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@@ -31,7 +31,7 @@
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@@ -30,7 +30,7 @@
<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="">3.0.1.9079</small>
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@@ -284,11 +284,6 @@ taxonomic codes. Let’s check this:</p>
<span><span class="co">#&gt; <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FFD787;">0.571</span>), and <span style="font-style: italic;">Enterobacter cloacae dissolvens</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.565</span>)</span></span>
<span><span class="co">#&gt; <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">"K. pneumoniae"</span> -&gt; <span style="font-weight: bold; font-style: italic;">Klebsiella pneumoniae</span> (B_KLBSL_PNMN, <span style="color: #080808; background-color: #5FD7AF;">0.786</span>)</span></span>
<span><span class="co">#&gt; Also matched: <span style="font-style: italic;">Klebsiella pneumoniae</span> complex<span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.707</span>), <span style="font-style: italic;">Klebsiella pneumoniae</span></span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">ozaenae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.707</span>), <span style="font-style: italic;">Klebsiella pneumoniae pneumoniae</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.688</span>), <span style="font-style: italic;">Klebsiella</span></span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">pneumoniae rhinoscleromatis</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFFF87;">0.658</span>), <span style="font-style: italic;">Klebsiella pasteurii</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.500</span>), <span style="font-style: italic;">Klebsiella</span></span></span>
<span><span class="co">#&gt; <span style="font-style: italic;">planticola</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.500</span>), <span style="font-style: italic;">Kosakonia pseudosacchari</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.471</span>), <span style="font-style: italic;">Kaistella palustris</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">(</span><span style="color: #080808; background-color: #FF5F5F;">0.435</span>), <span style="font-style: italic;">Kingella potus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.435</span>), and <span style="font-style: italic;">Kocuria palustris</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FF5F5F;">0.435</span>)</span></span>
<span><span class="co">#&gt; <span style="color: #B2B2B2;">-------------------------------------------------------------------------------</span></span></span>
<span><span class="co">#&gt; <span style="color: #0000BB;">"S. aureus"</span> -&gt; <span style="font-weight: bold; font-style: italic;">Staphylococcus aureus</span> (B_STPHY_AURS, <span style="color: #080808; background-color: #FFFF87;">0.690</span>)</span></span>
<span><span class="co">#&gt; Also matched: <span style="font-style: italic;">Staphylococcus aureus aureus</span><span style="color: #0000BB;"> (</span><span style="color: #080808; background-color: #FFD787;">0.643</span>), <span style="font-style: italic;">Staphylococcus argenteus</span></span></span>

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articles/AMR.md
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@@ -196,11 +196,6 @@ mo_uncertainties()
#> (0.571), and Enterobacter cloacae dissolvens (0.565)
#> -------------------------------------------------------------------------------
#> "K. pneumoniae" -> Klebsiella pneumoniae (B_KLBSL_PNMN, 0.786)
#> Also matched: Klebsiella pneumoniae complex (0.707), Klebsiella pneumoniae
#> ozaenae (0.707), Klebsiella pneumoniae pneumoniae (0.688), Klebsiella
#> pneumoniae rhinoscleromatis (0.658), Klebsiella pasteurii (0.500), Klebsiella
#> planticola (0.500), Kosakonia pseudosacchari (0.471), Kaistella palustris
#> (0.435), Kingella potus (0.435), and Kocuria palustris (0.435)
#> -------------------------------------------------------------------------------
#> "S. aureus" -> Staphylococcus aureus (B_STPHY_AURS, 0.690)
#> Also matched: Staphylococcus aureus aureus (0.643), Staphylococcus argenteus

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@@ -30,7 +30,7 @@
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@@ -30,7 +30,7 @@
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9079</small>
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authors.html
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@@ -7,7 +7,7 @@
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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="">3.0.1.9079</small>
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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="">3.0.1.9079</small>
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@@ -49,15 +49,15 @@
</div>
<div class="section level2">
<h2 class="pkg-version" data-toc-text="3.0.1.9079" id="amr-3019079">AMR 3.0.1.9079<a class="anchor" aria-label="anchor" href="#amr-3019079"></a></h2>
<h2 class="pkg-version" data-toc-text="3.0.1.9080" id="amr-3019080">AMR 3.0.1.9080<a class="anchor" aria-label="anchor" href="#amr-3019080"></a></h2>
<p>Planned as v3.1.0, end of June 2026.</p>
<div class="section level4">
<h4 id="breaking-changes-3-0-1-9079">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9079"></a></h4>
<h4 id="breaking-changes-3-0-1-9080">Breaking Changes<a class="anchor" aria-label="anchor" href="#breaking-changes-3-0-1-9080"></a></h4>
<ul><li>The former <em>kingdoms</em> Bacteria and Archaea are now each divided into four kingdoms with new top-level <em>domains</em> ‘Bacteria’ and ‘Archaea’ (Göker and Oren, 2024, DOI: 10.1099/ijsem.0.006242). Following this, a new <code>domain</code> column in the <code>microorganisms</code> data set was added, and more importantly, <code><a href="../reference/mo_property.html">mo_kingdom()</a></code> now returns the formal kingdom (e.g. <code>"Pseudomonadati"</code> instead of <code>"Bacteria"</code>). Use <code><a href="../reference/mo_property.html">mo_domain()</a></code> for the old behaviour. For non-prokaryotic kingdoms (Fungi, Protozoa, etc.), <code>kingdom</code> and <code>domain</code> are identical.</li>
<li>Faster parallel computing via the <code>future</code> package for <code><a href="../reference/as.sir.html">as.sir()</a></code> and <code><a href="../reference/antibiogram.html">wisca()</a></code>: a non-sequential plan (e.g. <code>future::plan(future::multisession)</code>) must be active before using <code>parallel = TRUE</code>.</li>
</ul></div>
<div class="section level4">
<h4 id="new-3-0-1-9079">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9079"></a></h4>
<h4 id="new-3-0-1-9080">New<a class="anchor" aria-label="anchor" href="#new-3-0-1-9080"></a></h4>
<ul><li>EUCAST 2026 and CLSI 2026 breakpoints: over 5,700 new breakpoints added to the <code>clinical_breakpoints</code> data set; EUCAST 2026 is now the default for all MIC and disk diffusion interpretations</li>
<li>Wildtype/Non-wildtype (WT/NWT) output when using ECOFF-based interpretation, by setting <code>breakpoint_type = "ECOFF"</code> in <code><a href="../reference/as.sir.html">as.sir()</a></code>; WT/NWT results are fully supported in all resistance/susceptibility functions and plots (<a href="https://github.com/msberends/AMR/issues/254" class="external-link">#254</a>)</li>
<li>
@@ -74,7 +74,7 @@
<li>New <code><a href="../reference/antibiogram.html">wisca_plot()</a></code> to assess the susceptibility and incidence distributions from the Monte Carlo simulations</li>
</ul></div>
<div class="section level4">
<h4 id="fixed-3-0-1-9079">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9079"></a></h4>
<h4 id="fixed-3-0-1-9080">Fixed<a class="anchor" aria-label="anchor" href="#fixed-3-0-1-9080"></a></h4>
<ul><li>Setting <code>options(AMR_guideline = "EUCAST 2012")</code> or any year-qualified value no longer causes errors or silent wrong behaviour in <code><a href="../reference/interpretive_rules.html">interpretive_rules()</a></code>, <code><a href="../reference/proportion.html">resistance()</a></code>, <code><a href="../reference/proportion.html">susceptibility()</a></code>, <code><a href="../reference/count.html">count_resistant()</a></code>, <code><a href="../reference/count.html">count_susceptible()</a></code>, and SIR plotting/printing functions (<a href="https://github.com/msberends/AMR/issues/298" class="external-link">#298</a>)</li>
<li>
<code><a href="../reference/as.sir.html">as.sir()</a></code>
@@ -93,6 +93,7 @@
<code><a href="../reference/as.mo.html">as.mo()</a></code>:
<ul><li>Input of the form <code>"X complex"</code> now falls back to <code>"X"</code> when the complex is not a distinct taxon in the database, preventing <code>NA</code> results for valid clinical descriptions such as <code>"Proteus vulgaris complex"</code> (<a href="https://github.com/msberends/AMR/issues/287" class="external-link">#287</a>)</li>
<li>Abbreviated-genus input (e.g. <code>"S. apiospermum"</code>) now correctly ranks candidates whose species epithet exactly matches the input above more-prevalent organisms whose species does not match; fixes <code>"S. apiospermum"</code> resolving to <em>Staphylococcus</em> instead of <em>Scedosporium apiospermum</em> (<a href="https://github.com/msberends/AMR/issues/288" class="external-link">#288</a>)</li>
<li>Abbreviated-genus input for species that have subspecies (e.g. <code>"P. ovale"</code>) now collapses to the species-rank record instead of incorrectly matching a more-prevalent organism; explicit subspecies queries (e.g. <code>"P. ovale curtisi"</code>) are preserved (<a href="https://github.com/msberends/AMR/issues/288" class="external-link">#288</a>)</li>
</ul></li>
<li>
<code>get_author_year()</code> in the microorganism reproduction script now strips <code>emend.</code> and everything after it, so <code>ref</code> reflects the combination authority rather than the emendation author (e.g. <em>Rhodococcus equi</em> now returns “Goodfellow et al., 1977” instead of “Nouioui et al., 2018”)</li>
@@ -102,7 +103,7 @@
</li>
</ul></div>
<div class="section level4">
<h4 id="updated-3-0-1-9079">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9079"></a></h4>
<h4 id="updated-3-0-1-9080">Updated<a class="anchor" aria-label="anchor" href="#updated-3-0-1-9080"></a></h4>
<ul><li>
<code><a href="../reference/top_n_microorganisms.html">top_n_microorganisms()</a></code>: new <code>property_for_each</code> argument for sub-grouping within top <em>n</em> groups; rank ordering enforced (only lower taxonomic ranks allowed); fixed <code>property = NULL</code> not being accepted; inner filter now tracks original row indices to prevent cross-group contamination</li>
<li>Taxonomic update for all microorganisms, now updated to June 2026</li>

7
news/index.md
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@@ -1,6 +1,6 @@
# Changelog
## AMR 3.0.1.9079
## AMR 3.0.1.9080
Planned as v3.1.0, end of June 2026.
@@ -117,6 +117,11 @@ Planned as v3.1.0, end of June 2026.
`"S. apiospermum"` resolving to *Staphylococcus* instead of
*Scedosporium apiospermum*
([\#288](https://github.com/msberends/AMR/issues/288))
- Abbreviated-genus input for species that have subspecies
(e.g. `"P. ovale"`) now collapses to the species-rank record instead
of incorrectly matching a more-prevalent organism; explicit
subspecies queries (e.g. `"P. ovale curtisi"`) are preserved
([\#288](https://github.com/msberends/AMR/issues/288))
- `get_author_year()` in the microorganism reproduction script now
strips `emend.` and everything after it, so `ref` reflects the
combination authority rather than the emendation author

2
pkgdown.yml
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@@ -10,7 +10,7 @@ articles:
PCA: PCA.html
WHONET: WHONET.html
WISCA: WISCA.html
last_built: 2026-06-27T12:34Z
last_built: 2026-06-27T13:26Z
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>
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reference/AMR-options.html
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@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
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@@ -21,7 +21,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
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@@ -7,7 +7,7 @@
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/ab_from_text.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9079</small>
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2
reference/ab_property.html
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@@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9079</small>
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2
reference/add_custom_antimicrobials.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9079</small>
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2
reference/add_custom_microorganisms.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9079</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="">3.0.1.9079</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="">3.0.1.9079</small>
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2
reference/amr-tidymodels.html
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@@ -7,7 +7,7 @@
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2
reference/amr_course.html
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@@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9079</small>
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2
reference/antibiogram.html
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@@ -13,7 +13,7 @@ All antibiogram types adhere to previously described approaches (see Source), an
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9079</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="">3.0.1.9079</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
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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>
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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="">3.0.1.9079</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>
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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>
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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="">3.0.1.9079</small>
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10
reference/as.sir.html
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@@ -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="">3.0.1.9079</small>
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@@ -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> 2026-06-27 <span style="color: #949494;">12:37:06</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> 2026-06-27 <span style="color: #949494;">12:37:06</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> 2026-06-27 <span style="color: #949494;">12:37:06</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> 2026-06-27 <span style="color: #949494;">12:37:07</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> 2026-06-27 <span style="color: #949494;">13:28:18</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> 2026-06-27 <span style="color: #949494;">13:28:18</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> 2026-06-27 <span style="color: #949494;">13:28:19</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> 2026-06-27 <span style="color: #949494;">13:28:19</span> 1 DISK genta Escherich… human 18 </span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 11 more variables: ab &lt;ab&gt;, mo &lt;mo&gt;, host &lt;chr&gt;, input &lt;chr&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># outcome &lt;sir&gt;, notes &lt;chr&gt;, guideline &lt;chr&gt;, ref_table &lt;chr&gt;, uti &lt;lgl&gt;,</span></span>
<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># breakpoint_S_R &lt;chr&gt;, site &lt;chr&gt;</span></span>

8
reference/as.sir.md
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@@ -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 2026-06-27 12:37:06 1 MIC amoxicillin Escherich… human 8
#> 2 2026-06-27 12:37:06 1 MIC cipro Escherich… human 0.256
#> 3 2026-06-27 12:37:06 1 DISK tobra Escherich… human 16
#> 4 2026-06-27 12:37:07 1 DISK genta Escherich… human 18
#> 1 2026-06-27 13:28:18 1 MIC amoxicillin Escherich… human 8
#> 2 2026-06-27 13:28:18 1 MIC cipro Escherich… human 0.256
#> 3 2026-06-27 13:28:19 1 DISK tobra Escherich… human 16
#> 4 2026-06-27 13:28:19 1 DISK genta Escherich… human 18
#> # ℹ 11 more variables: ab <ab>, mo <mo>, host <chr>, input <chr>,
#> # outcome <sir>, notes <chr>, guideline <chr>, ref_table <chr>, uti <lgl>,
#> # breakpoint_S_R <chr>, site <chr>

2
reference/atc_online.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9079</small>
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reference/av_from_text.html
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@@ -7,7 +7,7 @@
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reference/av_property.html
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@@ -7,7 +7,7 @@
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2
reference/availability.html
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@@ -7,7 +7,7 @@
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<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9079</small>
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reference/bug_drug_combinations.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/clinical_breakpoints.html
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@@ -21,7 +21,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/count.html
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@@ -9,7 +9,7 @@ count_resistant() should be used to count resistant isolates, count_susceptible(
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reference/custom_interpretive_rules.html
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@@ -7,7 +7,7 @@
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reference/custom_mdro_guideline.html
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@@ -7,7 +7,7 @@
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reference/dosage.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9079</small>
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reference/esbl_isolates.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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2
reference/example_isolates.html
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@@ -7,7 +7,7 @@
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reference/example_isolates_unclean.html
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@@ -7,7 +7,7 @@
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reference/export_ncbi_biosample.html
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@@ -7,7 +7,7 @@
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reference/first_isolate.html
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@@ -9,7 +9,7 @@
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reference/g.test.html
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@@ -7,7 +7,7 @@
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reference/get_episode.html
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@@ -7,7 +7,7 @@
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reference/ggplot_pca.html
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@@ -7,7 +7,7 @@
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reference/ggplot_sir.html
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@@ -7,7 +7,7 @@
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reference/guess_ab_col.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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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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>
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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>
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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>
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reference/join.html
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@@ -7,7 +7,7 @@
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reference/key_antimicrobials.html
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@@ -7,7 +7,7 @@
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reference/kurtosis.html
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@@ -7,7 +7,7 @@
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reference/like.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/mdro.html
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@@ -7,7 +7,7 @@
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reference/mean_amr_distance.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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reference/microorganisms.codes.html
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@@ -7,7 +7,7 @@
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reference/microorganisms.groups.html
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@@ -7,7 +7,7 @@
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reference/microorganisms.html
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@@ -9,7 +9,7 @@ This data set is carefully crafted, yet made 100% reproducible from public and a
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reference/mo_matching_score.html
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@@ -7,7 +7,7 @@
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reference/mo_property.html
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@@ -7,7 +7,7 @@
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reference/mo_source.html
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@@ -9,7 +9,7 @@ This is the fastest way to have your organisation (or analysis) specific codes p
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reference/pca.html
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@@ -7,7 +7,7 @@
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reference/plot.html
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@@ -9,7 +9,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
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reference/proportion.html
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@@ -9,7 +9,7 @@ resistance() should be used to calculate resistance, susceptibility() should be
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2
reference/random.html
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@@ -7,7 +7,7 @@
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
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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
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reference/skewness.html
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@@ -9,7 +9,7 @@ When negative ('left-skewed'): the left tail is longer; the mass of the distribu
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reference/top_n_microorganisms.html
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@@ -7,7 +7,7 @@
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reference/translate.html
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@@ -7,7 +7,7 @@
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search.json
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