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@ -30,7 +30,7 @@
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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="https://msberends.github.io/AMR/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="">2.1.1.9087</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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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="">2.1.1.9087</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
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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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<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="">2.1.1.9087</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
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@ -87,7 +87,7 @@
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website update since they are based on randomly created values and the
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website update since they are based on randomly created values and the
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page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
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page was written in <a href="https://rmarkdown.rstudio.com/" class="external-link">R
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Markdown</a>. However, the methodology remains unchanged. This page was
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Markdown</a>. However, the methodology remains unchanged. This page was
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generated on 02 October 2024.</p>
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generated on 06 October 2024.</p>
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<div class="section level2">
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<div class="section level2">
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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<h2 id="introduction">Introduction<a class="anchor" aria-label="anchor" href="#introduction"></a>
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</h2>
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</h2>
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@ -143,21 +143,21 @@ make the structure of your data generally look like this:</p>
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</tr></thead>
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</tr></thead>
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<tbody>
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<tbody>
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<tr class="odd">
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<tr class="odd">
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<td align="center">2024-10-02</td>
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<td align="center">2024-10-06</td>
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<td align="center">abcd</td>
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<td align="center">abcd</td>
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<td align="center">Escherichia coli</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">S</td>
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</tr>
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</tr>
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<tr class="even">
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<tr class="even">
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<td align="center">2024-10-02</td>
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<td align="center">2024-10-06</td>
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<td align="center">abcd</td>
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<td align="center">abcd</td>
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<td align="center">Escherichia coli</td>
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<td align="center">Escherichia coli</td>
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<td align="center">S</td>
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<td align="center">S</td>
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<td align="center">R</td>
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<td align="center">R</td>
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</tr>
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</tr>
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<tr class="odd">
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<tr class="odd">
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<td align="center">2024-10-02</td>
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<td align="center">2024-10-06</td>
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<td align="center">efgh</td>
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<td align="center">efgh</td>
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<td align="center">Escherichia coli</td>
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<td align="center">Escherichia coli</td>
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<td align="center">R</td>
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<td align="center">R</td>
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@ -272,10 +272,11 @@ taxonomic codes. Let’s check this:</p>
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<span><span class="co">#> --------------------------------------------------------------------------------</span></span>
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<span><span class="co">#> --------------------------------------------------------------------------------</span></span>
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<span><span class="co">#> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)</span></span>
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<span><span class="co">#> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)</span></span>
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<span><span class="co">#> Also matched: Enterococcus crotali (0.650), Escherichia coli coli</span></span>
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<span><span class="co">#> Also matched: Enterococcus crotali (0.650), Escherichia coli coli</span></span>
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<span><span class="co">#> (0.643), Escherichia coli expressing (0.611), Enterococcus columbae</span></span>
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<span><span class="co">#> (0.643), Escherichia coli expressing (0.611), Enterobacter cowanii</span></span>
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<span><span class="co">#> (0.595), Enterococcus camelliae (0.591), Enterococcus casseliflavus</span></span>
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<span><span class="co">#> (0.600), Enterococcus columbae (0.595), Enterococcus camelliae (0.591),</span></span>
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<span><span class="co">#> (0.577), Enterococcus canis (0.556), Enterococcus cecorum (0.550),</span></span>
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<span><span class="co">#> Enterococcus casseliflavus (0.577), Enterobacter cloacae cloacae</span></span>
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<span><span class="co">#> Enterococcus canintestini (0.540), and Enterobacter cowanii (0.522)</span></span>
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<span><span class="co">#> (0.571), Enterobacter cloacae complex (0.571), and Enterobacter cloacae</span></span>
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<span><span class="co">#> dissolvens (0.565)</span></span>
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<span><span class="co">#> --------------------------------------------------------------------------------</span></span>
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<span><span class="co">#> --------------------------------------------------------------------------------</span></span>
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<span><span class="co">#> "K. pneumoniae" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)</span></span>
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<span><span class="co">#> "K. pneumoniae" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)</span></span>
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<span><span class="co">#> Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella</span></span>
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<span><span class="co">#> Also matched: Klebsiella pneumoniae ozaenae (0.707), Klebsiella</span></span>
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<span><span class="co">#> --------------------------------------------------------------------------------</span></span>
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<span><span class="co">#> --------------------------------------------------------------------------------</span></span>
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<span><span class="co">#> "S. pneumoniae" -> Streptococcus pneumoniae (B_STRPT_PNMN, 0.750)</span></span>
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<span><span class="co">#> "S. pneumoniae" -> Streptococcus pneumoniae (B_STRPT_PNMN, 0.750)</span></span>
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<span><span class="co">#> Also matched: Streptococcus pseudopneumoniae (0.700), Streptococcus</span></span>
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<span><span class="co">#> Also matched: Streptococcus pseudopneumoniae (0.700), Streptococcus</span></span>
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<span><span class="co">#> phocae salmonis (0.552), Streptococcus pseudoporcinus (0.536),</span></span>
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<span><span class="co">#> phocae salmonis (0.552), Serratia proteamaculans quinovora (0.545),</span></span>
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<span><span class="co">#> Staphylococcus piscifermentans (0.533), Staphylococcus pseudintermedius</span></span>
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<span><span class="co">#> Streptococcus pseudoporcinus (0.536), Staphylococcus piscifermentans</span></span>
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<span><span class="co">#> (0.532), Streptococcus gallolyticus pasteurianus (0.526), Salmonella</span></span>
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<span><span class="co">#> (0.533), Staphylococcus pseudintermedius (0.532), Serratia</span></span>
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<span><span class="co">#> Portanigra (0.524), Streptococcus periodonticum (0.519), Streptococcus</span></span>
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<span><span class="co">#> proteamaculans proteamaculans (0.526), Streptococcus gallolyticus</span></span>
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<span><span class="co">#> phocae phocae (0.519), and Streptococcus pluranimalium (0.519)</span></span>
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<span><span class="co">#> pasteurianus (0.526), Salmonella Portanigra (0.524), and Streptococcus</span></span>
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<span><span class="co">#> periodonticum (0.519)</span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> </span></span>
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<span><span class="co">#> Only the first 10 other matches of each record are shown. Run</span></span>
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<span><span class="co">#> Only the first 10 other matches of each record are shown. Run</span></span>
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<span><span class="co">#> print(mo_uncertainties(), n = ...) to view more entries, or save</span></span>
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<span><span class="co">#> print(mo_uncertainties(), n = ...) to view more entries, or save</span></span>
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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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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</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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@ -98,7 +98,6 @@ data in your own Python environment. This post will guide you through
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setting up <code>rpy2</code> and show you how to use R functions from
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setting up <code>rpy2</code> and show you how to use R functions from
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<code>AMR</code> in Python to supercharge your antimicrobial resistance
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<code>AMR</code> in Python to supercharge your antimicrobial resistance
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analysis.</p>
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analysis.</p>
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<p><a href="https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant" class="external-link"><img src="../AMRforRGPT.svg" style="min-width: 300px; width: 10%;"></a></p>
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</div>
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</div>
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<div class="section level2">
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<div class="section level2">
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<h2 id="what-is-rpy2">What is <code>rpy2</code>?<a class="anchor" aria-label="anchor" href="#what-is-rpy2"></a>
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<h2 id="what-is-rpy2">What is <code>rpy2</code>?<a class="anchor" aria-label="anchor" href="#what-is-rpy2"></a>
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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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<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="">2.1.1.9087</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
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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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<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="">2.1.1.9087</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</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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@ -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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<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="">2.1.1.9087</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</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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@ -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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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</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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@ -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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<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="">2.1.1.9087</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</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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@ -76,7 +76,7 @@
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<main id="main" class="col-md-9"><div class="page-header">
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<main id="main" class="col-md-9"><div class="page-header">
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<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
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<img src="../logo.svg" class="logo" alt=""><h1>Data sets for download / own use</h1>
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<h4 data-toc-skip class="date">02 October 2024</h4>
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<h4 data-toc-skip class="date">06 October 2024</h4>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
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<small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/vignettes/datasets.Rmd" class="external-link"><code>vignettes/datasets.Rmd</code></a></small>
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<div class="d-none name"><code>datasets.Rmd</code></div>
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<div class="d-none name"><code>datasets.Rmd</code></div>
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@ -108,7 +108,7 @@ column names:<br><em>mo</em>, <em>fullname</em>, <em>status</em>, <em>kingdom</e
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<em>snomed</em>.</p>
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<em>snomed</em>.</p>
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<p>This data set is in R available as <code>microorganisms</code>, after
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<p>This data set is in R available as <code>microorganisms</code>, after
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you load the <code>AMR</code> package.</p>
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you load the <code>AMR</code> package.</p>
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<p>It was last updated on 2 October 2024 08:20:05 UTC. Find more info
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<p>It was last updated on 4 October 2024 13:28:44 UTC. Find more info
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about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
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about the structure of this data set <a href="https://msberends.github.io/AMR/reference/microorganisms.html">here</a>.</p>
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<p><strong>Direct download links:</strong></p>
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<p><strong>Direct download links:</strong></p>
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<ul>
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<ul>
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@ -7,7 +7,7 @@
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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||||||
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||||||
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9087</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
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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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<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="">2.1.1.9087</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">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -29,7 +29,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -29,7 +29,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -119,6 +119,10 @@ body.amr-for-python * {
|
|||||||
width: 150px;
|
width: 150px;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
.amr-gpt-assistant * {
|
||||||
|
width: 90%;
|
||||||
|
}
|
||||||
|
|
||||||
.template-reference-index .section-desc {
|
.template-reference-index .section-desc {
|
||||||
font-style: italic;
|
font-style: italic;
|
||||||
text-align: justify;
|
text-align: justify;
|
||||||
|
7
extra.js
7
extra.js
@ -30,8 +30,10 @@
|
|||||||
*/
|
*/
|
||||||
|
|
||||||
$(document).ready(function() {
|
$(document).ready(function() {
|
||||||
|
// add GPT assistant info
|
||||||
|
$('aside').prepend('<div class="amr-gpt-assistant"><a target="_blank" href="https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant"><img src="https://github.com/msberends/AMR/raw/main/pkgdown/assets/AMRforRGPT.svg"></a></div>');
|
||||||
|
|
||||||
// Replace 'Developers' with 'Maintainers' on the main page, and "Contributors" on the Authors page
|
// replace 'Developers' with 'Maintainers' on the main page, and "Contributors" on the Authors page
|
||||||
$(".developers h2").text("Maintainers");
|
$(".developers h2").text("Maintainers");
|
||||||
$(".citation h2:nth(0)").text("All contributors");
|
$(".citation h2:nth(0)").text("All contributors");
|
||||||
$(".citation h2:nth(1)").text("How to Cite");
|
$(".citation h2:nth(1)").text("How to Cite");
|
||||||
@ -43,6 +45,9 @@ $(document).ready(function() {
|
|||||||
$("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# }", ""));
|
$("#ref-examples ~ div pre").html($("#ref-examples ~ div pre").html().replaceAll("# }", ""));
|
||||||
}
|
}
|
||||||
|
|
||||||
|
// rename 'Package index' to 'Manual' (weird design choice to pick 'Package index')
|
||||||
|
|
||||||
|
|
||||||
// remove leading newline in code examples on changelog
|
// remove leading newline in code examples on changelog
|
||||||
if ($("body .template-news").length > 0) {
|
if ($("body .template-news").length > 0) {
|
||||||
$("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n<span', 'sourceCode R"><span'));
|
$("body .template-news").html($("body .template-news").html().replaceAll('sourceCode R">\n<span', 'sourceCode R"><span'));
|
||||||
|
@ -32,7 +32,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@ -91,7 +91,6 @@
|
|||||||
<li>100% free of costs and dependencies, highly suitable for places with <strong>limited resources</strong>
|
<li>100% free of costs and dependencies, highly suitable for places with <strong>limited resources</strong>
|
||||||
</li>
|
</li>
|
||||||
</ul>
|
</ul>
|
||||||
<p><a href="https://chatgpt.com/g/g-M4UNLwFi5-amr-for-r-assistant" class="external-link"><img src="AMRforRGPT.svg" style="min-width: 300px; width: 10%;"></a></p>
|
|
||||||
<div style="display: flex; font-size: 0.8em;">
|
<div style="display: flex; font-size: 0.8em;">
|
||||||
<p style="text-align:left; width: 50%;">
|
<p style="text-align:left; width: 50%;">
|
||||||
<small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small>
|
<small><a href="https://msberends.github.io/AMR/">https://msberends.github.io/AMR</a></small>
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@ -47,18 +47,18 @@
|
|||||||
</div>
|
</div>
|
||||||
|
|
||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
<h2 class="pkg-version" data-toc-text="2.1.1.9087" id="amr-2119087">AMR 2.1.1.9087<a class="anchor" aria-label="anchor" href="#amr-2119087"></a></h2>
|
<h2 class="pkg-version" data-toc-text="2.1.1.9092" id="amr-2119092">AMR 2.1.1.9092<a class="anchor" aria-label="anchor" href="#amr-2119092"></a></h2>
|
||||||
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
|
<p><em>(this beta version will eventually become v3.0. We’re happy to reach a new major milestone soon, which will be all about the new One Health support! Install this beta using <a href="https://msberends.github.io/AMR/#latest-development-version">the instructions here</a>.)</em></p>
|
||||||
<div class="section level5">
|
<div class="section level5">
|
||||||
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9087">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9087"></a></h5>
|
<h5 id="a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9092">A New Milestone: AMR v3.0 with One Health Support (= Human + Veterinary + Environmental)<a class="anchor" aria-label="anchor" href="#a-new-milestone-amr-v30-with-one-health-support--human--veterinary--environmental-2-1-1-9092"></a></h5>
|
||||||
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
|
<p>This package now supports not only tools for AMR data analysis in clinical settings, but also for veterinary and environmental microbiology. This was made possible through a collaboration with the <a href="https://www.upei.ca/avc" class="external-link">University of Prince Edward Island’s Atlantic Veterinary College</a>, Canada. To celebrate this great improvement of the package, we also updated the package logo to reflect this change.</p>
|
||||||
</div>
|
</div>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="breaking-2-1-1-9087">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9087"></a></h3>
|
<h3 id="breaking-2-1-1-9092">Breaking<a class="anchor" aria-label="anchor" href="#breaking-2-1-1-9092"></a></h3>
|
||||||
<ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over a year ago</li>
|
<ul><li>Removed all functions and references that used the deprecated <code>rsi</code> class, which were all replaced with their <code>sir</code> equivalents over a year ago</li>
|
||||||
</ul></div>
|
</ul></div>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="new-2-1-1-9087">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9087"></a></h3>
|
<h3 id="new-2-1-1-9092">New<a class="anchor" aria-label="anchor" href="#new-2-1-1-9092"></a></h3>
|
||||||
<ul><li>
|
<ul><li>
|
||||||
<strong>One Health implementation</strong>
|
<strong>One Health implementation</strong>
|
||||||
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
|
<ul><li>Function <code><a href="../reference/as.sir.html">as.sir()</a></code> now has extensive support for veterinary breakpoints from CLSI. Use <code>breakpoint_type = "animal"</code> and set the <code>host</code> argument to a variable that contains animal species names.</li>
|
||||||
@ -95,7 +95,7 @@
|
|||||||
</ul></li>
|
</ul></li>
|
||||||
</ul></div>
|
</ul></div>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="changed-2-1-1-9087">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9087"></a></h3>
|
<h3 id="changed-2-1-1-9092">Changed<a class="anchor" aria-label="anchor" href="#changed-2-1-1-9092"></a></h3>
|
||||||
<ul><li>SIR interpretation
|
<ul><li>SIR interpretation
|
||||||
<ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
|
<ul><li>It is now possible to use column names for argument <code>ab</code>, <code>mo</code>, and <code>uti</code>: <code>as.sir(..., ab = "column1", mo = "column2", uti = "column3")</code>. This greatly improves the flexibility for users.</li>
|
||||||
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
|
<li>Users can now set their own criteria (using regular expressions) as to what should be considered S, I, R, SDD, and NI.</li>
|
||||||
@ -146,13 +146,13 @@
|
|||||||
<li>Improved algorithm of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> when using the phenotype-based method, to prioritise records with the highest availability of SIR values</li>
|
<li>Improved algorithm of <code><a href="../reference/first_isolate.html">first_isolate()</a></code> when using the phenotype-based method, to prioritise records with the highest availability of SIR values</li>
|
||||||
</ul></div>
|
</ul></div>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="other-2-1-1-9087">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9087"></a></h3>
|
<h3 id="other-2-1-1-9092">Other<a class="anchor" aria-label="anchor" href="#other-2-1-1-9092"></a></h3>
|
||||||
<ul><li>Greatly updated and expanded documentation</li>
|
<ul><li>Greatly updated and expanded documentation</li>
|
||||||
<li>Added Larisse Bolton, Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
|
<li>Added Larisse Bolton, Jordan Stull, Matthew Saab, and Javier Sanchez as contributors, to thank them for their valuable input</li>
|
||||||
<li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li>
|
<li>Stopped support for SAS (<code>.xpt</code>) files, since their file structure and extremely inefficient and requires more disk space than GitHub allows in a single commit.</li>
|
||||||
</ul></div>
|
</ul></div>
|
||||||
<div class="section level3">
|
<div class="section level3">
|
||||||
<h3 id="older-versions-2-1-1-9087">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9087"></a></h3>
|
<h3 id="older-versions-2-1-1-9092">Older Versions<a class="anchor" aria-label="anchor" href="#older-versions-2-1-1-9092"></a></h3>
|
||||||
<p>This changelog only contains changes from AMR v3.0 (October 2024) and later.</p>
|
<p>This changelog only contains changes from AMR v3.0 (October 2024) and later.</p>
|
||||||
<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
|
<ul><li>For prior v2 versions, please see <a href="https://github.com/msberends/AMR/blob/v2.1.1/NEWS.md" class="external-link">our v2 archive</a>.</li>
|
||||||
<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>
|
<li>For prior v1 versions, please see <a href="https://github.com/msberends/AMR/blob/v1.8.2/NEWS.md" class="external-link">our v1 archive</a>.</li>
|
||||||
|
@ -12,7 +12,7 @@ articles:
|
|||||||
resistance_predict: resistance_predict.html
|
resistance_predict: resistance_predict.html
|
||||||
welcome_to_AMR: welcome_to_AMR.html
|
welcome_to_AMR: welcome_to_AMR.html
|
||||||
WHONET: WHONET.html
|
WHONET: WHONET.html
|
||||||
last_built: 2024-10-02T08:36Z
|
last_built: 2024-10-06T14:31Z
|
||||||
urls:
|
urls:
|
||||||
reference: https://msberends.github.io/AMR/reference
|
reference: https://msberends.github.io/AMR/reference
|
||||||
article: https://msberends.github.io/AMR/articles
|
article: https://msberends.github.io/AMR/articles
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@ -97,13 +97,7 @@
|
|||||||
<span class="r-in"><span><span class="co"># this will result in "Enterobacter cloacae cloacae",</span></span></span>
|
<span class="r-in"><span><span class="co"># this will result in "Enterobacter cloacae cloacae",</span></span></span>
|
||||||
<span class="r-in"><span><span class="co"># since it resembles the input best:</span></span></span>
|
<span class="r-in"><span><span class="co"># since it resembles the input best:</span></span></span>
|
||||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Enterobacter asburiae/cloacae"</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></span><span class="op">(</span><span class="st">"Enterobacter asburiae/cloacae"</span><span class="op">)</span></span></span>
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>No hits found for "Enterobacter asburiae/cloacae" with</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Enterobacter asburiae"</span>
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> minimum_matching_score = NULL (=0.538). Try setting this value lower or</span>
|
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> even to 0.</span>
|
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>The following input could not be coerced and was returned as "UNKNOWN":</span>
|
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> "Enterobacter asburiae/cloacae".</span>
|
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> You can retrieve this list with mo_failures().</span>
|
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] "(unknown name)"</span>
|
|
||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="co"># now add a custom entry - it will be considered by as.mo() and</span></span></span>
|
<span class="r-in"><span><span class="co"># now add a custom entry - it will be considered by as.mo() and</span></span></span>
|
||||||
<span class="r-in"><span><span class="co"># all mo_*() functions</span></span></span>
|
<span class="r-in"><span><span class="co"># all mo_*() functions</span></span></span>
|
||||||
@ -231,26 +225,11 @@
|
|||||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Added Citrobacter braakii complex and Citrobacter freundii complex to the</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Added Citrobacter braakii complex and Citrobacter freundii complex to the</span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> internal microorganisms data set.</span>
|
<span class="r-msg co"><span class="r-pr">#></span> internal microorganisms data set.</span>
|
||||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></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">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_name</a></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">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>No hits found for "C. freundii complex" with minimum_matching_score = NULL</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Citrobacter freundii complex" "Citrobacter braakii complex" </span>
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> (=0.16). Try setting this value lower or even to 0.</span>
|
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>The following input could not be coerced and was returned as "UNKNOWN": "C.</span>
|
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> freundii complex".</span>
|
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> You can retrieve this list with mo_failures().</span>
|
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] "(unknown name)" "Citrobacter braakii complex"</span>
|
|
||||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_species</a></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">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_species</a></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">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>No hits found for "C. freundii complex" with minimum_matching_score = NULL</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] "freundii complex" "braakii complex" </span>
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> (=0.16). Try setting this value lower or even to 0.</span>
|
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>The following input could not be coerced and was returned as "UNKNOWN": "C.</span>
|
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> freundii complex".</span>
|
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> You can retrieve this list with mo_failures().</span>
|
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] "(unknown species)" "braakii complex" </span>
|
|
||||||
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></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">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span>
|
<span class="r-in"><span><span class="fu"><a href="mo_property.html">mo_gramstain</a></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">"C. freundii complex"</span>, <span class="st">"C. braakii complex"</span><span class="op">)</span><span class="op">)</span></span></span>
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>No hits found for "C. freundii complex" with minimum_matching_score = NULL</span>
|
<span class="r-out co"><span class="r-pr">#></span> [1] "Gram-negative" "Gram-negative"</span>
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> (=0.16). Try setting this value lower or even to 0.</span>
|
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> <span class="warning">Warning: </span>The following input could not be coerced and was returned as "UNKNOWN": "C.</span>
|
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> freundii complex".</span>
|
|
||||||
<span class="r-wrn co"><span class="r-pr">#></span> You can retrieve this list with mo_failures().</span>
|
|
||||||
<span class="r-out co"><span class="r-pr">#></span> [1] NA "Gram-negative"</span>
|
|
||||||
<span class="r-in"><span><span class="co"># }</span></span></span>
|
<span class="r-in"><span><span class="co"># }</span></span></span>
|
||||||
</code></pre></div>
|
</code></pre></div>
|
||||||
</div>
|
</div>
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@ -110,16 +110,16 @@
|
|||||||
<span class="r-in"><span></span></span>
|
<span class="r-in"><span></span></span>
|
||||||
<span class="r-in"><span><span class="va">df</span></span></span>
|
<span class="r-in"><span><span class="va">df</span></span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
<span class="r-out co"><span class="r-pr">#></span> birth_date age age_exact age_at_y2k</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 1 1965-12-05 58 58.82514 34</span>
|
<span class="r-out co"><span class="r-pr">#></span> 1 1965-12-05 58 58.83607 34</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 2 1980-03-01 44 44.58743 19</span>
|
<span class="r-out co"><span class="r-pr">#></span> 2 1980-03-01 44 44.59836 19</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 3 1949-11-01 74 74.91803 50</span>
|
<span class="r-out co"><span class="r-pr">#></span> 3 1949-11-01 74 74.92896 50</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 4 1947-02-14 77 77.63115 52</span>
|
<span class="r-out co"><span class="r-pr">#></span> 4 1947-02-14 77 77.64208 52</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 5 1940-02-19 84 84.61749 59</span>
|
<span class="r-out co"><span class="r-pr">#></span> 5 1940-02-19 84 84.62842 59</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 6 1988-01-10 36 36.72678 11</span>
|
<span class="r-out co"><span class="r-pr">#></span> 6 1988-01-10 36 36.73770 11</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 7 1997-08-27 27 27.09836 2</span>
|
<span class="r-out co"><span class="r-pr">#></span> 7 1997-08-27 27 27.10929 2</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 8 1978-01-26 46 46.68306 21</span>
|
<span class="r-out co"><span class="r-pr">#></span> 8 1978-01-26 46 46.69399 21</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 9 1972-06-17 52 52.29235 27</span>
|
<span class="r-out co"><span class="r-pr">#></span> 9 1972-06-17 52 52.30328 27</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> 10 1986-08-10 38 38.14481 13</span>
|
<span class="r-out co"><span class="r-pr">#></span> 10 1986-08-10 38 38.15574 13</span>
|
||||||
</code></pre></div>
|
</code></pre></div>
|
||||||
</div>
|
</div>
|
||||||
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -9,7 +9,7 @@ In short, if you have a column name that resembles an antimicrobial drug, it wil
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@ -785,16 +785,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
|
|||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 57 × 16</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># A tibble: 57 × 16</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_given mo_given host_given ab mo </span>
|
<span class="r-out co"><span class="r-pr">#></span> datetime index ab_given mo_given host_given ab mo </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">*</span> <span style="color: #949494; font-style: italic;"><dttm></span> <span style="color: #949494; font-style: italic;"><int></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><ab></span> <span style="color: #949494; font-style: italic;"><mo></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2024-10-02 <span style="color: #949494;">08:37:04</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 1</span> 2024-10-06 <span style="color: #949494;">14:32:35</span> 4 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2024-10-02 <span style="color: #949494;">08:37:11</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 2</span> 2024-10-06 <span style="color: #949494;">14:32:42</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2024-10-02 <span style="color: #949494;">08:37:11</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 3</span> 2024-10-06 <span style="color: #949494;">14:32:42</span> 4 genta Escheri… human GEN B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2024-10-02 <span style="color: #949494;">08:37:12</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 4</span> 2024-10-06 <span style="color: #949494;">14:32:43</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2024-10-02 <span style="color: #949494;">08:37:12</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 5</span> 2024-10-06 <span style="color: #949494;">14:32:43</span> 4 genta Escheri… cattle GEN B_ESCHR_COLI </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2024-10-02 <span style="color: #949494;">08:37:04</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 6</span> 2024-10-06 <span style="color: #949494;">14:32:35</span> 3 AMX B_STRPT… human AMX B_STRPT_PNMN </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2024-10-02 <span style="color: #949494;">08:37:11</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 7</span> 2024-10-06 <span style="color: #949494;">14:32:42</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2024-10-02 <span style="color: #949494;">08:37:11</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 8</span> 2024-10-06 <span style="color: #949494;">14:32:42</span> 3 tobra Escheri… human TOB B_[ORD]_ENTRBCTR</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2024-10-02 <span style="color: #949494;">08:37:12</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;"> 9</span> 2024-10-06 <span style="color: #949494;">14:32:43</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2024-10-02 <span style="color: #949494;">08:37:12</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #BCBCBC;">10</span> 2024-10-06 <span style="color: #949494;">14:32:43</span> 3 tobra Escheri… horses TOB B_ESCHR_COLI </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 9 more variables: host <chr>, method <chr>, input <dbl>, outcome <sir>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># ℹ 9 more variables: host <chr>, method <chr>, input <dbl>, outcome <sir>,</span></span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
|
<span class="r-out co"><span class="r-pr">#></span> <span style="color: #949494;"># notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,</span></span>
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -9,7 +9,7 @@ To improve the interpretation of the antibiogram before EUCAST rules are applied
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -9,7 +9,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
@ -109,7 +109,7 @@
|
|||||||
<div class="section level2">
|
<div class="section level2">
|
||||||
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
|
||||||
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="as.mo.html">mo_reset_session</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="fu"><a href="as.mo.html">mo_reset_session</a></span><span class="op">(</span><span class="op">)</span></span></span>
|
||||||
<span class="r-msg co"><span class="r-pr">#></span> ℹ Reset 16 previously matched input values.</span>
|
<span class="r-msg co"><span class="r-pr">#></span> ℹ Reset 17 previously matched input values.</span>
|
||||||
<span class="r-in"><span></span></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-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-out co"><span class="r-pr">#></span> Class 'mo'</span>
|
<span class="r-out co"><span class="r-pr">#></span> Class 'mo'</span>
|
||||||
@ -121,10 +121,11 @@
|
|||||||
<span class="r-out co"><span class="r-pr">#></span> --------------------------------------------------------------------------------</span>
|
<span class="r-out co"><span class="r-pr">#></span> --------------------------------------------------------------------------------</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)</span>
|
<span class="r-out co"><span class="r-pr">#></span> "E. coli" -> Escherichia coli (B_ESCHR_COLI, 0.688)</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Also matched: Enterococcus crotali (0.650), Escherichia coli coli</span>
|
<span class="r-out co"><span class="r-pr">#></span> Also matched: Enterococcus crotali (0.650), Escherichia coli coli</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> (0.643), Escherichia coli expressing (0.611), Enterococcus columbae</span>
|
<span class="r-out co"><span class="r-pr">#></span> (0.643), Escherichia coli expressing (0.611), Enterobacter cowanii</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> (0.595), Enterococcus camelliae (0.591), Enterococcus casseliflavus</span>
|
<span class="r-out co"><span class="r-pr">#></span> (0.600), Enterococcus columbae (0.595), Enterococcus camelliae (0.591),</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> (0.577), Enterococcus canis (0.556), Enterococcus cecorum (0.550),</span>
|
<span class="r-out co"><span class="r-pr">#></span> Enterococcus casseliflavus (0.577), Enterobacter cloacae cloacae</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Enterococcus canintestini (0.540), and Enterobacter cowanii (0.522)</span>
|
<span class="r-out co"><span class="r-pr">#></span> (0.571), Enterobacter cloacae complex (0.571), and Enterobacter cloacae</span>
|
||||||
|
<span class="r-out co"><span class="r-pr">#></span> dissolvens (0.565)</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> </span>
|
<span class="r-out co"><span class="r-pr">#></span> </span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> Only the first 10 other matches of each record are shown. Run</span>
|
<span class="r-out co"><span class="r-pr">#></span> Only the first 10 other matches of each record are shown. Run</span>
|
||||||
<span class="r-out co"><span class="r-pr">#></span> print(mo_uncertainties(), n = ...) to view more entries, or save</span>
|
<span class="r-out co"><span class="r-pr">#></span> print(mo_uncertainties(), n = ...) to view more entries, or save</span>
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
||||||
|
@ -7,7 +7,7 @@
|
|||||||
|
|
||||||
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
|
<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="">2.1.1.9087</small>
|
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9092</small>
|
||||||
|
|
||||||
|
|
||||||
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">
|
<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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Loading…
Reference in New Issue
Block a user