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@ -7,7 +7,7 @@
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@ -21,7 +21,7 @@ The AMR package is available in English, Chinese, Czech, Danish, Dutch, Finnish,
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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reference/add_custom_antimicrobials.html
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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reference/age.html
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@ -7,7 +7,7 @@
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@ -111,16 +111,16 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="va">df</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> birth_date age age_exact age_at_y2k</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 59 59.25753 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 45 45.02192 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 75 75.35068 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 78 78.06301 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 85 85.04932 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 37 37.15890 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 27 27.53151 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 47 47.11507 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.72603 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 38 38.57808 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1965-12-05 59 59.26027 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1980-03-01 45 45.02466 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-11-01 75 75.35342 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1947-02-14 78 78.06575 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1940-02-19 85 85.05205 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1988-01-10 37 37.16164 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1997-08-27 27 27.53425 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1978-01-26 47 47.11781 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1972-06-17 52 52.72877 27</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1986-08-10 38 38.58082 13</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

2
reference/age_groups.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/antibiogram.html
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@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
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reference/antimicrobial_selectors.html
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@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
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reference/antimicrobials.html
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
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reference/as.sir.html
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@ -21,7 +21,7 @@ All breakpoints used for interpretation are available in our clinical_breakpoint
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@ -810,16 +810,16 @@ A microorganism is categorised as "Resistant" when there is a high likelihood of
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 57 × 16</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index ab_given mo_given host_given ab mo </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span> <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-03-09 <span style="color: #949494;">09:46:00</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-03-09 <span style="color: #949494;">09:46:00</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-03-09 <span style="color: #949494;">09:46:00</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2025-03-09 <span style="color: #949494;">09:46:00</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-03-09 <span style="color: #949494;">09:46:00</span> 2 cipro Escheri… dogs CIP <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-03-09 <span style="color: #949494;">09:46:00</span> 2 cipro Escheri… dogs CIP <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-03-09 <span style="color: #949494;">09:46:01</span> 2 nitrofu… E. coli human NIT <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-03-09 <span style="color: #949494;">09:46:01</span> 2 nitrofu… E. coli human NIT <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-03-09 <span style="color: #949494;">09:46:00</span> 1 genta bacteria human GEN <span style="color: #949494;">B_</span>[KNG]<span style="color: #949494;">_</span>BACTERIA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-03-09 <span style="color: #949494;">09:46:00</span> 1 cipro bacteria human CIP <span style="color: #949494;">B_</span>[KNG]<span style="color: #949494;">_</span>BACTERIA</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 2025-03-10 <span style="color: #949494;">11:24:34</span> 4 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> 2025-03-10 <span style="color: #949494;">11:24:41</span> 4 genta Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> 2025-03-10 <span style="color: #949494;">11:24:41</span> 4 genta Escheri… human GEN <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> 2025-03-10 <span style="color: #949494;">11:24:42</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> 2025-03-10 <span style="color: #949494;">11:24:42</span> 4 genta Escheri… cattle GEN <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> 2025-03-10 <span style="color: #949494;">11:24:34</span> 3 AMX B_STRPT… human AMX <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>PNMN </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> 2025-03-10 <span style="color: #949494;">11:24:41</span> 3 tobra Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 2025-03-10 <span style="color: #949494;">11:24:41</span> 3 tobra Escheri… human TOB <span style="color: #949494;">B_</span>[ORD]<span style="color: #949494;">_</span>ENTRBCTR</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 2025-03-10 <span style="color: #949494;">11:24:42</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 2025-03-10 <span style="color: #949494;">11:24:42</span> 3 tobra Escheri… horses TOB <span style="color: #949494;">B_</span>ESCHR<span style="color: #949494;">_</span>COLI </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 47 more rows</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 9 more variables: host &lt;chr&gt;, method &lt;chr&gt;, input &lt;chr&gt;, outcome &lt;sir&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>

2
reference/atc_online.html
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@ -7,7 +7,7 @@
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9190</small>
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2
reference/av_property.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9190</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9191</small>
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2
reference/availability.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9190</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9191</small>
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2
reference/bug_drug_combinations.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9190</small>
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reference/clinical_breakpoints.html
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@ -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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9190</small>
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reference/count.html
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@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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2
reference/custom_eucast_rules.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9190</small>
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2
reference/dosage.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9190</small>
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reference/eucast_rules.html
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@ -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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9190</small>
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2
reference/example_isolates.html
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@ -7,7 +7,7 @@
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2
reference/example_isolates_unclean.html
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@ -7,7 +7,7 @@
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reference/export_ncbi_biosample.html
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@ -7,7 +7,7 @@
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2
reference/first_isolate.html
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@ -9,7 +9,7 @@
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reference/g.test.html
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@ -7,7 +7,7 @@
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reference/get_episode.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/ggplot_pca.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/ggplot_sir.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/guess_ab_col.html
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@ -7,7 +7,7 @@
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2
reference/index.html
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@ -7,7 +7,7 @@
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reference/intrinsic_resistant.html
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@ -7,7 +7,7 @@
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reference/italicise_taxonomy.html
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@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9190</small>
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2
reference/join.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9190</small>
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2
reference/key_antimicrobials.html
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@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9190</small>
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2
reference/kurtosis.html
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@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9190</small>
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2
reference/like.html
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@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9190</small>
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2
reference/mdro.html
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@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9190</small>
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2
reference/mean_amr_distance.html
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@ -7,7 +7,7 @@
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2
reference/microorganisms.codes.html
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@ -7,7 +7,7 @@
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reference/microorganisms.groups.html
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@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">2.1.1.9190</small>
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2
reference/microorganisms.html
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@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
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2
reference/mo_matching_score.html
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@ -7,7 +7,7 @@
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2
reference/mo_property.html
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@ -7,7 +7,7 @@
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reference/mo_source.html
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@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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reference/pca.html
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@ -7,7 +7,7 @@
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2
reference/plot.html
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@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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2
reference/proportion.html
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@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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2
reference/random.html
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@ -7,7 +7,7 @@
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2
reference/resistance_predict.html
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@ -7,7 +7,7 @@
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reference/skewness.html
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@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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reference/top_n_microorganisms.html
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@ -7,7 +7,7 @@
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reference/translate.html
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@ -7,7 +7,7 @@
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