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@ -38,7 +38,7 @@
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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="">1.8.2.9095</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">1.8.2.9096</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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@ -196,46 +196,46 @@ is currently being developed.</strong></p>
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<span><span class="co"># $ gender <span style="color: #949494; font-style: italic;"><chr></span> "F", "F", "F", "F", "F", "F", "M", "M", "F", "F", "M", "M", "M…</span></span>
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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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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;"><rsi></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"># $ ERY <span style="color: #949494; font-style: italic;"><rsi></span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,…</span></span>
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<span><span class="co"># $ CLI <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, R, NA, NA, NA, NA, NA, NA, R, R, R, R, R, NA…</span></span>
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<span><span class="co"># $ AZM <span style="color: #949494; font-style: italic;"><rsi></span> R, R, R, R, R, R, S, S, R, S, S, S, R, R, R, R, R, R, R, R, S,…</span></span>
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<span><span class="co"># $ IPM <span style="color: #949494; font-style: italic;"><rsi></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"># $ MEM <span style="color: #949494; font-style: italic;"><rsi></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"># $ MTR <span style="color: #949494; font-style: italic;"><rsi></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"># $ CHL <span style="color: #949494; font-style: italic;"><rsi></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"># $ COL <span style="color: #949494; font-style: italic;"><rsi></span> NA, NA, R, R, R, R, R, R, R, R, R, R, NA, NA, NA, R, R, R, R, …</span></span>
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<span><span class="co"># $ MUP <span style="color: #949494; font-style: italic;"><rsi></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"># $ RIF <span style="color: #949494; font-style: italic;"><rsi></span> R, R, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, R, R, R, R, R, N…</span></span></code></pre></div>
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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"># $ 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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
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<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>
|
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<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>
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<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>
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<p>Now to transform this to a data set with only resistance percentages
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per taxonomic order and genus:</p>
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<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
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@ -244,7 +244,7 @@ per taxonomic order and genus:</p>
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<span> order <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_order</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span>, <span class="co"># group on anything, like order</span></span>
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<span> genus <span class="op">=</span> <span class="fu"><a href="../reference/mo_property.html">mo_genus</a></span><span class="op">(</span><span class="va">mo</span><span class="op">)</span></span>
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<span> <span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># and genus as we do here</span></span>
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<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html" class="external-link">summarise_if</a></span><span class="op">(</span><span class="va">is.rsi</span>, <span class="va">resistance</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># then get resistance of all drugs</span></span>
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<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/summarise_all.html" class="external-link">summarise_if</a></span><span class="op">(</span><span class="va">is.sir</span>, <span class="va">resistance</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%>%</a></span> <span class="co"># then get resistance of all drugs</span></span>
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<span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span></span>
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<span> <span class="va">order</span>, <span class="va">genus</span>, <span class="va">AMC</span>, <span class="va">CXM</span>, <span class="va">CTX</span>,</span>
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<span> <span class="va">CAZ</span>, <span class="va">GEN</span>, <span class="va">TOB</span>, <span class="va">TMP</span>, <span class="va">SXT</span></span>
|
||||
|
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Reference in New Issue
Block a user