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@@ -31,7 +31,7 @@
<a class="navbar-brand me-2" href="https://amr-for-r.org/index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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<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="">3.0.1.9050</small>
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@@ -73,7 +73,7 @@
<span><span class="fu">pkgdown</span><span class="fu">::</span><span class="fu"><a href="https://pkgdown.r-lib.org/reference/build_site.html" class="external-link">build_site</a></span><span class="op">(</span><span class="op">)</span></span>
<span></span>
<span><span class="co"># Code coverage report</span></span>
<span><span class="fu">covr</span><span class="fu">::</span><span class="fu">package_coverage</span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<span><span class="fu">covr</span><span class="fu">::</span><span class="fu"><a href="http://covr.r-lib.org/reference/package_coverage.html" class="external-link">package_coverage</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>From the shell:</p>
<div class="sourceCode" id="cb2"><pre class="sourceCode bash"><code class="sourceCode bash"><span id="cb2-1"><a href="#cb2-1" tabindex="-1"></a><span class="co"># CRAN check from parent directory</span></span>
<span id="cb2-2"><a href="#cb2-2" tabindex="-1"></a><span class="ex">R</span> CMD check AMR</span></code></pre></div>

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<a class="navbar-brand me-2" href="index.html">AMR (for R)</a>
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@@ -30,7 +30,7 @@
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<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="">3.0.1.9050</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
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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="">3.0.1.9050</small>
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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="">3.0.1.9050</small>
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index.html
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@@ -33,7 +33,7 @@
<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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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18
news/index.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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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@@ -49,9 +49,9 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9050" id="amr-3019050">AMR 3.0.1.9050<a class="anchor" aria-label="anchor" href="#amr-3019050"></a></h2>
<h2 class="pkg-version" data-toc-text="3.0.1.9052" id="amr-3019052">AMR 3.0.1.9052<a class="anchor" aria-label="anchor" href="#amr-3019052"></a></h2>
<div class="section level4">
<h4 id="new-3-0-1-9050">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9050"></a></h4>
<h4 id="new-3-0-1-9052">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9052"></a></h4>
<ul><li>Support for clinical breakpoints of 2026 of both CLSI and EUCAST, by adding all of their over 5,700 new clinical breakpoints to the <code>clinical_breakpoints</code> data set for usage in <code><a href="../reference/as.sir.html">as.sir()</a></code>. EUCAST 2026 is now the new default guideline for all MIC and disk diffusion interpretations.</li>
<li>Integration with the <strong>tidymodels</strong> framework to allow seamless use of SIR, MIC and disk data in modelling pipelines via <code>recipes</code>
<ul><li>
@@ -86,10 +86,8 @@
<li>Two new <code>NA</code> objects, <code>NA_ab_</code> and <code>NA_mo_</code>, analogous to base R’s <code>NA_character_</code> and <code>NA_integer_</code>, for use in pipelines that require typed missing values</li>
</ul></div>
<div class="section level4">
<h4 id="fixes-3-0-1-9050">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9050"></a></h4>
<ul><li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> with <code>reference_data</code>: custom guideline names now correctly classify values as R using EUCAST convention (<code>&gt; breakpoint_R</code> for MIC, <code>&lt; breakpoint_R</code> for disk); custom breakpoints with <code>host = NA</code> now serve as a host-agnostic fallback when no host-specific row matches (fixes <a href="https://github.com/msberends/AMR/issues/239" class="external-link">#239</a>)</li>
<li>Fixed multiple bugs in the <code>parallel = TRUE</code> mode of <code><a href="../reference/as.sir.html">as.sir()</a></code> for data frames: (1) PSOCK workers (Windows / R &lt; 4.0) now correctly load the AMR package before processing, with a graceful fallback to sequential mode when the package cannot be loaded; (2) resolved stale-environment issue where the PSOCK path read a frozen copy of <code>AMR_env</code> instead of the live one, causing the wrong log entries to be captured; (3) fixed log-entry duplication in the fork-based path (<code>mclapply</code>) where pre-existing <code>sir_interpretation_history</code> rows were included in every worker’s captured log; (4) removed use of non-exported internal functions (<code>%pm&gt;%</code>, <code>pm_pull</code>, <code>as.sir.default</code>) from the worker closure, which made PSOCK workers fail; (5) suppressed per-column progress messages inside workers to prevent interleaved console output; (6) fixed a malformed Unicode escape <code>\u00a</code> (3 digits) in the “DONE” status message</li>
<h4 id="fixes-3-0-1-9052">Fixes<a class="anchor" aria-label="anchor" href="#fixes-3-0-1-9052"></a></h4>
<ul><li>Fixed multiple bugs in the <code>parallel = TRUE</code> mode of <code><a href="../reference/as.sir.html">as.sir()</a></code> for data frames</li>
<li>Fixed a bug in <code><a href="../reference/as.sir.html">as.sir()</a></code> where values that were purely numeric (e.g., <code>"1"</code>) and matched the broad SIR-matching regex would be incorrectly stripped of all content by the Unicode letter filter</li>
<li>Fixed a bug in <code><a href="../reference/as.mic.html">as.mic()</a></code> where MIC values in scientific notation (e.g., <code>"1e-3"</code>) were incorrectly handled because the letter <code>e</code> was removed along with other Unicode letters; scientific notation <code>e</code> is now preserved</li>
<li>Fixed a bug in <code><a href="../reference/as.ab.html">as.ab()</a></code> where certain AB codes containing “PH” or “TH” (such as <code>ETH</code>, <code>MTH</code>, <code>PHE</code>, <code>PHN</code>, <code>STH</code>, <code>THA</code>, <code>THI1</code>) would incorrectly return <code>NA</code> when combined in a vector with any untranslatable value (<a href="https://github.com/msberends/AMR/issues/245" class="external-link">#245</a>)</li>
@@ -111,8 +109,10 @@
</li>
</ul></div>
<div class="section level4">
<h4 id="updates-3-0-1-9050">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9050"></a></h4>
<ul><li>Extensive <code>cli</code> integration for better message handling and clickable links in messages and warnings (<a href="https://github.com/msberends/AMR/issues/191" class="external-link">#191</a>, <a href="https://github.com/msberends/AMR/issues/265" class="external-link">#265</a>)</li>
<h4 id="updates-3-0-1-9052">Updates<a class="anchor" aria-label="anchor" href="#updates-3-0-1-9052"></a></h4>
<ul><li>
<code><a href="../reference/as.sir.html">as.sir()</a></code> with <code>reference_data</code>: custom guideline names now correctly classify values as R using EUCAST convention (<code>&gt; breakpoint_R</code> for MIC, <code>&lt; breakpoint_R</code> for disk); custom breakpoints with <code>host = NA</code> now serve as a host-agnostic fallback when no host-specific row matches (<a href="https://github.com/msberends/AMR/issues/239" class="external-link">#239</a>)</li>
<li>Extensive <code>cli</code> integration for better message handling and clickable links in messages and warnings (<a href="https://github.com/msberends/AMR/issues/191" class="external-link">#191</a>, <a href="https://github.com/msberends/AMR/issues/265" class="external-link">#265</a>)</li>
<li>
<code><a href="../reference/mdro.html">mdro()</a></code> now infers resistance for a <em>missing</em> base drug column from an <em>available</em> corresponding drug+inhibitor combination showing resistance (e.g., piperacillin is absent but required, while piperacillin/tazobactam available and resistant). Can be set with the new argument <code>infer_from_combinations</code>, which defaults to <code>TRUE</code> (<a href="https://github.com/msberends/AMR/issues/209" class="external-link">#209</a>). Note that this can yield a higher MDRO detection (which is a good thing as it has become more reliable).</li>
<li>

28
news/index.md
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@@ -1,6 +1,6 @@
# Changelog
## AMR 3.0.1.9050
## AMR 3.0.1.9052
#### New
@@ -63,27 +63,9 @@
#### Fixes
- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) with
`reference_data`: custom guideline names now correctly classify values
as R using EUCAST convention (`> breakpoint_R` for MIC,
`< breakpoint_R` for disk); custom breakpoints with `host = NA` now
serve as a host-agnostic fallback when no host-specific row matches
(fixes [\#239](https://github.com/msberends/AMR/issues/239))
- Fixed multiple bugs in the `parallel = TRUE` mode of
[`as.sir()`](https://amr-for-r.org/reference/as.sir.md) for data
frames: (1) PSOCK workers (Windows / R \< 4.0) now correctly load the
AMR package before processing, with a graceful fallback to sequential
mode when the package cannot be loaded; (2) resolved stale-environment
issue where the PSOCK path read a frozen copy of `AMR_env` instead of
the live one, causing the wrong log entries to be captured; (3) fixed
log-entry duplication in the fork-based path (`mclapply`) where
pre-existing `sir_interpretation_history` rows were included in every
worker’s captured log; (4) removed use of non-exported internal
functions (`%pm>%`, `pm_pull`, `as.sir.default`) from the worker
closure, which made PSOCK workers fail; (5) suppressed per-column
progress messages inside workers to prevent interleaved console
output; (6) fixed a malformed Unicode escape `\u00a` (3 digits) in the
“DONE” status message
frames
- Fixed a bug in [`as.sir()`](https://amr-for-r.org/reference/as.sir.md)
where values that were purely numeric (e.g., `"1"`) and matched the
broad SIR-matching regex would be incorrectly stripped of all content
@@ -145,6 +127,12 @@
#### Updates
- [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) with
`reference_data`: custom guideline names now correctly classify values
as R using EUCAST convention (`> breakpoint_R` for MIC,
`< breakpoint_R` for disk); custom breakpoints with `host = NA` now
serve as a host-agnostic fallback when no host-specific row matches
([\#239](https://github.com/msberends/AMR/issues/239))
- Extensive `cli` integration for better message handling and clickable
links in messages and warnings
([\#191](https://github.com/msberends/AMR/issues/191),

2
pkgdown.yml
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@@ -10,7 +10,7 @@ articles:
PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
last_built: 2026-04-25T12:44Z
last_built: 2026-04-25T14:24Z
urls:
reference: https://amr-for-r.org/reference
article: https://amr-for-r.org/articles

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reference/AMR-deprecated.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
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2
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="">3.0.1.9050</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="">3.0.1.9050</small>
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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="">3.0.1.9050</small>
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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="">3.0.1.9050</small>
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reference/ab_from_text.html
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@@ -7,7 +7,7 @@
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@@ -7,7 +7,7 @@
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reference/add_custom_antimicrobials.html
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@@ -7,7 +7,7 @@
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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="">3.0.1.9050</small>
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2
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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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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="">3.0.1.9050</small>
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2
reference/amr-tidymodels.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
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2
reference/amr_course.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="">3.0.1.9050</small>
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2
reference/antibiogram.html
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@@ -9,7 +9,7 @@ Adhering to previously described approaches (see Source) and especially the Baye
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
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2
reference/antimicrobial_selectors.html
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@@ -17,7 +17,7 @@ my_data_with_all_these_columns %&amp;gt;%
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
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2
reference/antimicrobials.html
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@@ -9,7 +9,7 @@ The antibiotics data set has been renamed to antimicrobials. The old name will b
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
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2
reference/as.ab.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
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2
reference/as.av.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
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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="">3.0.1.9050</small>
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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="">3.0.1.9050</small>
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2
reference/as.mo.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
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14
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="">3.0.1.9050</small>
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@@ -187,7 +187,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<dt id="arg-reference-data">reference_data<a class="anchor" aria-label="anchor" href="#arg-reference-data"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> to be used for interpretation, which defaults to the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set. Changing this argument allows for using own interpretation guidelines. This argument must contain a data set that is equal in structure to the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set (same column names and column types). Please note that the <code>guideline</code> argument will be ignored when <code>reference_data</code> is manually set.</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/data.frame.html" class="external-link">data.frame</a> to be used for interpretation, which defaults to the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set. Changing this argument allows for using own interpretation guidelines. This argument must have the same column names as the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set. Column types are coerced automatically where possible: the <code>mo</code> column is passed through <code><a href="as.mo.html">as.mo()</a></code>, the <code>ab</code> column through <code><a href="as.ab.html">as.ab()</a></code>, and plain character, numeric, or logical columns are cast to the expected type. When <code>reference_data</code> is manually set, the <code>guideline</code> argument is optional: if omitted (or if its value does not match any row in the custom data), all rows in <code>reference_data</code> are considered. If <code>guideline</code> is set to a value that exists in the <code>guideline</code> column of the custom data, only matching rows are used — useful when a single custom table contains multiple guidelines. For the R classification, the EUCAST convention is used by default: MIC values <code>&gt; breakpoint_R</code> and disk diffusion values <code>&lt; breakpoint_R</code> are classified as R, with values between <code>breakpoint_S</code> and <code>breakpoint_R</code> classified as I (or SDD). Only when using the standard <a href="clinical_breakpoints.html">clinical_breakpoints</a> with a CLSI guideline are the closed-interval rules (<code>&gt;= breakpoint_R</code> for MIC, <code>&lt;= breakpoint_R</code> for disk) applied; custom <code>reference_data</code> always uses the open-interval (EUCAST) convention regardless of the guideline name.</p></dd>
<dt id="arg-substitute-missing-r-breakpoint">substitute_missing_r_breakpoint<a class="anchor" aria-label="anchor" href="#arg-substitute-missing-r-breakpoint"></a></dt>
@@ -227,7 +227,7 @@ Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026,
<dt id="arg-parallel">parallel<a class="anchor" aria-label="anchor" href="#arg-parallel"></a></dt>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if parallel computing must be used, defaults to <code>FALSE</code>. This requires no additional packages, as the used <code>parallel</code> package is part of base <span style="R">R</span>. On Windows and on <span style="R">R</span> &lt; 4.0.0 <code><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">parallel::parLapply()</a></code> will be used, in all other cases the more efficient <code><a href="https://rdrr.io/r/parallel/mclapply.html" class="external-link">parallel::mclapply()</a></code> will be used.</p></dd>
<dd><p>A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to indicate if parallel computing must be used, defaults to <code>FALSE</code>. The <code>parallel</code> package is part of base <span style="R">R</span> and no additional packages are required. On Unix/macOS with <span style="R">R</span> &gt;= 4.0.0, <code><a href="https://rdrr.io/r/parallel/mclapply.html" class="external-link">parallel::mclapply()</a></code> (fork-based) is used; on Windows and <span style="R">R</span> &lt; 4.0.0, <code><a href="https://rdrr.io/r/parallel/clusterApply.html" class="external-link">parallel::parLapply()</a></code> with a PSOCK cluster is used (requires the AMR package to be installed, not just loaded via <code>devtools::load_all()</code>). Parallelism distributes columns across cores; it is most beneficial when there are many antibiotic columns and a large number of rows.</p></dd>
<dt id="arg-max-cores">max_cores<a class="anchor" aria-label="anchor" href="#arg-max-cores"></a></dt>
@@ -424,10 +424,10 @@ 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> 2026-04-25 <span style="color: #949494;">12:45:43</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> 2026-04-25 <span style="color: #949494;">12:45:43</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> 2026-04-25 <span style="color: #949494;">12:45:44</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> 2026-04-25 <span style="color: #949494;">12:45:44</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> 2026-04-25 <span style="color: #949494;">14:25:30</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> 2026-04-25 <span style="color: #949494;">14:25:30</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> 2026-04-25 <span style="color: #949494;">14:25:31</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> 2026-04-25 <span style="color: #949494;">14:25:31</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>

49
reference/as.sir.md
View File

@@ -247,12 +247,28 @@ disk diffusion diameters:
interpretation, which defaults to the
[clinical_breakpoints](https://amr-for-r.org/reference/clinical_breakpoints.md)
data set. Changing this argument allows for using own interpretation
guidelines. This argument must contain a data set that is equal in
structure to the
guidelines. This argument must have the same column names as the
[clinical_breakpoints](https://amr-for-r.org/reference/clinical_breakpoints.md)
data set (same column names and column types). Please note that the
`guideline` argument will be ignored when `reference_data` is manually
set.
data set. Column types are coerced automatically where possible: the
`mo` column is passed through
[`as.mo()`](https://amr-for-r.org/reference/as.mo.md), the `ab` column
through [`as.ab()`](https://amr-for-r.org/reference/as.ab.md), and
plain character, numeric, or logical columns are cast to the expected
type. When `reference_data` is manually set, the `guideline` argument
is optional: if omitted (or if its value does not match any row in the
custom data), all rows in `reference_data` are considered. If
`guideline` is set to a value that exists in the `guideline` column of
the custom data, only matching rows are used — useful when a single
custom table contains multiple guidelines. For the R classification,
the EUCAST convention is used by default: MIC values `> breakpoint_R`
and disk diffusion values `< breakpoint_R` are classified as R, with
values between `breakpoint_S` and `breakpoint_R` classified as I (or
SDD). Only when using the standard
[clinical_breakpoints](https://amr-for-r.org/reference/clinical_breakpoints.md)
with a CLSI guideline are the closed-interval rules (`>= breakpoint_R`
for MIC, `<= breakpoint_R` for disk) applied; custom `reference_data`
always uses the open-interval (EUCAST) convention regardless of the
guideline name.
- substitute_missing_r_breakpoint:
@@ -332,13 +348,16 @@ disk diffusion diameters:
- parallel:
A [logical](https://rdrr.io/r/base/logical.html) to indicate if
parallel computing must be used, defaults to `FALSE`. This requires no
additional packages, as the used `parallel` package is part of base R.
On Windows and on R \< 4.0.0
[`parallel::parLapply()`](https://rdrr.io/r/parallel/clusterApply.html)
will be used, in all other cases the more efficient
parallel computing must be used, defaults to `FALSE`. The `parallel`
package is part of base R and no additional packages are required. On
Unix/macOS with R \>= 4.0.0,
[`parallel::mclapply()`](https://rdrr.io/r/parallel/mclapply.html)
will be used.
(fork-based) is used; on Windows and R \< 4.0.0,
[`parallel::parLapply()`](https://rdrr.io/r/parallel/clusterApply.html)
with a PSOCK cluster is used (requires the AMR package to be
installed, not just loaded via `devtools::load_all()`). Parallelism
distributes columns across cores; it is most beneficial when there are
many antibiotic columns and a large number of rows.
- max_cores:
@@ -660,10 +679,10 @@ 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 2026-04-25 12:45:43 1 MIC amoxicillin Escherich… human 8
#> 2 2026-04-25 12:45:43 1 MIC cipro Escherich… human 0.256
#> 3 2026-04-25 12:45:44 1 DISK tobra Escherich… human 16
#> 4 2026-04-25 12:45:44 1 DISK genta Escherich… human 18
#> 1 2026-04-25 14:25:30 1 MIC amoxicillin Escherich… human 8
#> 2 2026-04-25 14:25:30 1 MIC cipro Escherich… human 0.256
#> 3 2026-04-25 14:25:31 1 DISK tobra Escherich… human 16
#> 4 2026-04-25 14:25:31 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="">3.0.1.9050</small>
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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="">3.0.1.9050</small>
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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="">3.0.1.9050</small>
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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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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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="">3.0.1.9050</small>
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2
reference/clinical_breakpoints.html
View File

@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
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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="">3.0.1.9050</small>
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2
reference/custom_eucast_rules.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/dosage.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/esbl_isolates.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/example_isolates.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
<button class="navbar-toggler" type="button" data-bs-toggle="collapse" data-bs-target="#navbar" aria-controls="navbar" aria-expanded="false" aria-label="Toggle navigation">

2
reference/example_isolates_unclean.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/export_ncbi_biosample.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/first_isolate.html
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@@ -9,7 +9,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/g.test.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/get_episode.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/ggplot_pca.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/ggplot_sir.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</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
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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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/index.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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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/interpretive_rules.html
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@@ -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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/intrinsic_resistant.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</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/italicise_taxonomy.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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/join.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</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
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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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</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
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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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/like.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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/mdro.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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</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
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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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/microorganisms.codes.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/microorganisms.groups.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/microorganisms.html
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@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
<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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/mo_matching_score.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/mo_property.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/mo_source.html
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@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/pca.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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/plot.html
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@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
<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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/proportion.html
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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
<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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/random.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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
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
<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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
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>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/top_n_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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
reference/translate.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="">3.0.1.9050</small>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9052</small>
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2
search.json
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