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@ -29,7 +29,7 @@
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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="">2.1.1.9120</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9121</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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@ -45,6 +45,7 @@
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<li><a class="dropdown-item" href="../reference/antibiogram.html"><span class="fa fa-file-prescription"></span> Generate Antibiogram (Trad./Syndromic/WISCA)</a></li>
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<li><a class="dropdown-item" href="../articles/resistance_predict.html"><span class="fa fa-dice"></span> Predict Antimicrobial Resistance</a></li>
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<li><a class="dropdown-item" href="../articles/datasets.html"><span class="fa fa-database"></span> Download Data Sets for Own Use</a></li>
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<li><a class="dropdown-item" href="../articles/AMR_with_tidymodels.html"><span class="fa fa-square-root-variable"></span> Use AMR for Predictive Modelling (tidymodels)</a></li>
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<li><a class="dropdown-item" href="../reference/AMR-options.html"><span class="fa fa-gear"></span> Set User- Or Team-specific Package Settings</a></li>
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<li><a class="dropdown-item" href="../articles/PCA.html"><span class="fa fa-compress"></span> Conduct Principal Component Analysis for AMR</a></li>
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<li><a class="dropdown-item" href="../articles/MDR.html"><span class="fa fa-skull-crossbones"></span> Determine Multi-Drug Resistance (MDR)</a></li>
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@ -96,6 +97,8 @@ is currently being developed.</strong></p>
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<code>example_isolates</code> data set in this package looks like:</p>
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<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
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<code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://msberends.github.io/AMR/">AMR</a></span><span class="op">)</span></span>
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<span><span class="co">#> Error in get(paste0(generic, ".", class), envir = get_method_env()) : </span></span>
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<span><span class="co">#> object 'type_sum.accel' not found</span></span>
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<span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://dplyr.tidyverse.org" class="external-link">dplyr</a></span><span class="op">)</span></span>
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<span><span class="fu"><a href="https://pillar.r-lib.org/reference/glimpse.html" class="external-link">glimpse</a></span><span class="op">(</span><span class="va">example_isolates</span><span class="op">)</span></span>
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<span><span class="co">#> Rows: 2,000</span></span>
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@ -107,45 +110,45 @@ is currently being developed.</strong></p>
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<span><span class="co">#> $ ward <span style="color: #949494; font-style: italic;"><chr></span> "Clinical", "Clinical", "ICU", "ICU", "ICU", "ICU", "Clinical"…</span></span>
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<span><span class="co">#> $ mo <span style="color: #949494; font-style: italic;"><mo></span> "B_ESCHR_COLI", "B_ESCHR_COLI", "B_STPHY_EPDR", "B_STPHY_EPDR",…</span></span>
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<span><span class="co">#> $ PEN <span style="color: #949494; font-style: italic;"><sir></span> R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, R, S,…</span></span>
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<span><span class="co">#> $ OXA <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
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<span><span class="co">#> $ FLC <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, R, R, R, R, S, S, R, S, S, S, NA, NA, NA, NA, NA, R, R…</span></span>
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<span><span class="co">#> $ AMX <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N…</span></span>
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<span><span class="co">#> $ AMC <span style="color: #949494; font-style: italic;"><sir></span> I, I, NA, NA, NA, NA, S, S, NA, NA, S, S, I, I, R, I, I, NA, N…</span></span>
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<span><span class="co">#> $ AMP <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, R, R, NA, NA, NA, NA, NA, NA, R, NA, N…</span></span>
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<span><span class="co">#> $ TZP <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
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<span><span class="co">#> $ CZO <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,…</span></span>
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<span><span class="co">#> $ FEP <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
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<span><span class="co">#> $ CXM <span style="color: #949494; font-style: italic;"><sir></span> I, I, R, R, R, R, S, S, R, S, S, S, S, S, NA, S, S, R, R, S, S…</span></span>
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<span><span class="co">#> $ FOX <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, NA,…</span></span>
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<span><span class="co">#> $ CTX <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
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<span><span class="co">#> $ CAZ <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, S, S, R, R, …</span></span>
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<span><span class="co">#> $ CRO <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
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<span><span class="co">#> $ GEN <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
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<span><span class="co">#> $ TOB <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, S, S, NA, NA, NA…</span></span>
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<span><span class="co">#> $ AMK <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
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<span><span class="co">#> $ KAN <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
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<span><span class="co">#> $ TMP <span style="color: #949494; font-style: italic;"><sir></span> R, R, S, S, R, R, R, R, S, S, NA, NA, S, S, S, S, S, R, R, R, …</span></span>
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<span><span class="co">#> $ SXT <span style="color: #949494; font-style: italic;"><sir></span> R, R, S, S, NA, NA, NA, NA, S, S, NA, NA, S, S, S, S, S, NA, N…</span></span>
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<span><span class="co">#> $ NIT <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R,…</span></span>
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<span><span class="co">#> $ FOS <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
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<span><span class="co">#> $ LNZ <span style="color: #949494; font-style: italic;"><sir></span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span>
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<span><span class="co">#> $ CIP <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, NA, NA, NA, NA, S, S…</span></span>
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<span><span class="co">#> $ MFX <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
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<span><span class="co">#> $ VAN <span style="color: #949494; font-style: italic;"><sir></span> R, R, S, S, S, S, S, S, S, S, NA, NA, R, R, R, R, R, S, S, S, …</span></span>
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<span><span class="co">#> $ TEC <span style="color: #949494; font-style: italic;"><sir></span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span>
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<span><span class="co">#> $ TCY <span style="color: #949494; font-style: italic;"><sir></span> R, R, S, S, S, S, S, S, S, I, S, S, NA, NA, I, R, R, S, I, R, …</span></span>
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<span><span class="co">#> $ TGC <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA…</span></span>
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<span><span class="co">#> $ DOX <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, S, S, S, S, S, S, S, NA, S, S, NA, NA, NA, R, R, S, NA…</span></span>
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<span><span class="co">#> $ OXA <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
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<span><span class="co">#> $ FLC <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, S, S, R, S, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R…</span></span>
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<span><span class="co">#> $ AMX <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">N</span>…</span></span>
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<span><span class="co">#> $ AMC <span style="color: #949494; font-style: italic;"><sir></span> I, I, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, I, I, R, I, I, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">N</span>…</span></span>
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<span><span class="co">#> $ AMP <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">N</span>…</span></span>
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<span><span class="co">#> $ TZP <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
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<span><span class="co">#> $ CZO <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, <span style="color: #BB0000;">NA</span>,…</span></span>
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<span><span class="co">#> $ FEP <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
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<span><span class="co">#> $ CXM <span style="color: #949494; font-style: italic;"><sir></span> I, I, R, R, R, R, S, S, R, S, S, S, S, S, <span style="color: #BB0000;">NA</span>, S, S, R, R, S, S…</span></span>
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<span><span class="co">#> $ FOX <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, <span style="color: #BB0000;">NA</span>,…</span></span>
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<span><span class="co">#> $ CTX <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, S, S…</span></span>
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<span><span class="co">#> $ CAZ <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, R, R, R, R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, R, R, …</span></span>
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<span><span class="co">#> $ CRO <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, S, S…</span></span>
|
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<span><span class="co">#> $ GEN <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
|
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<span><span class="co">#> $ TOB <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
|
||||
<span><span class="co">#> $ AMK <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
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<span><span class="co">#> $ KAN <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
|
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<span><span class="co">#> $ TMP <span style="color: #949494; font-style: italic;"><sir></span> R, R, S, S, R, R, R, R, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, S, S, S, R, R, R, …</span></span>
|
||||
<span><span class="co">#> $ SXT <span style="color: #949494; font-style: italic;"><sir></span> R, R, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, S, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">N</span>…</span></span>
|
||||
<span><span class="co">#> $ NIT <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R,…</span></span>
|
||||
<span><span class="co">#> $ FOS <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
|
||||
<span><span class="co">#> $ LNZ <span style="color: #949494; font-style: italic;"><sir></span> R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, <span style="color: #BB0000;">N</span>…</span></span>
|
||||
<span><span class="co">#> $ CIP <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S…</span></span>
|
||||
<span><span class="co">#> $ MFX <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
|
||||
<span><span class="co">#> $ VAN <span style="color: #949494; font-style: italic;"><sir></span> R, R, S, S, S, S, S, S, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, S, S, S, …</span></span>
|
||||
<span><span class="co">#> $ TEC <span style="color: #949494; font-style: italic;"><sir></span> R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, <span style="color: #BB0000;">N</span>…</span></span>
|
||||
<span><span class="co">#> $ TCY <span style="color: #949494; font-style: italic;"><sir></span> R, R, S, S, S, S, S, S, S, I, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, I, R, R, S, I, R, …</span></span>
|
||||
<span><span class="co">#> $ TGC <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, S, S, S, S, S, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, S, <span style="color: #BB0000;">NA</span>…</span></span>
|
||||
<span><span class="co">#> $ DOX <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, S, S, S, S, S, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, S, <span style="color: #BB0000;">NA</span>…</span></span>
|
||||
<span><span class="co">#> $ ERY <span style="color: #949494; font-style: italic;"><sir></span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,…</span></span>
|
||||
<span><span class="co">#> $ CLI <span style="color: #949494; font-style: italic;"><sir></span> R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, R, R, NA…</span></span>
|
||||
<span><span class="co">#> $ CLI <span style="color: #949494; font-style: italic;"><sir></span> R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, <span style="color: #BB0000;">NA</span>…</span></span>
|
||||
<span><span class="co">#> $ AZM <span style="color: #949494; font-style: italic;"><sir></span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,…</span></span>
|
||||
<span><span class="co">#> $ IPM <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, S, S, NA, S, S…</span></span>
|
||||
<span><span class="co">#> $ MEM <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co">#> $ MTR <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co">#> $ CHL <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co">#> $ COL <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R, R, R, …</span></span>
|
||||
<span><span class="co">#> $ MUP <span style="color: #949494; font-style: italic;"><sir></span> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA…</span></span>
|
||||
<span><span class="co">#> $ RIF <span style="color: #949494; font-style: italic;"><sir></span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span></code></pre></div>
|
||||
<span><span class="co">#> $ IPM <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, S, S, <span style="color: #BB0000;">NA</span>, S, S…</span></span>
|
||||
<span><span class="co">#> $ MEM <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
|
||||
<span><span class="co">#> $ MTR <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
|
||||
<span><span class="co">#> $ CHL <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
|
||||
<span><span class="co">#> $ COL <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, R, R, R, R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, …</span></span>
|
||||
<span><span class="co">#> $ MUP <span style="color: #949494; font-style: italic;"><sir></span> <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>…</span></span>
|
||||
<span><span class="co">#> $ RIF <span style="color: #949494; font-style: italic;"><sir></span> R, R, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, <span style="color: #BB0000;">NA</span>, R, R, R, R, R, <span style="color: #BB0000;">N</span>…</span></span></code></pre></div>
|
||||
<p>Now to transform this to a data set with only resistance percentages
|
||||
per taxonomic order and genus:</p>
|
||||
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
|
||||
|
Reference in New Issue
Block a user