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reference/AMR-deprecated.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
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reference/AMR-options.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
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2
reference/AMR.html
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@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
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2
reference/WHOCC.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
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reference/WHONET.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
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2
reference/ab_from_text.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
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2
reference/ab_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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
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2
reference/add_custom_antimicrobials.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
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2
reference/add_custom_microorganisms.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

22
reference/age.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">
@@ -112,16 +112,16 @@
<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 1980-02-27 45 45.94795 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.53973 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 76 76.43562 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 39 39.51781 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 93 93.22192 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.86301 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.63014 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 62 62.39726 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.73425 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 73 73.23562 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1980-02-27 45 45.95068 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.54247 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 76 76.43836 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 39 39.52055 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 93 93.22466 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.86575 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.63288 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 62 62.40000 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.73699 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 73 73.23836 47</span>
</code></pre></div>
</div>
</main><aside class="col-md-3"><nav id="toc" aria-label="Table of contents"><h2>On this page</h2>

20
reference/age.md
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@@ -81,14 +81,14 @@ df$age_at_y2k <- age(df$birth_date, "2000-01-01")
df
#> birth_date age age_exact age_at_y2k
#> 1 1980-02-27 45 45.94795 19
#> 2 1953-07-26 72 72.53973 46
#> 3 1949-09-02 76 76.43562 50
#> 4 1986-08-03 39 39.51781 13
#> 5 1932-11-19 93 93.22192 67
#> 6 1949-03-30 76 76.86301 50
#> 7 1996-06-23 29 29.63014 3
#> 8 1963-09-16 62 62.39726 36
#> 9 1952-05-16 73 73.73425 47
#> 10 1952-11-14 73 73.23562 47
#> 1 1980-02-27 45 45.95068 19
#> 2 1953-07-26 72 72.54247 46
#> 3 1949-09-02 76 76.43836 50
#> 4 1986-08-03 39 39.52055 13
#> 5 1932-11-19 93 93.22466 67
#> 6 1949-03-30 76 76.86575 50
#> 7 1996-06-23 29 29.63288 3
#> 8 1963-09-16 62 62.40000 36
#> 9 1952-05-16 73 73.73699 47
#> 10 1952-11-14 73 73.23836 47
```

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reference/age_groups.html
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reference/age_groups.md
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2
reference/amr-tidymodels.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

2
reference/antibiogram.html
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@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
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2
reference/antimicrobial_selectors.html
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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

2
reference/antimicrobials.html
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
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2
reference/as.ab.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
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2
reference/as.av.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

2
reference/as.disk.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

2
reference/as.mic.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

2
reference/as.mo.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

10
reference/as.sir.html
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@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">
@@ -424,10 +424,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> datetime index method ab_given mo_given host_given input_given</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;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-02-08 <span style="color: #949494;">22:25:52</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-02-08 <span style="color: #949494;">22:25:53</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-02-08 <span style="color: #949494;">22:25:53</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-02-08 <span style="color: #949494;">22:25:54</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-02-09 <span style="color: #949494;">12:50:16</span> 1 MIC amoxicillin Escherich… human 8 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-02-09 <span style="color: #949494;">12:50:17</span> 1 MIC cipro Escherich… human 0.256 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-02-09 <span style="color: #949494;">12:50:17</span> 1 DISK tobra Escherich… human 16 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-02-09 <span style="color: #949494;">12:50:17</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>

8
reference/as.sir.md
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@@ -660,10 +660,10 @@ sir_interpretation_history()
#> # A tibble: 4 × 18
#> datetime index method ab_given mo_given host_given input_given
#> <dttm> <int> <chr> <chr> <chr> <chr> <chr>
#> 1 2026-02-08 22:25:52 1 MIC amoxicillin Escherich… human 8
#> 2 2026-02-08 22:25:53 1 MIC cipro Escherich… human 0.256
#> 3 2026-02-08 22:25:53 1 DISK tobra Escherich… human 16
#> 4 2026-02-08 22:25:54 1 DISK genta Escherich… human 18
#> 1 2026-02-09 12:50:16 1 MIC amoxicillin Escherich… human 8
#> 2 2026-02-09 12:50:17 1 MIC cipro Escherich… human 0.256
#> 3 2026-02-09 12:50:17 1 DISK tobra Escherich… human 16
#> 4 2026-02-09 12:50:17 1 DISK genta Escherich… human 18
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr>

2
reference/atc_online.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</small>
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2
reference/av_from_text.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

2
reference/clinical_breakpoints.html
View File

@@ -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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

2
reference/count.html
View File

@@ -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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

2
reference/custom_mdro_guideline.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

2
reference/esbl_isolates.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

2
reference/example_isolates.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

2
reference/example_isolates_unclean.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

2
reference/export_ncbi_biosample.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

6803
reference/first_isolate.html
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6801
reference/first_isolate.md
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File diff suppressed because it is too large Load Diff

2
reference/g.test.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

2
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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

2
reference/ggplot_pca.html
View File

@@ -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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

9
reference/ggplot_sir.html
View File

@@ -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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">
@@ -257,13 +257,6 @@
<span class="r-in"><span> <span class="fu"><a href="https://dplyr.tidyverse.org/reference/select.html" class="external-link">select</a></span><span class="op">(</span><span class="va">age_group</span>, <span class="va">CIP</span><span class="op">)</span> <span class="op"><a href="https://magrittr.tidyverse.org/reference/pipe.html" class="external-link">%&gt;%</a></span></span></span>
<span class="r-in"><span> <span class="fu">ggplot_sir</span><span class="op">(</span>x <span class="op">=</span> <span class="st">"age_group"</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 1131 warnings in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `first_isolate = first_isolate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> in <span style="background-color: #444444;">`as.sir()`</span>: 7 results in column 'first_isolate' truncated (18%) that</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> were invalid antimicrobial interpretations: "."</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 1130 remaining warnings.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 6 rows containing missing values or values outside the scale range</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> (`geom_col()`).</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>Removed 6 rows containing missing values or values outside the scale range</span>

7
reference/ggplot_sir.md
View File

@@ -267,13 +267,6 @@ if (require("ggplot2") && require("dplyr")) {
select(age_group, CIP) %>%
ggplot_sir(x = "age_group")
}
#> Warning: There were 1131 warnings in `mutate()`.
#> The first warning was:
#> ℹ In argument: `first_isolate = first_isolate()`.
#> Caused by warning:
#> ! in `as.sir()`: 7 results in column 'first_isolate' truncated (18%) that
#> were invalid antimicrobial interpretations: "."
#> ℹ Run `dplyr::last_dplyr_warnings()` to see the 1130 remaining warnings.
#> Warning: Removed 6 rows containing missing values or values outside the scale range
#> (`geom_col()`).
#> Warning: Removed 6 rows containing missing values or values outside the scale range

2
reference/guess_ab_col.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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

2
reference/index.html
View File

@@ -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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">

26
reference/interpretive_rules.html
View File

@@ -13,7 +13,7 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
<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="">3.0.1.9019</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9020</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">
@@ -64,19 +64,21 @@ To improve the interpretation of the antibiogram before CLSI/EUCAST interpretive
<div class="section level2">
<h2 id="ref-usage">Usage<a class="anchor" aria-label="anchor" href="#ref-usage"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">interpretive_rules</span><span class="op">(</span><span class="va">x</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>,</span>
<span> <span class="st">"EUCAST"</span><span class="op">)</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
<div class="sourceCode"><pre class="sourceCode r"><code><span><span class="fu">interpretive_rules</span><span class="op">(</span><span class="va">x</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> rules <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_interpretive_rules"</span>, default <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">"breakpoints"</span>,</span>
<span> <span class="st">"expected_phenotypes"</span><span class="op">)</span><span class="op">)</span>, verbose <span class="op">=</span> <span class="cn">FALSE</span>, version_breakpoints <span class="op">=</span> <span class="fl">15</span>,</span>
<span> <span class="st">"expected_phenotypes"</span><span class="op">)</span><span class="op">)</span>, guideline <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_guideline"</span>, <span class="st">"EUCAST"</span><span class="op">)</span>,</span>
<span> verbose <span class="op">=</span> <span class="cn">FALSE</span>, version_breakpoints <span class="op">=</span> <span class="fl">15</span>,</span>
<span> version_expected_phenotypes <span class="op">=</span> <span class="fl">1.2</span>, version_expertrules <span class="op">=</span> <span class="fl">3.3</span>,</span>
<span> ampc_cephalosporin_resistance <span class="op">=</span> <span class="cn">NA</span>, only_sir_columns <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/any.html" class="external-link">any</a></span><span class="op">(</span><span class="fu"><a href="as.sir.html">is.sir</a></span><span class="op">(</span><span class="va">x</span><span class="op">)</span><span class="op">)</span>,</span>
<span> custom_rules <span class="op">=</span> <span class="cn">NULL</span>, overwrite <span class="op">=</span> <span class="cn">FALSE</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">eucast_rules</span><span class="op">(</span><span class="va">x</span>, rules <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_interpretive_rules"</span>, default <span class="op">=</span></span>
<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">"breakpoints"</span>, <span class="st">"expected_phenotypes"</span><span class="op">)</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">eucast_rules</span><span class="op">(</span><span class="va">x</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> rules <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_interpretive_rules"</span>, default <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">"breakpoints"</span>,</span>
<span> <span class="st">"expected_phenotypes"</span><span class="op">)</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">clsi_rules</span><span class="op">(</span><span class="va">x</span>, rules <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_interpretive_rules"</span>, default <span class="op">=</span></span>
<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">"breakpoints"</span>, <span class="st">"expected_phenotypes"</span><span class="op">)</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span><span class="fu">clsi_rules</span><span class="op">(</span><span class="va">x</span>, col_mo <span class="op">=</span> <span class="cn">NULL</span>, info <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/interactive.html" class="external-link">interactive</a></span><span class="op">(</span><span class="op">)</span>,</span>
<span> rules <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/options.html" class="external-link">getOption</a></span><span class="op">(</span><span class="st">"AMR_interpretive_rules"</span>, default <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">"breakpoints"</span>,</span>
<span> <span class="st">"expected_phenotypes"</span><span class="op">)</span><span class="op">)</span>, <span class="va">...</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">eucast_dosage</span><span class="op">(</span><span class="va">ab</span>, administration <span class="op">=</span> <span class="st">"iv"</span>, version_breakpoints <span class="op">=</span> <span class="fl">15</span><span class="op">)</span></span></code></pre></div>
</div>
@@ -106,10 +108,6 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dd><p>Column name of the names or codes of the microorganisms (see <code><a href="as.mo.html">as.mo()</a></code>) - the default is the first column of class <code><a href="as.mo.html">mo</a></code>. Values will be coerced using <code><a href="as.mo.html">as.mo()</a></code>.</p></dd>
<dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt>
<dd><p>A guideline name, either "EUCAST" (default) or "CLSI". This can be set with the package option <code><a href="AMR-options.html">AMR_guideline</a></code>.</p></dd>
<dt id="arg-info">info<a class="anchor" aria-label="anchor" href="#arg-info"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate whether progress should be printed to the console - the default is only print while in interactive sessions.</p></dd>
@@ -118,6 +116,10 @@ Leclercq et al. <strong>EUCAST expert rules in antimicrobial susceptibility test
<dd><p>A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> vector that specifies which rules should be applied. Must be one or more of <code>"breakpoints"</code>, <code>"expected_phenotypes"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expected_phenotypes")</code>. The default value can be set to another value using the package option <code><a href="AMR-options.html">AMR_interpretive_rules</a></code>: <code>options(AMR_interpretive_rules = "all")</code>. If using <code>"custom"</code>, be sure to fill in argument <code>custom_rules</code> too. Custom rules can be created with <code><a href="custom_eucast_rules.html">custom_eucast_rules()</a></code>.</p></dd>
<dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt>
<dd><p>A guideline name, either "EUCAST" (default) or "CLSI". This can be set with the package option <code><a href="AMR-options.html">AMR_guideline</a></code>.</p></dd>
<dt id="arg-verbose">verbose<a class="anchor" aria-label="anchor" href="#arg-verbose"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.</p></dd>

28
reference/interpretive_rules.md
View File

@@ -22,19 +22,21 @@ at default, see *Details*.
## Usage
``` r
interpretive_rules(x, col_mo = NULL, guideline = getOption("AMR_guideline",
"EUCAST"), info = interactive(),
interpretive_rules(x, col_mo = NULL, info = interactive(),
rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
"expected_phenotypes")), verbose = FALSE, version_breakpoints = 15,
"expected_phenotypes")), guideline = getOption("AMR_guideline", "EUCAST"),
verbose = FALSE, version_breakpoints = 15,
version_expected_phenotypes = 1.2, version_expertrules = 3.3,
ampc_cephalosporin_resistance = NA, only_sir_columns = any(is.sir(x)),
custom_rules = NULL, overwrite = FALSE, ...)
eucast_rules(x, rules = getOption("AMR_interpretive_rules", default =
c("breakpoints", "expected_phenotypes")), ...)
eucast_rules(x, col_mo = NULL, info = interactive(),
rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
"expected_phenotypes")), ...)
clsi_rules(x, rules = getOption("AMR_interpretive_rules", default =
c("breakpoints", "expected_phenotypes")), ...)
clsi_rules(x, col_mo = NULL, info = interactive(),
rules = getOption("AMR_interpretive_rules", default = c("breakpoints",
"expected_phenotypes")), ...)
eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
```
@@ -87,12 +89,6 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
[`mo`](https://amr-for-r.org/reference/as.mo.md). Values will be
coerced using [`as.mo()`](https://amr-for-r.org/reference/as.mo.md).
- guideline:
A guideline name, either "EUCAST" (default) or "CLSI". This can be set
with the package option
[`AMR_guideline`](https://amr-for-r.org/reference/AMR-options.md).
- info:
A [logical](https://rdrr.io/r/base/logical.html) to indicate whether
@@ -113,6 +109,12 @@ eucast_dosage(ab, administration = "iv", version_breakpoints = 15)
created with
[`custom_eucast_rules()`](https://amr-for-r.org/reference/custom_eucast_rules.md).
- guideline:
A guideline name, either "EUCAST" (default) or "CLSI". This can be set
with the package option
[`AMR_guideline`](https://amr-for-r.org/reference/AMR-options.md).
- verbose:
A [logical](https://rdrr.io/r/base/logical.html) to turn Verbose mode

2
reference/intrinsic_resistant.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="">3.0.1.9019</small>
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reference/italicise_taxonomy.html
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@@ -7,7 +7,7 @@
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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="">3.0.1.9019</small>
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14
reference/key_antimicrobials.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="">3.0.1.9019</small>
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@@ -168,14 +168,10 @@
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="co"># those strings can be compared with:</span></span></span>
<span class="r-in"><span><span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #444444;">`as.sir()`</span>: 4 results truncated (33%) that were invalid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretations: "."</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] TRUE</span>
<span class="r-in"><span><span class="co"># TRUE, because I is ignored (as well as missing values)</span></span></span>
<span class="r-in"><span></span></span>
<span class="r-in"><span><span class="fu">antimicrobials_equal</span><span class="op">(</span><span class="va">strainA</span>, <span class="va">strainB</span>, type <span class="op">=</span> <span class="st">"keyantimicrobials"</span>, ignore_I <span class="op">=</span> <span class="cn">FALSE</span><span class="op">)</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>in <span style="background-color: #444444;">`as.sir()`</span>: 4 results truncated (33%) that were invalid antimicrobial</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> interpretations: "."</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] FALSE</span>
<span class="r-in"><span><span class="co"># FALSE, because I is not ignored and so the 4th [character] differs</span></span></span>
<span class="r-in"><span></span></span>
@@ -195,14 +191,6 @@
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_regular</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span> <span class="fu"><a href="https://rdrr.io/r/base/sum.html" class="external-link">sum</a></span><span class="op">(</span><span class="va">my_patients</span><span class="op">$</span><span class="va">first_weighted</span>, na.rm <span class="op">=</span> <span class="cn">TRUE</span><span class="op">)</span></span></span>
<span class="r-in"><span><span class="op">}</span></span></span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span class="warning">Warning: </span>There were 823 warnings in `mutate()`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> The first warning was:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> In argument: `first_weighted = first_isolate(col_keyantimicrobials =</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> "keyab")`.</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> Caused by warning:</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #BBBB00;">!</span> in <span style="background-color: #444444;">`as.sir()`</span>: 1 result in column 'first_weighted' truncated (8%) that were</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> invalid antimicrobial interpretations: "."</span>
<span class="r-wrn co"><span class="r-pr">#&gt;</span> <span style="color: #00BBBB;">ℹ</span> Run `dplyr::last_dplyr_warnings()` to see the 822 remaining warnings.</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> [1] 1383</span>
<span class="r-in"><span><span class="co"># }</span></span></span>
</code></pre></div>

12
reference/key_antimicrobials.md
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@@ -195,14 +195,10 @@ strainB <- "SSSIRSSSRSSS"
# those strings can be compared with:
antimicrobials_equal(strainA, strainB, type = "keyantimicrobials")
#> Warning: in `as.sir()`: 4 results truncated (33%) that were invalid antimicrobial
#> interpretations: "."
#> [1] TRUE
# TRUE, because I is ignored (as well as missing values)
antimicrobials_equal(strainA, strainB, type = "keyantimicrobials", ignore_I = FALSE)
#> Warning: in `as.sir()`: 4 results truncated (33%) that were invalid antimicrobial
#> interpretations: "."
#> [1] FALSE
# FALSE, because I is not ignored and so the 4th [character] differs
@@ -222,14 +218,6 @@ if (require("dplyr")) {
sum(my_patients$first_regular, na.rm = TRUE)
sum(my_patients$first_weighted, na.rm = TRUE)
}
#> Warning: There were 823 warnings in `mutate()`.
#> The first warning was:
#> ℹ In argument: `first_weighted = first_isolate(col_keyantimicrobials =
#> "keyab")`.
#> Caused by warning:
#> ! in `as.sir()`: 1 result in column 'first_weighted' truncated (8%) that were
#> invalid antimicrobial interpretations: "."
#> ℹ Run `dplyr::last_dplyr_warnings()` to see the 822 remaining warnings.
#> [1] 1383
# }
```

2
reference/kurtosis.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="">3.0.1.9019</small>
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reference/like.html
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@@ -7,7 +7,7 @@
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@@ -7,7 +7,7 @@
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reference/mean_amr_distance.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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2
reference/microorganisms.codes.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="">3.0.1.9019</small>
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2
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="">3.0.1.9019</small>
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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
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/mo_matching_score.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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2
reference/mo_property.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/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
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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@@ -7,7 +7,7 @@
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reference/plot.html
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@@ -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>
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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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reference/random.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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