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2
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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
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reference/AMR-options.html
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@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
<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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
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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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
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8
reference/NA_ab_.html Normal file
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@@ -0,0 +1,8 @@
<html>
<head>
<meta http-equiv="refresh" content="0;URL=https://amr-for-r.org/reference/as.ab.html" />
<meta name="robots" content="noindex">
<link rel="canonical" href="https://amr-for-r.org/reference/as.ab.html">
</head>
</html>

8
reference/NA_mo_.html Normal file
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@@ -0,0 +1,8 @@
<html>
<head>
<meta http-equiv="refresh" content="0;URL=https://amr-for-r.org/reference/as.mo.html" />
<meta name="robots" content="noindex">
<link rel="canonical" href="https://amr-for-r.org/reference/as.mo.html">
</head>
</html>

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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
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2
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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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/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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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/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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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/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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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/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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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 46 46.01370 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.60548 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 76 76.50137 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 39 39.58356 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 93 93.28767 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.92877 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.69589 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 62 62.46301 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.80000 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 73 73.30137 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1980-02-27 46 46.01918 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1953-07-26 72 72.61096 46</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1949-09-02 76 76.50685 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1986-08-03 39 39.58904 13</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1932-11-19 93 93.29315 67</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1949-03-30 76 76.93425 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1996-06-23 29 29.70137 3</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1963-09-16 62 62.46849 36</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1952-05-16 73 73.80548 47</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1952-11-14 73 73.30685 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
View File

@@ -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 46 46.01370 19
#> 2 1953-07-26 72 72.60548 46
#> 3 1949-09-02 76 76.50137 50
#> 4 1986-08-03 39 39.58356 13
#> 5 1932-11-19 93 93.28767 67
#> 6 1949-03-30 76 76.92877 50
#> 7 1996-06-23 29 29.69589 3
#> 8 1963-09-16 62 62.46301 36
#> 9 1952-05-16 73 73.80000 47
#> 10 1952-11-14 73 73.30137 47
#> 1 1980-02-27 46 46.01918 19
#> 2 1953-07-26 72 72.61096 46
#> 3 1949-09-02 76 76.50685 50
#> 4 1986-08-03 39 39.58904 13
#> 5 1932-11-19 93 93.29315 67
#> 6 1949-03-30 76 76.93425 50
#> 7 1996-06-23 29 29.70137 3
#> 8 1963-09-16 62 62.46849 36
#> 9 1952-05-16 73 73.80548 47
#> 10 1952-11-14 73 73.30685 47
```

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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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/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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
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2
reference/antibiogram.html
View File

@@ -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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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/antimicrobial_selectors.html
View File

@@ -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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</small>
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2
reference/antimicrobials.html
View File

@@ -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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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">

7
reference/as.ab.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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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">
@@ -60,7 +60,9 @@
<span></span>
<span><span class="fu">is.ab</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">ab_reset_session</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu">ab_reset_session</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="va">NA_ab_</span></span></code></pre></div>
</div>
<div class="section level2">
@@ -101,6 +103,7 @@
</ul><p>Use the <code><a href="ab_property.html">ab_*</a></code> functions to get properties based on the returned antibiotic ID, see <em>Examples</em>.</p>
<p>Note: the <code>as.ab()</code> and <code><a href="ab_property.html">ab_*</a></code> functions may use very long regular expression to match brand names of antimicrobial drugs. This may fail on some systems.</p>
<p>You can add your own manual codes to be considered by <code>as.ab()</code> and all <code><a href="ab_property.html">ab_*</a></code> functions, see <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p>
<p><code>NA_ab_</code> is a missing value of the new <code>ab</code> class, analogous to e.g. base <span style="R">R</span>'s <code><a href="https://rdrr.io/r/base/NA.html" class="external-link">NA_character_</a></code>.</p>
</div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>

5
reference/as.ab.md
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@@ -15,6 +15,8 @@ as.ab(x, flag_multiple_results = TRUE, language = get_AMR_locale(),
is.ab(x)
ab_reset_session()
NA_ab_
```
## Arguments
@@ -91,6 +93,9 @@ You can add your own manual codes to be considered by `as.ab()` and all
[`ab_*`](https://amr-for-r.org/reference/ab_property.md) functions, see
[`add_custom_antimicrobials()`](https://amr-for-r.org/reference/add_custom_antimicrobials.md).
`NA_ab_` is a missing value of the new `ab` class, analogous to e.g.
base R's [`NA_character_`](https://rdrr.io/r/base/NA.html).
## Source
World Health Organization (WHO) Collaborating Centre for Drug Statistics

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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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">

7
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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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">
@@ -74,7 +74,9 @@
<span></span>
<span><span class="fu">mo_reset_session</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="fu">mo_cleaning_regex</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu">mo_cleaning_regex</span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="va">NA_mo_</span></span></code></pre></div>
</div>
<div class="section level2">
@@ -201,6 +203,7 @@
</ul><p>This is based on:</p><ul><li><p>Lancefield RC (1933). <strong>A serological differentiation of human and other groups of hemolytic streptococci.</strong> <em>J Exp Med.</em> 57(4): 571-95; <a href="https://doi.org/10.1084/jem.57.4.571" class="external-link">doi:10.1084/jem.57.4.571</a></p></li>
</ul></div>
<p><code>NA_mo_</code> is a missing value of the new <code>mo</code> class, analogous to e.g. base <span style="R">R</span>'s <code><a href="https://rdrr.io/r/base/NA.html" class="external-link">NA_character_</a></code>.</p>
</div>
<div class="section level2">
<h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>

5
reference/as.mo.md
View File

@@ -32,6 +32,8 @@ mo_failures()
mo_reset_session()
mo_cleaning_regex()
NA_mo_
```
## Arguments
@@ -338,6 +340,9 @@ This is based on:
other groups of hemolytic streptococci.** *J Exp Med.* 57(4): 571-95;
[doi:10.1084/jem.57.4.571](https://doi.org/10.1084/jem.57.4.571)
`NA_mo_` is a missing value of the new `mo` class, analogous to e.g.
base R's [`NA_character_`](https://rdrr.io/r/base/NA.html).
## Source
- Berends MS *et al.* (2022). **AMR: An R Package for Working with

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="">3.0.1.9023</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9026</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> 2026-03-04 <span style="color: #949494;">08:07:22</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> 2026-03-04 <span style="color: #949494;">08:07:22</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> 2026-03-04 <span style="color: #949494;">08:07:23</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> 2026-03-04 <span style="color: #949494;">08:07:23</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> 2026-03-06 <span style="color: #949494;">11:51:54</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> 2026-03-06 <span style="color: #949494;">11:51:54</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> 2026-03-06 <span style="color: #949494;">11:51:55</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> 2026-03-06 <span style="color: #949494;">11:51:55</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 2026-03-04 08:07:22 1 MIC amoxicillin Escherich… human 8
#> 2 2026-03-04 08:07:22 1 MIC cipro Escherich… human 0.256
#> 3 2026-03-04 08:07:23 1 DISK tobra Escherich… human 16
#> 4 2026-03-04 08:07:23 1 DISK genta Escherich… human 18
#> 1 2026-03-06 11:51:54 1 MIC amoxicillin Escherich… human 8
#> 2 2026-03-06 11:51:54 1 MIC cipro Escherich… human 0.256
#> 3 2026-03-06 11:51:55 1 DISK tobra Escherich… human 16
#> 4 2026-03-06 11:51:55 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="">3.0.1.9023</small>
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2
reference/av_from_text.html
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@@ -7,7 +7,7 @@
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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>
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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="">3.0.1.9023</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="">3.0.1.9023</small>
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2
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>
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2
reference/count.html
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@@ -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>
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2
reference/custom_eucast_rules.html
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@@ -7,7 +7,7 @@
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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>
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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>
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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>
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reference/example_isolates.html
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@@ -7,7 +7,7 @@
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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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reference/first_isolate.html
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@@ -9,7 +9,7 @@
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2
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 @@
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reference/ggplot_pca.html
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@@ -7,7 +7,7 @@
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2
reference/ggplot_sir.html
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@@ -7,7 +7,7 @@
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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>
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6
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="">3.0.1.9023</small>
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@@ -75,7 +75,7 @@
<dl><dt>
<code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_reset_session()</a></code> <code><a href="as.mo.html">mo_cleaning_regex()</a></code>
<code><a href="as.mo.html">as.mo()</a></code> <code><a href="as.mo.html">is.mo()</a></code> <code><a href="as.mo.html">mo_uncertainties()</a></code> <code><a href="as.mo.html">mo_renamed()</a></code> <code><a href="as.mo.html">mo_failures()</a></code> <code><a href="as.mo.html">mo_reset_session()</a></code> <code><a href="as.mo.html">mo_cleaning_regex()</a></code> <code><a href="as.mo.html">NA_mo_</a></code>
</dt>
<dd>Transform Arbitrary Input to Valid Microbial Taxonomy</dd>
@@ -112,7 +112,7 @@
<dl><dt>
<code><a href="as.ab.html">as.ab()</a></code> <code><a href="as.ab.html">is.ab()</a></code> <code><a href="as.ab.html">ab_reset_session()</a></code>
<code><a href="as.ab.html">as.ab()</a></code> <code><a href="as.ab.html">is.ab()</a></code> <code><a href="as.ab.html">ab_reset_session()</a></code> <code><a href="as.ab.html">NA_ab_</a></code>
</dt>
<dd>Transform Input to an Antibiotic ID</dd>

10
reference/index.md
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@@ -29,8 +29,9 @@ to add your own custom microorganisms to this package.
[`mo_renamed()`](https://amr-for-r.org/reference/as.mo.md)
[`mo_failures()`](https://amr-for-r.org/reference/as.mo.md)
[`mo_reset_session()`](https://amr-for-r.org/reference/as.mo.md)
[`mo_cleaning_regex()`](https://amr-for-r.org/reference/as.mo.md) :
Transform Arbitrary Input to Valid Microbial Taxonomy
[`mo_cleaning_regex()`](https://amr-for-r.org/reference/as.mo.md)
[`NA_mo_`](https://amr-for-r.org/reference/as.mo.md) : Transform
Arbitrary Input to Valid Microbial Taxonomy
- [`mo_name()`](https://amr-for-r.org/reference/mo_property.md)
[`mo_fullname()`](https://amr-for-r.org/reference/mo_property.md)
[`mo_shortname()`](https://amr-for-r.org/reference/mo_property.md)
@@ -85,8 +86,9 @@ from clinical text records, using
- [`as.ab()`](https://amr-for-r.org/reference/as.ab.md)
[`is.ab()`](https://amr-for-r.org/reference/as.ab.md)
[`ab_reset_session()`](https://amr-for-r.org/reference/as.ab.md) :
Transform Input to an Antibiotic ID
[`ab_reset_session()`](https://amr-for-r.org/reference/as.ab.md)
[`NA_ab_`](https://amr-for-r.org/reference/as.ab.md) : Transform Input
to an Antibiotic ID
- [`ab_name()`](https://amr-for-r.org/reference/ab_property.md)
[`ab_cid()`](https://amr-for-r.org/reference/ab_property.md)
[`ab_synonyms()`](https://amr-for-r.org/reference/ab_property.md)

2
reference/interpretive_rules.html
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@@ -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>
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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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@@ -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/microorganisms.codes.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/microorganisms.groups.html
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@@ -7,7 +7,7 @@
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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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
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reference/mo_matching_score.html
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@@ -7,7 +7,7 @@
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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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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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
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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/resistance_predict.html
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@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9023</small>
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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
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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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