P281424/AMR
1
0
Fork 0
mirror of https://github.com/msberends/AMR.git synced 2026-09-11 16:58:56 +02:00
Code Releases Activity

Built site for AMR@3.0.1.9088: bbdd3a9

Browse Source
This commit is contained in:
github-actions
2026-09-03 12:36:14 +00:00
parent 8fbf4f8f0b
commit 9a21a80414
96 changed files with 272 additions and 272 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
reference/AMR-deprecated.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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-options.html
View File

@@ -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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">

5
reference/AMR.html
View File

@@ -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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">
@@ -112,7 +112,8 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
<div class="section level2">
<h2 id="author">Author<a class="anchor" aria-label="anchor" href="#author"></a></h2>
<p><strong>Maintainer</strong>: Matthijs S. Berends <a href="mailto:m.s.berends@umcg.nl">m.s.berends@umcg.nl</a> (<a href="https://orcid.org/0000-0001-7620-1800" class="external-link">ORCID</a>)</p>
<p>Authors:</p><ul><li><p>Dennis Souverein (<a href="https://orcid.org/0000-0003-0455-0336" class="external-link">ORCID</a>) [contributor]</p></li>
<p>Authors:</p><ul><li><p>Matthijs S. Berends <a href="mailto:m.s.berends@umcg.nl">m.s.berends@umcg.nl</a> (<a href="https://orcid.org/0000-0001-7620-1800" class="external-link">ORCID</a>)</p></li>
<li><p>Dennis Souverein (<a href="https://orcid.org/0000-0003-0455-0336" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Erwin E. A. Hassing [contributor]</p></li>
</ul><p>Other contributors:</p><ul><li><p>Aislinn Cook (<a href="https://orcid.org/0000-0002-9189-7815" class="external-link">ORCID</a>) [contributor]</p></li>
<li><p>Andrew P. Norgan (<a href="https://orcid.org/0000-0002-2955-2066" class="external-link">ORCID</a>) [contributor]</p></li>

3
reference/AMR.md
View File

@@ -102,6 +102,9 @@ Useful links:
Authors:
- Matthijs S. Berends <m.s.berends@umcg.nl>
([ORCID](https://orcid.org/0000-0001-7620-1800))
- Dennis Souverein ([ORCID](https://orcid.org/0000-0003-0455-0336))
\[contributor\]

2
reference/WHOCC.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/WHONET.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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
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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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
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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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
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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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
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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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
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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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 1999-06-30 27 27.13973 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.55616 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.70685 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.47123 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.80000 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.51233 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.49863 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.60822 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 28 28.98082 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.56438 21</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 1 1999-06-30 27 27.17808 0</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 2 1968-01-29 58 58.59452 31</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 3 1965-12-05 60 60.74521 34</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 4 1980-03-01 46 46.50959 19</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 5 1949-11-01 76 76.83836 50</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 6 1947-02-14 79 79.55068 52</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 7 1940-02-19 86 86.53699 59</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 8 1988-01-10 38 38.64658 11</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 9 1997-08-27 29 29.01918 2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26 48 48.60274 21</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 1999-06-30 27 27.13973 0
#> 2 1968-01-29 58 58.55616 31
#> 3 1965-12-05 60 60.70685 34
#> 4 1980-03-01 46 46.47123 19
#> 5 1949-11-01 76 76.80000 50
#> 6 1947-02-14 79 79.51233 52
#> 7 1940-02-19 86 86.49863 59
#> 8 1988-01-10 38 38.60822 11
#> 9 1997-08-27 28 28.98082 2
#> 10 1978-01-26 48 48.56438 21
#> 1 1999-06-30 27 27.17808 0
#> 2 1968-01-29 58 58.59452 31
#> 3 1965-12-05 60 60.74521 34
#> 4 1980-03-01 46 46.50959 19
#> 5 1949-11-01 76 76.83836 50
#> 6 1947-02-14 79 79.55068 52
#> 7 1940-02-19 86 86.53699 59
#> 8 1988-01-10 38 38.64658 11
#> 9 1997-08-27 29 29.01918 2
#> 10 1978-01-26 48 48.60274 21
```

2
reference/age_groups.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">

6
reference/amr-tidymodels.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">
@@ -202,10 +202,10 @@ may affect the computations for subsequent operations.</p></dd>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">broom </span> 1.0.13 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">rsample </span> 1.3.2 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">dials </span> 1.4.4 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tailor </span> 0.1.0 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">infer </span> 1.1.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tidyr </span> 1.3.2 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata </span> 1.5.1 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune </span> 2.1.0 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">modeldata </span> 1.6.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">tune </span> 2.1.0 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">parsnip </span> 1.6.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflows </span> 1.3.0 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">purrr </span> 1.2.2 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">workflowsets</span> 1.1.1 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes </span> 1.3.3 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick </span> 1.4.0 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">recipes </span> 1.4.0 <span style="color: #00BB00;">✔</span> <span style="color: #0000BB;">yardstick </span> 1.4.0 </span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> ── <span style="font-weight: bold;">Conflicts</span> ───────────────────────────────────────── tidymodels_conflicts() ──</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">purrr</span>::<span style="color: #00BB00;">discard()</span> masks <span style="color: #0000BB;">scales</span>::discard()</span>
<span class="r-msg co"><span class="r-pr">#&gt;</span> <span style="color: #BB0000;">✖</span> <span style="color: #0000BB;">dplyr</span>::<span style="color: #00BB00;">filter()</span> masks <span style="color: #0000BB;">stats</span>::filter()</span>

4
reference/amr-tidymodels.md
View File

@@ -181,10 +181,10 @@ if (require("tidymodels")) {
#> ✔ broom 1.0.13 ✔ rsample 1.3.2
#> ✔ dials 1.4.4 ✔ tailor 0.1.0
#> ✔ infer 1.1.0 ✔ tidyr 1.3.2
#> ✔ modeldata 1.5.1 ✔ tune 2.1.0
#> ✔ modeldata 1.6.0 ✔ tune 2.1.0
#> ✔ parsnip 1.6.0 ✔ workflows 1.3.0
#> ✔ purrr 1.2.2 ✔ workflowsets 1.1.1
#> ✔ recipes 1.3.3 ✔ yardstick 1.4.0
#> ✔ recipes 1.4.0 ✔ yardstick 1.4.0
#> ── Conflicts ───────────────────────────────────────── tidymodels_conflicts() ──
#> ✖ purrr::discard() masks scales::discard()
#> ✖ dplyr::filter() masks stats::filter()

2
reference/amr_course.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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
View File

@@ -13,7 +13,7 @@ All antibiogram types adhere to previously described approaches (see Source), an
<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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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
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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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.av.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">

6
reference/as.disk.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">
@@ -62,10 +62,6 @@
<span><span class="fu">is.disk</span><span class="op">(</span><span class="va">x</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>An object of class <code>disk</code> (inherits from <code>integer</code>) of length 1.</p>
</div>
<div class="section level2">
<h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>

4
reference/as.disk.md
View File

@@ -14,10 +14,6 @@ NA_disk_
is.disk(x)
```
## Format
An object of class `disk` (inherits from `integer`) of length 1.
## Arguments
- x:

2
reference/as.mic.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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
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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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
View File

@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">
@@ -462,10 +462,10 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<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> 2026-08-20 <span style="color: #949494;">12:34:53</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> 2026-08-20 <span style="color: #949494;">12:34:53</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> 2026-08-20 <span style="color: #949494;">12:34:53</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> 2026-08-20 <span style="color: #949494;">12:34:53</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> 2026-09-03 <span style="color: #949494;">12:31:42</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> 2026-09-03 <span style="color: #949494;">12:31:42</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> 2026-09-03 <span style="color: #949494;">12:31:42</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> 2026-09-03 <span style="color: #949494;">12:31:43</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
View File

@@ -712,10 +712,10 @@ 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 2026-08-20 12:34:53 1 MIC amoxicillin Escherich… human 8
#> 2 2026-08-20 12:34:53 1 MIC cipro Escherich… human 0.256
#> 3 2026-08-20 12:34:53 1 DISK tobra Escherich… human 16
#> 4 2026-08-20 12:34:53 1 DISK genta Escherich… human 18
#> 1 2026-09-03 12:31:42 1 MIC amoxicillin Escherich… human 8
#> 2 2026-09-03 12:31:42 1 MIC cipro Escherich… human 0.256
#> 3 2026-09-03 12:31:42 1 DISK tobra Escherich… human 16
#> 4 2026-09-03 12:31:43 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
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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/av_from_text.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/av_property.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/availability.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/bug_drug_combinations.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">
@@ -108,7 +108,10 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<h3 id="imported-from-whonet">Imported From WHONET<a class="anchor" aria-label="anchor" href="#imported-from-whonet"></a></h3>
<p>Clinical breakpoints in this package were validated through and imported from <a href="https://whonet.org" class="external-link">WHONET</a>, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on <a href="https://whonet.org" class="external-link">their website</a>. The developers of WHONET and this <code>AMR</code> package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software.</p>
<p>Some breakpoints in this package were validated through and imported from <a href="https://whonet.org" class="external-link">WHONET</a>, a free desktop Windows application developed and supported by the WHO Collaborating Centre for Surveillance of Antimicrobial Resistance. More can be read on <a href="https://whonet.org" class="external-link">their website</a>. The developers of WHONET and this <code>AMR</code> package have been in contact about sharing their work. We highly appreciate their great development on the WHONET software.</p>
<p>From WHONET, imported were:</p><ul><li><p>All CLSI breakpoints, including ECOFF</p></li>
<li><p>EUCAST breakpoints between 2011 and 2018</p></li>
</ul><p>EUCAST breakpoints from 2019 onwards, were retrieved directly from <a href="https://www.eucast.org" class="external-link">https://www.eucast.org</a>.</p>
<p>Our import and reproduction script can be found here: <a href="https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R" class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R</a>.</p>
</div>

11
reference/clinical_breakpoints.md
View File

@@ -100,7 +100,7 @@ to interpret raw data using a specific breakpoint type, e.g.
### Imported From WHONET
Clinical breakpoints in this package were validated through and imported
Some breakpoints in this package were validated through and imported
from [WHONET](https://whonet.org), a free desktop Windows application
developed and supported by the WHO Collaborating Centre for Surveillance
of Antimicrobial Resistance. More can be read on [their
@@ -108,6 +108,15 @@ website](https://whonet.org). The developers of WHONET and this `AMR`
package have been in contact about sharing their work. We highly
appreciate their great development on the WHONET software.
From WHONET, imported were:
- All CLSI breakpoints, including ECOFF
- EUCAST breakpoints between 2011 and 2018
EUCAST breakpoints from 2019 onwards, were retrieved directly from
<https://www.eucast.org>.
Our import and reproduction script can be found here:
<https://github.com/msberends/AMR/blob/main/data-raw/_reproduction_scripts/reproduction_of_clinical_breakpoints.R>.

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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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_interpretive_rules.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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
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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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
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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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
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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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
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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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
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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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
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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/first_isolate.html
View File

@@ -9,7 +9,7 @@
<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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/g.test.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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
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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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_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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/guess_ab_col.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/interpretive_rules.html
View File

@@ -9,7 +9,7 @@ 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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">

33
reference/intrinsic_resistant.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">
@@ -60,12 +60,13 @@
<div class="section level2">
<h2 id="format">Format<a class="anchor" aria-label="anchor" href="#format"></a></h2>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 294 079 observations and 2 variables:</p><ul><li><p><code>mo</code><br> Microorganism ID which occurs in <code><a href="microorganisms.html">microorganisms$mo</a></code>. Names can be retrieved using <code><a href="mo_property.html">mo_name()</a></code>.</p></li>
<p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 294 079 observations and 3 variables:</p><ul><li><p><code>mo</code><br> Microorganism ID which occurs in <code><a href="microorganisms.html">microorganisms$mo</a></code>. Names can be retrieved using <code><a href="mo_property.html">mo_name()</a></code>.</p></li>
<li><p><code>ab</code><br> Antimicrobial ID which occurs in <code><a href="antimicrobials.html">antimicrobials$ab</a></code>. Names can be retrieved using <code><a href="ab_property.html">ab_name()</a></code>.</p></li>
<li><p><code>version</code><br> Guideline name and version.</p></li>
</ul></div>
<div class="section level2">
<h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
<p>This data set is currently based on <a href="https://www.eucast.org/bacteria/important-additional-information/expert-rules/" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023).</p>
<p>This data set is currently strictly follows <a href="https://www.eucast.org/bacteria/important-additional-information/expert-rules/" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023). The</p>
<p>This data set is internally used by:</p><ul><li><p><code><a href="antimicrobial_selectors.html">not_intrinsic_resistant()</a></code> (an <a href="antimicrobial_selectors.html">antimicrobial selector</a>)</p></li>
<li><p><code><a href="mo_property.html">mo_is_intrinsic_resistant()</a></code></p></li>
<li><p><code><a href="antibiogram.html">wisca()</a></code> to model \(\beta(1, 9999)\) for resistant bug-drug combinations, per <a href="https://doi.org/10.1093/jac/dkv397" class="external-link">doi:10.1093/jac/dkv397</a></p></li>
@@ -82,19 +83,19 @@
<div class="section level2">
<h2 id="ref-examples">Examples<a class="anchor" aria-label="anchor" href="#ref-examples"></a></h2>
<div class="sourceCode"><pre class="sourceCode r"><code><span class="r-in"><span><span class="va">intrinsic_resistant</span></span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 294,079 × 2</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&gt;</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> <span style="color: #949494;">B_</span>GRAMP ATM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>GRAMP COL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>GRAMP NAL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>GRAMP PLB </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>GRAMP TEM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">B_</span>ANAER-POS ATM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">B_</span>ANAER-POS COL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ANAER-POS NAL </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>ANAER-POS PLB </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ANAER-POS TEM </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 294,079 × 3</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> mo ab version </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span> <span style="color: #949494; font-style: italic;">&lt;ab&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> <span style="color: #949494;">B_</span>GRAMP ATM 'EUCAST Expected Resistant Phenotypes' v1.2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> <span style="color: #949494;">B_</span>GRAMP COL 'EUCAST Expected Resistant Phenotypes' v1.2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> <span style="color: #949494;">B_</span>GRAMP NAL 'EUCAST Expected Resistant Phenotypes' v1.2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> <span style="color: #949494;">B_</span>GRAMP PLB 'EUCAST Expected Resistant Phenotypes' v1.2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> <span style="color: #949494;">B_</span>GRAMP TEM 'EUCAST Expected Resistant Phenotypes' v1.2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> <span style="color: #949494;">B_</span>ANAER-POS ATM 'EUCAST Expected Resistant Phenotypes' v1.2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> <span style="color: #949494;">B_</span>ANAER-POS COL 'EUCAST Expected Resistant Phenotypes' v1.2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> <span style="color: #949494;">B_</span>ANAER-POS NAL 'EUCAST Expected Resistant Phenotypes' v1.2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> <span style="color: #949494;">B_</span>ANAER-POS PLB 'EUCAST Expected Resistant Phenotypes' v1.2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> <span style="color: #949494;">B_</span>ANAER-POS TEM 'EUCAST Expected Resistant Phenotypes' v1.2</span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 294,069 more rows</span></span>
</code></pre></div>
</div>

35
reference/intrinsic_resistant.md
View File

@@ -15,7 +15,7 @@ intrinsic_resistant
## Format
A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 294
079 observations and 2 variables:
079 observations and 3 variables:
- `mo`
Microorganism ID which occurs in
@@ -29,12 +29,15 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 294
Names can be retrieved using
[`ab_name()`](https://amr-for-r.org/reference/ab_property.md).
- `version`
Guideline name and version.
## Details
This data set is currently based on ['EUCAST Expected Resistant
This data set is currently strictly follows ['EUCAST Expected Resistant
Phenotypes'
v1.2](https://www.eucast.org/bacteria/important-additional-information/expert-rules/)
(2023).
(2023). The
This data set is internally used by:
@@ -68,18 +71,18 @@ repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).
``` r
intrinsic_resistant
#> # A tibble: 294,079 × 2
#> mo ab
#> <mo> <ab>
#> 1 B_GRAMP ATM
#> 2 B_GRAMP COL
#> 3 B_GRAMP NAL
#> 4 B_GRAMP PLB
#> 5 B_GRAMP TEM
#> 6 B_ANAER-POS ATM
#> 7 B_ANAER-POS COL
#> 8 B_ANAER-POS NAL
#> 9 B_ANAER-POS PLB
#> 10 B_ANAER-POS TEM
#> # A tibble: 294,079 × 3
#> mo ab version
#> <mo> <ab> <chr>
#> 1 B_GRAMP ATM 'EUCAST Expected Resistant Phenotypes' v1.2
#> 2 B_GRAMP COL 'EUCAST Expected Resistant Phenotypes' v1.2
#> 3 B_GRAMP NAL 'EUCAST Expected Resistant Phenotypes' v1.2
#> 4 B_GRAMP PLB 'EUCAST Expected Resistant Phenotypes' v1.2
#> 5 B_GRAMP TEM 'EUCAST Expected Resistant Phenotypes' v1.2
#> 6 B_ANAER-POS ATM 'EUCAST Expected Resistant Phenotypes' v1.2
#> 7 B_ANAER-POS COL 'EUCAST Expected Resistant Phenotypes' v1.2
#> 8 B_ANAER-POS NAL 'EUCAST Expected Resistant Phenotypes' v1.2
#> 9 B_ANAER-POS PLB 'EUCAST Expected Resistant Phenotypes' v1.2
#> 10 B_ANAER-POS TEM 'EUCAST Expected Resistant Phenotypes' v1.2
#> # ℹ 294,069 more rows
```

2
reference/italicise_taxonomy.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/join.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/key_antimicrobials.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/kurtosis.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/like.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/mdro.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/mean_amr_distance.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/microorganisms.codes.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/microorganisms.groups.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/microorganisms.html
View File

@@ -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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/mo_matching_score.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/mo_property.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">
@@ -375,15 +375,15 @@
<li><p><code>mo_ref("Enterobacter aerogenes")</code> will return <code>"Tindall et al., 2017"</code> (with a note about the renaming)</p></li>
<li><p><code>mo_ref("Enterobacter aerogenes", keep_synonyms = TRUE)</code> will return <code>"Hormaeche et al., 1960"</code> (with a once-per-session warning that the name is outdated)</p></li>
</ul><p><code>mo_ref()</code> returns the abbreviated authority of the nomenclatural act that created the queried name combination. When <code>keep_synonyms = FALSE</code> (default), this is the authority of the currently accepted name. When <code>keep_synonyms = TRUE</code>, this is the authority under which the queried (possibly outdated) name was published. Emendations (changes to the species description without a name change) are not reflected; only the combination or original description authority is returned.</p>
<p>The short name (<code>mo_shortname()</code>) returns the first character of the genus and the full species, such as <code>"E. coli"</code>, for species and subspecies. Exceptions are abbreviations of staphylococci (such as <em>"CoNS"</em>, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as <em>"GBS"</em>, Group B Streptococci). Please bear in mind that e.g. <em>E. coli</em> could mean <em>Escherichia coli</em> (kingdom of Bacteria) as well as <em>Entamoeba coli</em> (kingdom of Protozoa). Returning to the full name will be done using <code><a href="as.mo.html">as.mo()</a></code> internally, giving priority to bacteria and human pathogens, i.e. <code>"E. coli"</code> will always be considered <em>Escherichia coli</em>. As a result, <code>mo_fullname(mo_shortname("Entamoeba coli"))</code> returns <code>"Escherichia coli"</code>.</p>
<p>The short name (<code>mo_shortname()</code>) returns the first character of the genus and the full species, such as <code>"E. coli"</code>, for species and subspecies. Exceptions are abbreviations of staphylococci (such as <em>"CoNS"</em>, Coagulase-Negative Staphylococci) and beta-haemolytic streptococci (such as <em>"GBS"</em>, Group B Streptococci). Please bear in mind that e.g. <em>E. coli</em> could mean <em>Escherichia coli</em> (domain of Bacteria) as well as <em>Entamoeba coli</em> (domain of Protozoa). Returning to the full name will be done using <code><a href="as.mo.html">as.mo()</a></code> internally, giving priority to bacteria and human pathogens, i.e. <code>"E. coli"</code> will always be considered <em>Escherichia coli</em>. As a result, <code>mo_fullname(mo_shortname("Entamoeba coli"))</code> returns <code>"Escherichia coli"</code>.</p>
<p>Following the formal introduction of the new kingdom rank into prokaryotic nomenclature in 2024 (<a href="https://doi.org/10.1099/ijsem.0.006242" class="external-link">doi:10.1099/ijsem.0.006242</a>
), <code>mo_kingdom()</code> and <code>mo_domain()</code> return different results for bacteria and archaea: <code>mo_kingdom()</code> returns the new formal kingdom (e.g. "Pseudomonadati", "Bacillati"), while <code>mo_domain()</code> returns the new domain (e.g. "Bacteria", "Archaea"). For non-prokaryotic organisms, both functions return identical results.</p>
<p>Determination of human pathogenicity (<code>mo_pathogenicity()</code>) is strongly based on Bartlett <em>et al.</em> (2022, <a href="https://doi.org/10.1099/mic.0.001269" class="external-link">doi:10.1099/mic.0.001269</a>
). This function returns a <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a> with the levels <em>Pathogenic</em>, <em>Potentially pathogenic</em>, <em>Non-pathogenic</em>, and <em>Unknown</em>.</p>
<p>Determination of the Gram stain (<code>mo_gramstain()</code> is based on the taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, <a href="https://pubmed.ncbi.nlm.nih.gov/11837318/" class="external-link">PMID 11837318</a>), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, <a href="https://pubmed.ncbi.nlm.nih.gov/34694987/" class="external-link">PMID 34694987</a>). Bacteria in these phyla are considered Gram-positive in this <code>AMR</code> package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
<p>Determination of yeasts (<code>mo_is_yeast()</code>) is based on the taxonomic kingdom and class. <em>Budding yeasts</em> are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. <em>True yeasts</em> quite specifically refers to yeasts in the underlying order Saccharomycetales (such as <em>Saccharomyces cerevisiae</em>). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
<p>Determination of the Gram stain (<code>mo_gramstain()</code> is based on the taxonomic domain and phylum. Originally, Cavalier-Smith defined the so-called subkingdoms Negibacteria and Posibacteria (2002, <a href="https://pubmed.ncbi.nlm.nih.gov/11837318/" class="external-link">PMID 11837318</a>), and only considered these phyla as Posibacteria: Actinobacteria, Chloroflexi, Firmicutes, and Tenericutes. These phyla were later renamed to Actinomycetota, Chloroflexota, Bacillota, and Mycoplasmatota (2021, <a href="https://pubmed.ncbi.nlm.nih.gov/34694987/" class="external-link">PMID 34694987</a>). Bacteria in these phyla are considered Gram-positive in this <code>AMR</code> package, except for members of the class Negativicutes (within phylum Bacillota) which are Gram-negative. All other bacteria are considered Gram-negative. Species outside the kingdom of Bacteria will return a value <code>NA</code>. Functions <code>mo_is_gram_negative()</code> and <code>mo_is_gram_positive()</code> always return <code>TRUE</code> or <code>FALSE</code> (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>), thus always return <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
<p>Determination of yeasts (<code>mo_is_yeast()</code>) is based on the taxonomic domain and class. <em>Budding yeasts</em> are yeasts that reproduce asexually through a process called budding, where a new cell develops from a small protrusion on the parent cell. Taxonomically, these are members of the phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes) or Pichiomycetes. <em>True yeasts</em> quite specifically refers to yeasts in the underlying order Saccharomycetales (such as <em>Saccharomyces cerevisiae</em>). Thus, for all microorganisms that are member of the taxonomic class Saccharomycetes or Pichiomycetes, the function will return <code>TRUE</code>. It returns <code>FALSE</code> otherwise (or <code>NA</code> when the input is <code>NA</code> or the MO code is <code>UNKNOWN</code>).</p>
<p>Determination of intrinsic resistance (<code>mo_is_intrinsic_resistant()</code>) is based on the <a href="intrinsic_resistant.html">intrinsic_resistant</a> data set, which is based on <a href="https://www.eucast.org/bacteria/important-additional-information/expert-rules/" class="external-link">'EUCAST Expected Resistant Phenotypes' v1.2</a> (2023). The <code>mo_is_intrinsic_resistant()</code> function can be vectorised over both argument <code>x</code> (input for microorganisms) and <code>ab</code> (input for antimicrobials).</p>
<p>Determination of both bacterial oxygen tolerance (<code>mo_oxygen_tolerance()</code>) and morphology (<code>mo_morphology()</code>) are based on BacDive, see <em>Source</em>. The function <code>mo_is_anaerobic()</code> only returns <code>TRUE</code> if the oxygen tolerance is <code>"anaerobe"</code>, indicating an obligate anaerobic species or genus. It always returns <code>FALSE</code> for species outside the taxonomic kingdom of Bacteria.</p>
<p>Determination of both bacterial oxygen tolerance (<code>mo_oxygen_tolerance()</code>) and morphology (<code>mo_morphology()</code>) are based on BacDive, see <em>Source</em>. The function <code>mo_is_anaerobic()</code> only returns <code>TRUE</code> if the oxygen tolerance is <code>"anaerobe"</code>, indicating an obligate anaerobic species or genus. It always returns <code>FALSE</code> for species outside the taxonomic domain of Bacteria.</p>
<p>The function <code>mo_url()</code> will return the direct URL to the online database entry, which also shows the scientific reference of the concerned species. <a href="https://www.mycobank.org" class="external-link">This MycoBank URL</a> is used for fungi wherever available , <a href="https://www.mycobank.org" class="external-link">this LPSN URL</a> for bacteria wherever available, and <a href="https://www.gbif.org" class="external-link">this GBIF link</a> otherwise.</p>
<p>SNOMED codes (<code>mo_snomed()</code>) was last updated on 16th of July, 2024. See <em>Source</em> and the <a href="microorganisms.html">microorganisms</a> data set for more info.</p>
<p>Old taxonomic names (so-called 'synonyms') can be retrieved with <code>mo_synonyms()</code> (which will have the scientific reference as <a href="https://rdrr.io/r/base/names.html" class="external-link">name</a>), the current taxonomic name can be retrieved with <code>mo_current()</code>. Both functions return full names.</p>

12
reference/mo_property.md
View File

@@ -400,9 +400,9 @@ genus and the full species, such as `"E. coli"`, for species and
subspecies. Exceptions are abbreviations of staphylococci (such as
*"CoNS"*, Coagulase-Negative Staphylococci) and beta-haemolytic
streptococci (such as *"GBS"*, Group B Streptococci). Please bear in
mind that e.g. *E. coli* could mean *Escherichia coli* (kingdom of
Bacteria) as well as *Entamoeba coli* (kingdom of Protozoa). Returning
to the full name will be done using
mind that e.g. *E. coli* could mean *Escherichia coli* (domain of
Bacteria) as well as *Entamoeba coli* (domain of Protozoa). Returning to
the full name will be done using
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md) internally, giving
priority to bacteria and human pathogens, i.e. `"E. coli"` will always
be considered *Escherichia coli*. As a result,
@@ -426,7 +426,7 @@ function returns a
*Pathogenic*, *Potentially pathogenic*, *Non-pathogenic*, and *Unknown*.
Determination of the Gram stain (`mo_gramstain()` is based on the
taxonomic kingdom and phylum. Originally, Cavalier-Smith defined the
taxonomic domain and phylum. Originally, Cavalier-Smith defined the
so-called subkingdoms Negibacteria and Posibacteria (2002, [PMID
11837318](https://pubmed.ncbi.nlm.nih.gov/11837318/)), and only
considered these phyla as Posibacteria: Actinobacteria, Chloroflexi,
@@ -443,7 +443,7 @@ is `UNKNOWN`), thus always return `FALSE` for species outside the
taxonomic kingdom of Bacteria.
Determination of yeasts (`mo_is_yeast()`) is based on the taxonomic
kingdom and class. *Budding yeasts* are yeasts that reproduce asexually
domain and class. *Budding yeasts* are yeasts that reproduce asexually
through a process called budding, where a new cell develops from a small
protrusion on the parent cell. Taxonomically, these are members of the
phylum Ascomycota, class Saccharomycetes (also called Hemiascomycetes)
@@ -468,7 +468,7 @@ Determination of both bacterial oxygen tolerance
on BacDive, see *Source*. The function `mo_is_anaerobic()` only returns
`TRUE` if the oxygen tolerance is `"anaerobe"`, indicating an obligate
anaerobic species or genus. It always returns `FALSE` for species
outside the taxonomic kingdom of Bacteria.
outside the taxonomic domain of Bacteria.
The function `mo_url()` will return the direct URL to the online
database entry, which also shows the scientific reference of the

2
reference/mo_source.html
View File

@@ -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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/plot.html
View File

@@ -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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/proportion.html
View File

@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/random.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/resistance_predict.html
View File

@@ -9,7 +9,7 @@ NOTE: These functions are deprecated and will be removed in a future version. Us
<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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/skewness.html
View File

@@ -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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/top_n_microorganisms.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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/translate.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="">3.0.1.9087</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9088</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">