../index.html">AMR (for R)</a>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9006</span>
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<span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Latest development version">1.3.0.9015</span>
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</span>
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</div>
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@@ -79,7 +79,7 @@
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<a href="../articles/datasets.html">
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<span class="fa fa-database"></span>
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Download our reference data sets for own use
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Data sets for download / own use
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</a>
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</li>
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<li>
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@@ -224,46 +224,46 @@
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<span class="co"># $ gender <chr> "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M"…</span>
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<span class="co"># $ patient_id <chr> "A77334", "A77334", "067927", "067927", "067927", "06…</span>
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<span class="co"># $ mo <mo> "B_ESCHR_COLI", "B_ESCHR_COLI", "B_STPHY_EPDR", "B_STP…</span>
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<span class="co"># $ PEN <ord> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R,…</span>
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<span class="co"># $ OXA <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ FLC <ord> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA,…</span>
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<span class="co"># $ AMX <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ AMC <ord> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I,…</span>
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<span class="co"># $ AMP <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ TZP <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ CZO <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ FEP <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ CXM <ord> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R…</span>
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<span class="co"># $ FOX <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ CTX <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
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<span class="co"># $ CAZ <ord> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, …</span>
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<span class="co"># $ CRO <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
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<span class="co"># $ GEN <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ TOB <ord> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, N…</span>
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<span class="co"># $ AMK <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ KAN <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ TMP <ord> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, …</span>
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<span class="co"># $ SXT <ord> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S,…</span>
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<span class="co"># $ NIT <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ FOS <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ LNZ <ord> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
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<span class="co"># $ CIP <ord> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA,…</span>
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<span class="co"># $ MFX <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ VAN <ord> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, …</span>
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<span class="co"># $ TEC <ord> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
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<span class="co"># $ TCY <ord> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, …</span>
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<span class="co"># $ TGC <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ DOX <ord> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R,…</span>
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<span class="co"># $ ERY <ord> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
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<span class="co"># $ CLI <ord> NA, NA, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, NA, NA…</span>
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<span class="co"># $ AZM <ord> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
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<span class="co"># $ IPM <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
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<span class="co"># $ MEM <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ MTR <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ CHL <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ COL <ord> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, …</span>
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<span class="co"># $ MUP <ord> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ RIF <ord> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
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<span class="co"># $ PEN <rsi> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R,…</span>
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<span class="co"># $ OXA <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ FLC <rsi> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA,…</span>
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<span class="co"># $ AMX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ AMC <rsi> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I,…</span>
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<span class="co"># $ AMP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ TZP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ CZO <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ FEP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ CXM <rsi> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R…</span>
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<span class="co"># $ FOX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ CTX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
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<span class="co"># $ CAZ <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, …</span>
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<span class="co"># $ CRO <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
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<span class="co"># $ GEN <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ TOB <rsi> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, N…</span>
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<span class="co"># $ AMK <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ KAN <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ TMP <rsi> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, …</span>
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<span class="co"># $ SXT <rsi> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S,…</span>
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<span class="co"># $ NIT <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ FOS <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ LNZ <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
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<span class="co"># $ CIP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA,…</span>
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<span class="co"># $ MFX <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ VAN <rsi> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, …</span>
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<span class="co"># $ TEC <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
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<span class="co"># $ TCY <rsi> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, …</span>
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<span class="co"># $ TGC <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ DOX <rsi> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R,…</span>
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<span class="co"># $ ERY <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
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<span class="co"># $ CLI <rsi> NA, NA, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, NA, NA…</span>
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<span class="co"># $ AZM <rsi> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R,…</span>
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<span class="co"># $ IPM <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S,…</span>
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<span class="co"># $ MEM <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ MTR <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ CHL <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ COL <rsi> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, …</span>
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<span class="co"># $ MUP <rsi> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, N…</span>
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<span class="co"># $ RIF <rsi> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R…</span>
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</pre></div>
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<p>Now to transform this to a data set with only resistance percentages per taxonomic order and genus:</p>
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<div class="sourceCode" id="cb2"><pre class="downlit">
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