Built site for AMR@3.0.1.9041: 3a736bc

2026-03-31 00:16:08 +02:00 · 2026-03-30 08:18:09 +00:00
parent d55d073ae9
commit d6c59896e9
105 changed files with 320 additions and 313 deletions
--- a/reference/AMR-deprecated.html
+++ b/reference/AMR-deprecated.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/AMR-options.html
+++ b/reference/AMR-options.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
@@ -68,12 +68,12 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
 <li><p><code>AMR_custom_ab</code> <br> A file location to an RDS file, to use custom antimicrobial drugs with this package. This is explained in <code><a href="add_custom_antimicrobials.html">add_custom_antimicrobials()</a></code>.</p></li>
 <li><p><code>AMR_custom_mo</code> <br> A file location to an RDS file, to use custom microorganisms with this package. This is explained in <code><a href="add_custom_microorganisms.html">add_custom_microorganisms()</a></code>.</p></li>
 <li><p><code>AMR_eucastrules</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the default types of rules for <code><a href="interpretive_rules.html">eucast_rules()</a></code> function, must be one or more of: <code>"breakpoints"</code>, <code>"expert"</code>, <code>"other"</code>, <code>"custom"</code>, <code>"all"</code>, and defaults to <code>c("breakpoints", "expert")</code>.</p></li>
-<li><p><code>AMR_guideline</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the default guideline used throughout the <code>AMR</code> package wherever a <code>guideline</code> argument is available. This option is used as the default in e.g. <code><a href="as.sir.html">as.sir()</a></code>, <code><a href="proportion.html">resistance()</a></code>, <code><a href="proportion.html">susceptibility()</a></code>, <code><a href="interpretive_rules.html">interpretive_rules()</a></code> and many plotting functions. <strong>While unset</strong>, the AMR package uses the latest implemented EUCAST guideline (currently EUCAST 2025).</p><ul><li><p>For <code><a href="as.sir.html">as.sir()</a></code>, this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., <code>"CLSI"</code> or <code>"EUCAST"</code>) or the name including a year (e.g., <code>"CLSI 2019"</code>). Supported guidelines are EUCAST 2011 to 2025, and CLSI 2011 to 2025.</p></li>
+<li><p><code>AMR_guideline</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the default guideline used throughout the <code>AMR</code> package wherever a <code>guideline</code> argument is available. This option is used as the default in e.g. <code><a href="as.sir.html">as.sir()</a></code>, <code><a href="proportion.html">resistance()</a></code>, <code><a href="proportion.html">susceptibility()</a></code>, <code><a href="interpretive_rules.html">interpretive_rules()</a></code> and many plotting functions. <strong>While unset</strong>, the AMR package uses the latest implemented EUCAST guideline (currently EUCAST 2026).</p><ul><li><p>For <code><a href="as.sir.html">as.sir()</a></code>, this determines which clinical breakpoint guideline is used to interpret MIC values and disk diffusion diameters. It can be either the guideline name (e.g., <code>"CLSI"</code> or <code>"EUCAST"</code>) or the name including a year (e.g., <code>"CLSI 2019"</code>). Supported guidelines are EUCAST 2011 to 2026, and CLSI 2011 to 2026.</p></li>
 <li><p>For <code><a href="proportion.html">resistance()</a></code> and <code><a href="proportion.html">susceptibility()</a></code>, this setting determines how the <code>"I"</code> (Intermediate / Increased exposure) category is handled in calculations. Under CLSI, <code>"I"</code> is considered <em>resistant</em> in susceptibility calculations; under EUCAST, <code>"I"</code> is considered <em>susceptible</em> in susceptibility calculations. Explicitly setting this option ensures reproducible AMR proportion estimates.</p></li>
 <li><p>For <code><a href="interpretive_rules.html">interpretive_rules()</a></code>, this determines which guideline-specific interpretive (expert) rules are applied to antimicrobial test results, either EUCAST or CLSI.</p></li>
-<li><p>For many plotting functions (e.g., for MIC or disk diffusion values), supplying <code>mo</code> and <code>ab</code> enables automatic SIR-based interpretative colouring. These colours are derived from <code><a href="as.sir.html">as.sir()</a></code> in the background and therefore depend on the active <code>guideline</code> setting, which again uses EUCAST 2025 if not set explicitly.</p></li>
+<li><p>For many plotting functions (e.g., for MIC or disk diffusion values), supplying <code>mo</code> and <code>ab</code> enables automatic SIR-based interpretative colouring. These colours are derived from <code><a href="as.sir.html">as.sir()</a></code> in the background and therefore depend on the active <code>guideline</code> setting, which again uses EUCAST 2026 if not set explicitly.</p></li>
 </ul></li>
-<li><p><code>AMR_guideline</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the default guideline for interpreting MIC values and disk diffusion diameters with <code><a href="as.sir.html">as.sir()</a></code>. Can be only the guideline name (e.g., <code>"CLSI"</code>) or the name with a year (e.g. <code>"CLSI 2019"</code>). The default to the latest implemented EUCAST guideline, currently <code>"EUCAST 2025"</code>. Supported guideline are currently EUCAST (2011-2025) and CLSI (2011-2025).</p></li>
+<li><p><code>AMR_guideline</code> <br> A <a href="https://rdrr.io/r/base/character.html" class="external-link">character</a> to set the default guideline for interpreting MIC values and disk diffusion diameters with <code><a href="as.sir.html">as.sir()</a></code>. Can be only the guideline name (e.g., <code>"CLSI"</code>) or the name with a year (e.g. <code>"CLSI 2019"</code>). The default to the latest implemented EUCAST guideline, currently <code>"EUCAST 2026"</code>. Supported guideline are currently EUCAST (2011-2026) and CLSI (2011-2026).</p></li>
 <li><p><code>AMR_ignore_pattern</code> <br> A <a href="https://rdrr.io/r/base/regex.html" class="external-link">regular expression</a> to ignore (i.e., make <code>NA</code>) any match given in <code><a href="as.mo.html">as.mo()</a></code> and all <code><a href="mo_property.html">mo_*</a></code> functions.</p></li>
 <li><p><code>AMR_include_PKPD</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that PK/PD clinical breakpoints must be applied as a last resort - the default is <code>TRUE</code>.</p></li>
 <li><p><code>AMR_substitute_missing_r_breakpoint</code> <br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> to use in <code><a href="as.sir.html">as.sir()</a></code>, to indicate that missing R breakpoints must be substituted with <code>"R"</code> - the default is <code>FALSE</code>.</p></li>
--- a/reference/AMR-options.md
+++ b/reference/AMR-options.md
@@ -63,14 +63,14 @@ the `AMR` package. Set them using the
  [`susceptibility()`](https://amr-for-r.org/reference/proportion.md),
  [`interpretive_rules()`](https://amr-for-r.org/reference/interpretive_rules.md)
  and many plotting functions. **While unset**, the AMR package uses the
-  latest implemented EUCAST guideline (currently EUCAST 2025).
+  latest implemented EUCAST guideline (currently EUCAST 2026).

  - For [`as.sir()`](https://amr-for-r.org/reference/as.sir.md), this
    determines which clinical breakpoint guideline is used to interpret
    MIC values and disk diffusion diameters. It can be either the
    guideline name (e.g., `"CLSI"` or `"EUCAST"`) or the name including
    a year (e.g., `"CLSI 2019"`). Supported guidelines are EUCAST 2011
-    to 2025, and CLSI 2011 to 2025.
+    to 2026, and CLSI 2011 to 2026.

  - For [`resistance()`](https://amr-for-r.org/reference/proportion.md)
    and
@@ -92,7 +92,7 @@ the `AMR` package. Set them using the
    interpretative colouring. These colours are derived from
    [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) in the
    background and therefore depend on the active `guideline` setting,
-    which again uses EUCAST 2025 if not set explicitly.
+    which again uses EUCAST 2026 if not set explicitly.

 - `AMR_guideline`  
  A [character](https://rdrr.io/r/base/character.html) to set the
@@ -101,8 +101,8 @@ the `AMR` package. Set them using the
  [`as.sir()`](https://amr-for-r.org/reference/as.sir.md). Can be only
  the guideline name (e.g., `"CLSI"`) or the name with a year (e.g.
  `"CLSI 2019"`). The default to the latest implemented EUCAST
-  guideline, currently `"EUCAST 2025"`. Supported guideline are
-  currently EUCAST (2011-2025) and CLSI (2011-2025).
+  guideline, currently `"EUCAST 2026"`. Supported guideline are
+  currently EUCAST (2011-2026) and CLSI (2011-2026).

 - `AMR_ignore_pattern`  
  A [regular expression](https://rdrr.io/r/base/regex.html) to ignore
--- a/reference/AMR.html
+++ b/reference/AMR.html
@@ -5,14 +5,14 @@ This work was published in the Journal of Statistical Software (Volume 104(3); d
 ) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
 and doi:10.33612/diss.192486375
 ).
-After installing this package, R knows ~79 000 distinct microbial species (updated June 2024) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2025 and EUCAST 2011-2025 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
+After installing this package, R knows ~79 000 distinct microbial species (updated June 2024) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
 The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:description" content="Welcome to the AMR package.
 The AMR package is a peer-reviewed, free and open-source R package with zero dependencies to simplify the analysis and prediction of Antimicrobial Resistance (AMR) and to work with microbial and antimicrobial data and properties, by using evidence-based methods. Our aim is to provide a standard for clean and reproducible AMR data analysis, that can therefore empower epidemiological analyses to continuously enable surveillance and treatment evaluation in any setting. We are a team of many different researchers from around the globe to make this a successful and durable project!
 This work was published in the Journal of Statistical Software (Volume 104(3); doi:10.18637/jss.v104.i03
 ) and formed the basis of two PhD theses (doi:10.33612/diss.177417131
 and doi:10.33612/diss.192486375
 ).
-After installing this package, R knows ~79 000 distinct microbial species (updated June 2024) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2025 and EUCAST 2011-2025 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
+After installing this package, R knows ~79 000 distinct microbial species (updated June 2024) and all ~620 antimicrobial and antiviral drugs by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). It was designed to work in any setting, including those with very limited resources. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the University of Groningen and the University Medical Center Groningen.
 The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>

@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
@@ -70,7 +70,7 @@ The AMR package is available in English, Arabic, Bengali, Chinese, Czech, Danish
 ) and formed the basis of two PhD theses (<a href="https://doi.org/10.33612/diss.177417131" class="external-link">doi:10.33612/diss.177417131</a>
 and <a href="https://doi.org/10.33612/diss.192486375" class="external-link">doi:10.33612/diss.192486375</a>
 ).</p>
-<p>After installing this package, R knows <a href="https://amr-for-r.org/reference/microorganisms.html"><strong>~79 000 distinct microbial species</strong></a> (updated June 2024) and all <a href="https://amr-for-r.org/reference/antimicrobials.html"><strong>~620 antimicrobial and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2025 and EUCAST 2011-2025 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
+<p>After installing this package, R knows <a href="https://amr-for-r.org/reference/microorganisms.html"><strong>~79 000 distinct microbial species</strong></a> (updated June 2024) and all <a href="https://amr-for-r.org/reference/antimicrobials.html"><strong>~620 antimicrobial and antiviral drugs</strong></a> by name and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED CT), and knows all about valid SIR and MIC values. The integral clinical breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are included, even with epidemiological cut-off (ECOFF) values. It supports and can read any data format, including WHONET data. This package works on Windows, macOS and Linux with all versions of R since R-3.0 (April 2013). <strong>It was designed to work in any setting, including those with very limited resources</strong>. It was created for both routine data analysis and academic research at the Faculty of Medical Sciences of the <a href="https://www.rug.nl" class="external-link">University of Groningen</a> and the <a href="https://www.umcg.nl" class="external-link">University Medical Center Groningen</a>.</p>
 <p>The <code>AMR</code> package is available in English, Arabic, Bengali, Chinese, Czech, Danish, Dutch, Finnish, French, German, Greek, Hindi, Indonesian, Italian, Japanese, Korean, Norwegian, Polish, Portuguese, Romanian, Russian, Spanish, Swahili, Swedish, Turkish, Ukrainian, Urdu, and Vietnamese. Antimicrobial drug (group) names and colloquial microorganism names are provided in these languages.</p>
    </div>

--- a/reference/AMR.md
+++ b/reference/AMR.md
@@ -29,7 +29,7 @@ June 2024) and all [**~620 antimicrobial and antiviral
 drugs**](https://amr-for-r.org/reference/antimicrobials.html) by name
 and code (including ATC, EARS-Net, ASIARS-Net, PubChem, LOINC and SNOMED
 CT), and knows all about valid SIR and MIC values. The integral clinical
-breakpoint guidelines from CLSI 2011-2025 and EUCAST 2011-2025 are
+breakpoint guidelines from CLSI 2011-2026 and EUCAST 2011-2026 are
 included, even with epidemiological cut-off (ECOFF) values. It supports
 and can read any data format, including WHONET data. This package works
 on Windows, macOS and Linux with all versions of R since R-3.0 (April
--- a/reference/WHOCC.html
+++ b/reference/WHOCC.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/WHONET.html
+++ b/reference/WHONET.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/ab_from_text.html
+++ b/reference/ab_from_text.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/ab_property.html
+++ b/reference/ab_property.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/add_custom_antimicrobials.html
+++ b/reference/add_custom_antimicrobials.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/add_custom_microorganisms.html
+++ b/reference/add_custom_microorganisms.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/age.html
+++ b/reference/age.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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  26  26.73151          0</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1968-01-29  58  58.14795         31</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1965-12-05  60  60.29863         34</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1980-03-01  46  46.06301         19</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1949-11-01  76  76.39178         50</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1947-02-14  79  79.10411         52</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1940-02-19  86  86.09041         59</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1988-01-10  38  38.20000         11</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1997-08-27  28  28.57260          2</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26  48  48.15616         21</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 1  1999-06-30  26  26.74795          0</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 2  1968-01-29  58  58.16438         31</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 3  1965-12-05  60  60.31507         34</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 4  1980-03-01  46  46.07945         19</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 5  1949-11-01  76  76.40822         50</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 6  1947-02-14  79  79.12055         52</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 7  1940-02-19  86  86.10685         59</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 8  1988-01-10  38  38.21644         11</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 9  1997-08-27  28  28.58904          2</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> 10 1978-01-26  48  48.17260         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>
--- a/reference/age.md
+++ b/reference/age.md
@@ -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  26  26.73151          0
-#> 2  1968-01-29  58  58.14795         31
-#> 3  1965-12-05  60  60.29863         34
-#> 4  1980-03-01  46  46.06301         19
-#> 5  1949-11-01  76  76.39178         50
-#> 6  1947-02-14  79  79.10411         52
-#> 7  1940-02-19  86  86.09041         59
-#> 8  1988-01-10  38  38.20000         11
-#> 9  1997-08-27  28  28.57260          2
-#> 10 1978-01-26  48  48.15616         21
+#> 1  1999-06-30  26  26.74795          0
+#> 2  1968-01-29  58  58.16438         31
+#> 3  1965-12-05  60  60.31507         34
+#> 4  1980-03-01  46  46.07945         19
+#> 5  1949-11-01  76  76.40822         50
+#> 6  1947-02-14  79  79.12055         52
+#> 7  1940-02-19  86  86.10685         59
+#> 8  1988-01-10  38  38.21644         11
+#> 9  1997-08-27  28  28.58904          2
+#> 10 1978-01-26  48  48.17260         21
 ```
--- a/reference/age_groups.html
+++ b/reference/age_groups.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/amr-tidymodels.html
+++ b/reference/amr-tidymodels.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</small>


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--- a/reference/amr_course.html
+++ b/reference/amr_course.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</small>


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--- a/reference/antibiogram.html
+++ b/reference/antibiogram.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</small>


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--- a/reference/antimicrobial_selectors.html
+++ b/reference/antimicrobial_selectors.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</small>


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--- a/reference/antimicrobials.html
+++ b/reference/antimicrobials.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</small>


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--- a/reference/as.ab.html
+++ b/reference/as.ab.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/as.av.html
+++ b/reference/as.av.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/as.disk.html
+++ b/reference/as.disk.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/as.mic-2.png
+++ b/reference/as.mic-2.png
--- a/reference/as.mic-3.png
+++ b/reference/as.mic-3.png
--- a/reference/as.mic-4.png
+++ b/reference/as.mic-4.png
--- a/reference/as.mic.html
+++ b/reference/as.mic.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
@@ -111,7 +111,7 @@
    </div>
    <div class="section level2">
    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
-    <p>To interpret MIC values as SIR values, use <code><a href="as.sir.html">as.sir()</a></code> on MIC values. It supports guidelines from EUCAST (2011-2025) and CLSI (2011-2025).</p>
+    <p>To interpret MIC values as SIR values, use <code><a href="as.sir.html">as.sir()</a></code> on MIC values. It supports guidelines from EUCAST (2011-2026) and CLSI (2011-2026).</p>
 <p>This class for MIC values is a quite a special data type: formally it is an ordered <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a> with valid MIC values as <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a> levels (to make sure only valid MIC values are retained), but for any mathematical operation it acts as decimal numbers:</p>
 <p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a>x <span class="ot">&lt;-</span> <span class="fu">random_mic</span>(<span class="dv">10</span>)</span>
 <span id="cb1-2"><a href="#cb1-2" tabindex="-1"></a>x</span>
--- a/reference/as.mic.md
+++ b/reference/as.mic.md
@@ -85,7 +85,7 @@ the outcome of any mathematical operation on MICs will return a

 To interpret MIC values as SIR values, use
 [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) on MIC values.
-It supports guidelines from EUCAST (2011-2025) and CLSI (2011-2025).
+It supports guidelines from EUCAST (2011-2026) and CLSI (2011-2026).

 This class for MIC values is a quite a special data type: formally it is
 an ordered [factor](https://rdrr.io/pkg/data.table/man/fctr.html) with
--- a/reference/as.mo.html
+++ b/reference/as.mo.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/as.sir.html
+++ b/reference/as.sir.html
@@ -1,7 +1,7 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data — as.sir • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Interpret MIC and Disk Diffusion as SIR, or Clean Existing SIR Data — as.sir"><meta name="description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, NI.
-Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025, see Details. All breakpoints used for interpretation are available in our clinical_breakpoints data set."><meta property="og:description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, NI.
-Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025, see Details. All breakpoints used for interpretation are available in our clinical_breakpoints data set."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
+Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026, see Details. All breakpoints used for interpretation are available in our clinical_breakpoints data set."><meta property="og:description" content="Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. as.sir() transforms the input to a new class sir, which is an ordered factor containing the levels S, SDD, I, R, NI.
+Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026, see Details. All breakpoints used for interpretation are available in our clinical_breakpoints data set."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>


@@ -9,7 +9,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,

    <a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>

-    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
@@ -53,7 +53,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,

    <div class="ref-description section level2">
    <p>Clean up existing SIR values, or interpret minimum inhibitory concentration (MIC) values and disk diffusion diameters according to EUCAST or CLSI. <code>as.sir()</code> transforms the input to a new class <code>sir</code>, which is an ordered <a href="https://rdrr.io/pkg/data.table/man/fctr.html" class="external-link">factor</a> containing the levels <code>S</code>, <code>SDD</code>, <code>I</code>, <code>R</code>, <code>NI</code>.</p>
-<p>Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025, see <em>Details</em>. All breakpoints used for interpretation are available in our <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set.</p>
+<p>Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI 2011-2026, see <em>Details</em>. All breakpoints used for interpretation are available in our <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set.</p>
    </div>

    <div class="section level2">
@@ -118,11 +118,11 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,

    <div class="section level2">
    <h2 id="source">Source<a class="anchor" aria-label="anchor" href="#source"></a></h2>
-    <p>For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:</p><ul><li><p><strong>CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data</strong>, 2011-2025, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
-<li><p><strong>CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2011-2025, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m100/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m100/</a>.</p></li>
-<li><p><strong>CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals</strong>, 2019-2025, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/veterinary-medicine/documents/vet01/" class="external-link">https://clsi.org/standards/products/veterinary-medicine/documents/vet01/</a>.</p></li>
-<li><p><strong>EUCAST Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2025, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/" class="external-link">https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/</a>.</p></li>
-<li><p><strong>WHONET</strong> as a source for machine-reading the clinical breakpoints (<a href="https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet">read more here</a>), 1989-2025, <em>WHO Collaborating Centre for Surveillance of Antimicrobial Resistance</em>. <a href="https://whonet.org/" class="external-link">https://whonet.org/</a>.</p></li>
+    <p>For interpretations of minimum inhibitory concentration (MIC) values and disk diffusion diameters:</p><ul><li><p><strong>CLSI M39: Analysis and Presentation of Cumulative Antimicrobial Susceptibility Test Data</strong>, 2011-2026, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m39/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m39/</a>.</p></li>
+<li><p><strong>CLSI M100: Performance Standard for Antimicrobial Susceptibility Testing</strong>, 2011-2026, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/microbiology/documents/m100/" class="external-link">https://clsi.org/standards/products/microbiology/documents/m100/</a>.</p></li>
+<li><p><strong>CLSI VET01: Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated From Animals</strong>, 2019-2026, <em>Clinical and Laboratory Standards Institute</em> (CLSI). <a href="https://clsi.org/standards/products/veterinary-medicine/documents/vet01/" class="external-link">https://clsi.org/standards/products/veterinary-medicine/documents/vet01/</a>.</p></li>
+<li><p><strong>EUCAST Breakpoint tables for interpretation of MICs and zone diameters</strong>, 2011-2026, <em>European Committee on Antimicrobial Susceptibility Testing</em> (EUCAST). <a href="https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/" class="external-link">https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/</a>.</p></li>
+<li><p><strong>WHONET</strong> as a source for machine-reading the clinical breakpoints (<a href="https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet">read more here</a>), 1989-2026, <em>WHO Collaborating Centre for Surveillance of Antimicrobial Resistance</em>. <a href="https://whonet.org/" class="external-link">https://whonet.org/</a>.</p></li>
 </ul></div>
    <div class="section level2">
    <h2 id="arguments">Arguments<a class="anchor" aria-label="anchor" href="#arguments"></a></h2>
@@ -158,7 +158,7 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,


 <dt id="arg-guideline">guideline<a class="anchor" aria-label="anchor" href="#arg-guideline"></a></dt>
-<dd><p>A guideline name (or column name) to use for SIR interpretation. Defaults to EUCAST 2025 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the package option <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2011-2025) and CLSI (2011-2025), see <em>Details</em>. Using a column name allows for straightforward interpretation of historical data, which must be analysed in the context of, for example, different years.</p></dd>
+<dd><p>A guideline name (or column name) to use for SIR interpretation. Defaults to EUCAST 2026 (the latest implemented EUCAST guideline in the <a href="clinical_breakpoints.html">clinical_breakpoints</a> data set), but can be set with the package option <code><a href="AMR-options.html">AMR_guideline</a></code>. Currently supports EUCAST (2011-2026) and CLSI (2011-2026), see <em>Details</em>. Using a column name allows for straightforward interpretation of historical data, which must be analysed in the context of, for example, different years.</p></dd>


 <dt id="arg-uti">uti<a class="anchor" aria-label="anchor" href="#arg-uti"></a></dt>
@@ -283,10 +283,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
 <h3 id="supported-guidelines">Supported Guidelines<a class="anchor" aria-label="anchor" href="#supported-guidelines"></a></h3>


-<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2025 and CLSI 2011-2025;</p></li>
-<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2025 and CLSI 2019-2025;</p></li>
-<li><p>For <strong>ECOFFs</strong> (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.</p></li>
-</ul><p>The <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2025"</code> or <code>"CLSI 2025"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. Importantly, using a column name of your data instead, allows for straightforward interpretation of historical data that must be analysed in the context of, for example, different years.</p>
+<p>For interpreting MIC values as well as disk diffusion diameters, currently implemented guidelines are:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2026 and CLSI 2011-2026;</p></li>
+<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2026 and CLSI 2019-2026;</p></li>
+<li><p>For <strong>ECOFFs</strong> (Epidemiological Cut-off Values): EUCAST 2020-2026 and CLSI 2022-2026.</p></li>
+</ul><p>The <code>guideline</code> argument must be set to e.g., <code>"EUCAST 2026"</code> or <code>"CLSI 2026"</code>. By simply using <code>"EUCAST"</code> (the default) or <code>"CLSI"</code> as input, the latest included version of that guideline will automatically be selected. Importantly, using a column name of your data instead, allows for straightforward interpretation of historical data that must be analysed in the context of, for example, different years.</p>
 <p>You can set your own data set using the <code>reference_data</code> argument. The <code>guideline</code> argument will then be ignored.</p>
 <p>It is also possible to set the default guideline with the package option <code><a href="AMR-options.html">AMR_guideline</a></code> (e.g. in your <code>.Rprofile</code> file), such as:</p>
 <p></p><div class="sourceCode"><pre><code><span id="cb1-1"><a href="#cb1-1" tabindex="-1"></a>  <span class="fu">options</span>(<span class="at">AMR_guideline =</span> <span class="st">"CLSI"</span>)</span>
@@ -424,10 +424,10 @@ Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI 2011-2025,
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 4 × 18</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   datetime            index method ab_given    mo_given   host_given input_given</span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>   <span style="color: #949494; font-style: italic;">&lt;dttm&gt;</span>              <span style="color: #949494; font-style: italic;">&lt;int&gt;</span> <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>  <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>       <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span>      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-03-24 <span style="color: #949494;">12:30:17</span>     1 MIC    amoxicillin Escherich… human      8          </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-03-24 <span style="color: #949494;">12:30:17</span>     1 MIC    cipro       Escherich… human      0.256      </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-03-24 <span style="color: #949494;">12:30:18</span>     1 DISK   tobra       Escherich… human      16         </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-03-24 <span style="color: #949494;">12:30:18</span>     1 DISK   genta       Escherich… human      18         </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">1</span> 2026-03-30 <span style="color: #949494;">08:14:10</span>     1 MIC    amoxicillin Escherich… human      8          </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">2</span> 2026-03-30 <span style="color: #949494;">08:14:10</span>     1 MIC    cipro       Escherich… human      0.256      </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">3</span> 2026-03-30 <span style="color: #949494;">08:14:10</span>     1 DISK   tobra       Escherich… human      16         </span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">4</span> 2026-03-30 <span style="color: #949494;">08:14:11</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>
--- a/reference/as.sir.md
+++ b/reference/as.sir.md
@@ -7,8 +7,8 @@ which is an ordered
 [factor](https://rdrr.io/pkg/data.table/man/fctr.html) containing the
 levels `S`, `SDD`, `I`, `R`, `NI`.

-Breakpoints are currently implemented from EUCAST 2011-2025 and CLSI
-2011-2025, see *Details*. All breakpoints used for interpretation are
+Breakpoints are currently implemented from EUCAST 2011-2026 and CLSI
+2011-2026, see *Details*. All breakpoints used for interpretation are
 available in our
 [clinical_breakpoints](https://amr-for-r.org/reference/clinical_breakpoints.md)
 data set.
@@ -80,29 +80,29 @@ For interpretations of minimum inhibitory concentration (MIC) values and
 disk diffusion diameters:

 - **CLSI M39: Analysis and Presentation of Cumulative Antimicrobial
-  Susceptibility Test Data**, 2011-2025, *Clinical and Laboratory
+  Susceptibility Test Data**, 2011-2026, *Clinical and Laboratory
  Standards Institute* (CLSI).
  <https://clsi.org/standards/products/microbiology/documents/m39/>.

 - **CLSI M100: Performance Standard for Antimicrobial Susceptibility
-  Testing**, 2011-2025, *Clinical and Laboratory Standards Institute*
+  Testing**, 2011-2026, *Clinical and Laboratory Standards Institute*
  (CLSI).
  <https://clsi.org/standards/products/microbiology/documents/m100/>.

 - **CLSI VET01: Performance Standards for Antimicrobial Disk and
  Dilution Susceptibility Tests for Bacteria Isolated From Animals**,
-  2019-2025, *Clinical and Laboratory Standards Institute* (CLSI).
+  2019-2026, *Clinical and Laboratory Standards Institute* (CLSI).
  <https://clsi.org/standards/products/veterinary-medicine/documents/vet01/>.

 - **EUCAST Breakpoint tables for interpretation of MICs and zone
-  diameters**, 2011-2025, *European Committee on Antimicrobial
+  diameters**, 2011-2026, *European Committee on Antimicrobial
  Susceptibility Testing* (EUCAST).
  <https://www.eucast.org/bacteria/clinical-breakpoints-and-interpretation/clinical-breakpoint-tables/>.

 - **WHONET** as a source for machine-reading the clinical breakpoints
  ([read more
  here](https://amr-for-r.org/reference/clinical_breakpoints.html#imported-from-whonet)),
-  1989-2025, *WHO Collaborating Centre for Surveillance of Antimicrobial
+  1989-2026, *WHO Collaborating Centre for Surveillance of Antimicrobial
  Resistance*. <https://whonet.org/>.

 ## Arguments
@@ -162,12 +162,12 @@ disk diffusion diameters:
 - guideline:

  A guideline name (or column name) to use for SIR interpretation.
-  Defaults to EUCAST 2025 (the latest implemented EUCAST guideline in
+  Defaults to EUCAST 2026 (the latest implemented EUCAST guideline in
  the
  [clinical_breakpoints](https://amr-for-r.org/reference/clinical_breakpoints.md)
  data set), but can be set with the package option
  [`AMR_guideline`](https://amr-for-r.org/reference/AMR-options.md).
-  Currently supports EUCAST (2011-2025) and CLSI (2011-2025), see
+  Currently supports EUCAST (2011-2026) and CLSI (2011-2026), see
  *Details*. Using a column name allows for straightforward
  interpretation of historical data, which must be analysed in the
  context of, for example, different years.
@@ -457,15 +457,15 @@ interpretation, and the exact input and output values.
 For interpreting MIC values as well as disk diffusion diameters,
 currently implemented guidelines are:

- For **clinical microbiology**: EUCAST 2011-2025 and CLSI 2011-2025;
+- For **clinical microbiology**: EUCAST 2011-2026 and CLSI 2011-2026;

- For **veterinary microbiology**: EUCAST 2021-2025 and CLSI 2019-2025;
+- For **veterinary microbiology**: EUCAST 2021-2026 and CLSI 2019-2026;

- For **ECOFFs** (Epidemiological Cut-off Values): EUCAST 2020-2025 and
-  CLSI 2022-2025.
+- For **ECOFFs** (Epidemiological Cut-off Values): EUCAST 2020-2026 and
+  CLSI 2022-2026.

-The `guideline` argument must be set to e.g., `"EUCAST 2025"` or
-`"CLSI 2025"`. By simply using `"EUCAST"` (the default) or `"CLSI"` as
+The `guideline` argument must be set to e.g., `"EUCAST 2026"` or
+`"CLSI 2026"`. By simply using `"EUCAST"` (the default) or `"CLSI"` as
 input, the latest included version of that guideline will automatically
 be selected. Importantly, using a column name of your data instead,
 allows for straightforward interpretation of historical data that must
@@ -660,10 +660,10 @@ sir_interpretation_history()
 #> # A tibble: 4 × 18
 #>   datetime            index method ab_given    mo_given   host_given input_given
 #>   <dttm>              <int> <chr>  <chr>       <chr>      <chr>      <chr>      
-#> 1 2026-03-24 12:30:17     1 MIC    amoxicillin Escherich… human      8          
-#> 2 2026-03-24 12:30:17     1 MIC    cipro       Escherich… human      0.256      
-#> 3 2026-03-24 12:30:18     1 DISK   tobra       Escherich… human      16         
-#> 4 2026-03-24 12:30:18     1 DISK   genta       Escherich… human      18         
+#> 1 2026-03-30 08:14:10     1 MIC    amoxicillin Escherich… human      8          
+#> 2 2026-03-30 08:14:10     1 MIC    cipro       Escherich… human      0.256      
+#> 3 2026-03-30 08:14:10     1 DISK   tobra       Escherich… human      16         
+#> 4 2026-03-30 08:14:11     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>
--- a/reference/atc_online.html
+++ b/reference/atc_online.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/av_from_text.html
+++ b/reference/av_from_text.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/av_property.html
+++ b/reference/av_property.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/availability.html
+++ b/reference/availability.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/bug_drug_combinations.html
+++ b/reference/bug_drug_combinations.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/clinical_breakpoints.html
+++ b/reference/clinical_breakpoints.html
@@ -1,16 +1,16 @@
 <!DOCTYPE html>
 <!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with Clinical Breakpoints for SIR Interpretation — clinical_breakpoints"><meta name="description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This data set contains breakpoints for humans, 7 different animal groups, and ECOFFs.
 These breakpoints are currently implemented:
-For clinical microbiology: EUCAST 2011-2025 and CLSI 2011-2025;
-For veterinary microbiology: EUCAST 2021-2025 and CLSI 2019-2025;
-For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
+For clinical microbiology: EUCAST 2011-2026 and CLSI 2011-2026;
+For veterinary microbiology: EUCAST 2021-2026 and CLSI 2019-2026;
+For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2026 and CLSI 2022-2026.


 Use as.sir() to transform MICs or disks measurements to SIR values."><meta property="og:description" content="Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This data set contains breakpoints for humans, 7 different animal groups, and ECOFFs.
 These breakpoints are currently implemented:
-For clinical microbiology: EUCAST 2011-2025 and CLSI 2011-2025;
-For veterinary microbiology: EUCAST 2021-2025 and CLSI 2019-2025;
-For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.
+For clinical microbiology: EUCAST 2011-2026 and CLSI 2011-2026;
+For veterinary microbiology: EUCAST 2021-2026 and CLSI 2019-2026;
+For ECOFFs (Epidemiological Cut-off Values): EUCAST 2020-2026 and CLSI 2022-2026.


 Use as.sir() to transform MICs or disks measurements to SIR values."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
@@ -65,9 +65,9 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope

    <div class="ref-description section level2">
    <p>Data set containing clinical breakpoints to interpret MIC and disk diffusion to SIR values, according to international guidelines. This data set contains breakpoints for humans, 7 different animal groups, and ECOFFs.</p>
-<p>These breakpoints are currently implemented:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2025 and CLSI 2011-2025;</p></li>
-<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2025 and CLSI 2019-2025;</p></li>
-<li><p>For <strong>ECOFFs</strong> (Epidemiological Cut-off Values): EUCAST 2020-2025 and CLSI 2022-2025.</p></li>
+<p>These breakpoints are currently implemented:</p><ul><li><p>For <strong>clinical microbiology</strong>: EUCAST 2011-2026 and CLSI 2011-2026;</p></li>
+<li><p>For <strong>veterinary microbiology</strong>: EUCAST 2021-2026 and CLSI 2019-2026;</p></li>
+<li><p>For <strong>ECOFFs</strong> (Epidemiological Cut-off Values): EUCAST 2020-2026 and CLSI 2022-2026.</p></li>
 </ul><p>Use <code><a href="as.sir.html">as.sir()</a></code> to transform MICs or disks measurements to SIR values.</p>
    </div>

@@ -78,7 +78,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope

    <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 40 217 observations and 14 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
+    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 45 797 observations and 14 variables:</p><ul><li><p><code>guideline</code><br> Name of the guideline</p></li>
 <li><p><code>type</code><br> Breakpoint type, either "ECOFF", "animal", or "human"</p></li>
 <li><p><code>host</code><br> Host of infectious agent. This is mostly useful for veterinary breakpoints and is either "ECOFF", "aquatic", "cats", "cattle", "dogs", "horse", "human", "poultry", or "swine"</p></li>
 <li><p><code>method</code><br> Testing method, either "DISK" or "MIC"</p></li>
@@ -91,7 +91,7 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
 <li><p><code>breakpoint_S</code><br> Lowest MIC value or highest number of millimetres that leads to "S"</p></li>
 <li><p><code>breakpoint_R</code><br> Highest MIC value or lowest number of millimetres that leads to "R", can be <code>NA</code></p></li>
 <li><p><code>uti</code><br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> value (<code>TRUE</code>/<code>FALSE</code>) to indicate whether the rule applies to a urinary tract infection (UTI)</p></li>
-<li><p><code>is_SDD</code><br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> value (<code>TRUE</code>/<code>FALSE</code>) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to 48 breakpoints.</p></li>
+<li><p><code>is_SDD</code><br> A <a href="https://rdrr.io/r/base/logical.html" class="external-link">logical</a> value (<code>TRUE</code>/<code>FALSE</code>) to indicate whether the intermediate range between "S" and "R" should be interpreted as "SDD", instead of "I". This currently applies to 72 breakpoints.</p></li>
 </ul></div>
    <div class="section level2">
    <h2 id="details">Details<a class="anchor" aria-label="anchor" href="#details"></a></h2>
@@ -143,20 +143,20 @@ Use as.sir() to transform MICs or disks measurements to SIR values."><meta prope
    <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">clinical_breakpoints</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 40,217 × 14</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 45,797 × 14</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    guideline   type  host  method site    mo            rank_index ab   ref_tbl </span>
 <span class="r-out co"><span class="r-pr">#&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 style="color: #949494; font-style: italic;">&lt;mo&gt;</span>               <span style="color: #949494; font-style: italic;">&lt;dbl&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> EUCAST 2025 human human DISK   <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS          2 MEM  A. xylo…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2025 human human MIC    <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS          2 MEM  A. xylo…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2025 human human DISK   <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS          2 SXT  A. xylo…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2025 human human MIC    <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS          2 SXT  A. xylo…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2025 human human DISK   <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS          2 TZP  A. xylo…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2025 human human MIC    <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS          2 TZP  A. xylo…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2025 human human DISK   <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACNTB                3 AMK  Acineto…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2025 human human DISK   Uncomp… <span style="color: #949494;">B_</span>ACNTB                3 AMK  Acineto…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2025 human human MIC    <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACNTB                3 AMK  Acineto…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> EUCAST 2025 human human MIC    Uncomp… <span style="color: #949494;">B_</span>ACNTB                3 AMK  Acineto…</span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 40,207 more rows</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> EUCAST 2026 human human DISK   <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS          2 MEM  A. xylo…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 2</span> EUCAST 2026 human human MIC    <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS          2 MEM  A. xylo…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 3</span> EUCAST 2026 human human DISK   <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS          2 SXT  A. xylo…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 4</span> EUCAST 2026 human human MIC    <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS          2 SXT  A. xylo…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 5</span> EUCAST 2026 human human DISK   <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS          2 TZP  A. xylo…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 6</span> EUCAST 2026 human human MIC    <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACHRMB<span style="color: #949494;">_</span>XYLS          2 TZP  A. xylo…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 7</span> EUCAST 2026 human human DISK   <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACNTB                3 AMK  Acineto…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> EUCAST 2026 human human DISK   Uncomp… <span style="color: #949494;">B_</span>ACNTB                3 AMK  Acineto…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> EUCAST 2026 human human MIC    <span style="color: #BB0000;">NA</span>      <span style="color: #949494;">B_</span>ACNTB                3 AMK  Acineto…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> EUCAST 2026 human human MIC    Uncomp… <span style="color: #949494;">B_</span>ACNTB                3 AMK  Acineto…</span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 45,787 more rows</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 5 more variables: disk_dose &lt;chr&gt;, breakpoint_S &lt;dbl&gt;, breakpoint_R &lt;dbl&gt;,</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;">#   uti &lt;lgl&gt;, is_SDD &lt;lgl&gt;</span></span>
 </code></pre></div>
--- a/reference/clinical_breakpoints.md
+++ b/reference/clinical_breakpoints.md
@@ -7,12 +7,12 @@ ECOFFs.

 These breakpoints are currently implemented:

- For **clinical microbiology**: EUCAST 2011-2025 and CLSI 2011-2025;
+- For **clinical microbiology**: EUCAST 2011-2026 and CLSI 2011-2026;

- For **veterinary microbiology**: EUCAST 2021-2025 and CLSI 2019-2025;
+- For **veterinary microbiology**: EUCAST 2021-2026 and CLSI 2019-2026;

- For **ECOFFs** (Epidemiological Cut-off Values): EUCAST 2020-2025 and
-  CLSI 2022-2025.
+- For **ECOFFs** (Epidemiological Cut-off Values): EUCAST 2020-2026 and
+  CLSI 2022-2026.

 Use [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) to transform
 MICs or disks measurements to SIR values.
@@ -25,8 +25,8 @@ clinical_breakpoints

 ## Format

-A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 40
-217 observations and 14 variables:
+A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 45
+797 observations and 14 variables:

 - `guideline`  
  Name of the guideline
@@ -80,7 +80,7 @@ A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 40
  A [logical](https://rdrr.io/r/base/logical.html) value
  (`TRUE`/`FALSE`) to indicate whether the intermediate range between
  "S" and "R" should be interpreted as "SDD", instead of "I". This
-  currently applies to 48 breakpoints.
+  currently applies to 72 breakpoints.

 ## Details

@@ -154,20 +154,20 @@ repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).

 ``` r
 clinical_breakpoints
-#> # A tibble: 40,217 × 14
+#> # A tibble: 45,797 × 14
 #>    guideline   type  host  method site    mo            rank_index ab   ref_tbl 
 #>    <chr>       <chr> <chr> <chr>  <chr>   <mo>               <dbl> <ab> <chr>   
-#>  1 EUCAST 2025 human human DISK   NA      B_ACHRMB_XYLS          2 MEM  A. xylo…
-#>  2 EUCAST 2025 human human MIC    NA      B_ACHRMB_XYLS          2 MEM  A. xylo…
-#>  3 EUCAST 2025 human human DISK   NA      B_ACHRMB_XYLS          2 SXT  A. xylo…
-#>  4 EUCAST 2025 human human MIC    NA      B_ACHRMB_XYLS          2 SXT  A. xylo…
-#>  5 EUCAST 2025 human human DISK   NA      B_ACHRMB_XYLS          2 TZP  A. xylo…
-#>  6 EUCAST 2025 human human MIC    NA      B_ACHRMB_XYLS          2 TZP  A. xylo…
-#>  7 EUCAST 2025 human human DISK   NA      B_ACNTB                3 AMK  Acineto…
-#>  8 EUCAST 2025 human human DISK   Uncomp… B_ACNTB                3 AMK  Acineto…
-#>  9 EUCAST 2025 human human MIC    NA      B_ACNTB                3 AMK  Acineto…
-#> 10 EUCAST 2025 human human MIC    Uncomp… B_ACNTB                3 AMK  Acineto…
-#> # ℹ 40,207 more rows
+#>  1 EUCAST 2026 human human DISK   NA      B_ACHRMB_XYLS          2 MEM  A. xylo…
+#>  2 EUCAST 2026 human human MIC    NA      B_ACHRMB_XYLS          2 MEM  A. xylo…
+#>  3 EUCAST 2026 human human DISK   NA      B_ACHRMB_XYLS          2 SXT  A. xylo…
+#>  4 EUCAST 2026 human human MIC    NA      B_ACHRMB_XYLS          2 SXT  A. xylo…
+#>  5 EUCAST 2026 human human DISK   NA      B_ACHRMB_XYLS          2 TZP  A. xylo…
+#>  6 EUCAST 2026 human human MIC    NA      B_ACHRMB_XYLS          2 TZP  A. xylo…
+#>  7 EUCAST 2026 human human DISK   NA      B_ACNTB                3 AMK  Acineto…
+#>  8 EUCAST 2026 human human DISK   Uncomp… B_ACNTB                3 AMK  Acineto…
+#>  9 EUCAST 2026 human human MIC    NA      B_ACNTB                3 AMK  Acineto…
+#> 10 EUCAST 2026 human human MIC    Uncomp… B_ACNTB                3 AMK  Acineto…
+#> # ℹ 45,787 more rows
 #> # ℹ 5 more variables: disk_dose <chr>, breakpoint_S <dbl>, breakpoint_R <dbl>,
 #> #   uti <lgl>, is_SDD <lgl>
 ```
--- a/reference/count.html
+++ b/reference/count.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/custom_eucast_rules.html
+++ b/reference/custom_eucast_rules.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/custom_mdro_guideline.html
+++ b/reference/custom_mdro_guideline.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/dosage.html
+++ b/reference/dosage.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/esbl_isolates.html
+++ b/reference/esbl_isolates.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/example_isolates.html
+++ b/reference/example_isolates.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/example_isolates_unclean.html
+++ b/reference/example_isolates_unclean.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/export_ncbi_biosample.html
+++ b/reference/export_ncbi_biosample.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/first_isolate.html
+++ b/reference/first_isolate.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/g.test.html
+++ b/reference/g.test.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/get_episode.html
+++ b/reference/get_episode.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/ggplot_pca.html
+++ b/reference/ggplot_pca.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/ggplot_sir.html
+++ b/reference/ggplot_sir.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/guess_ab_col.html
+++ b/reference/guess_ab_col.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/index.html
+++ b/reference/index.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
@@ -421,7 +421,7 @@
          <code><a href="microorganisms.codes.html">microorganisms.codes</a></code>

        </dt>
-        <dd>Data Set with 6 036 Common Microorganism Codes</dd>
+        <dd>Data Set with 6 050 Common Microorganism Codes</dd>

        <dt>

--- a/reference/index.md
+++ b/reference/index.md
@@ -402,7 +402,7 @@ information about how to work with functions in this package.
 - [`esbl_isolates`](https://amr-for-r.org/reference/esbl_isolates.md) :
  Data Set with 500 ESBL Isolates
 - [`microorganisms.codes`](https://amr-for-r.org/reference/microorganisms.codes.md)
-  : Data Set with 6 036 Common Microorganism Codes
+  : Data Set with 6 050 Common Microorganism Codes
 - [`microorganisms.groups`](https://amr-for-r.org/reference/microorganisms.groups.md)
  : Data Set with 534 Microorganisms In Species Groups
 - [`intrinsic_resistant`](https://amr-for-r.org/reference/intrinsic_resistant.md)
--- a/reference/interpretive_rules.html
+++ b/reference/interpretive_rules.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/intrinsic_resistant.html
+++ b/reference/intrinsic_resistant.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/italicise_taxonomy.html
+++ b/reference/italicise_taxonomy.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/join.html
+++ b/reference/join.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/key_antimicrobials.html
+++ b/reference/key_antimicrobials.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/kurtosis.html
+++ b/reference/kurtosis.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/like.html
+++ b/reference/like.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/mdro.html
+++ b/reference/mdro.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/mean_amr_distance.html
+++ b/reference/mean_amr_distance.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/microorganisms.codes.html
+++ b/reference/microorganisms.codes.html
@@ -1,5 +1,5 @@
 <!DOCTYPE html>
-<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Set with 6 036 Common Microorganism Codes — microorganisms.codes • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 6 036 Common Microorganism Codes — microorganisms.codes"><meta name="description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions."><meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
+<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><title>Data Set with 6 050 Common Microorganism Codes — microorganisms.codes • AMR (for R)</title><!-- favicons --><link rel="icon" type="image/png" sizes="96x96" href="../favicon-96x96.png"><link rel="icon" type="”image/svg+xml”" href="../favicon.svg"><link rel="apple-touch-icon" sizes="180x180" href="../apple-touch-icon.png"><link rel="icon" sizes="any" href="../favicon.ico"><link rel="manifest" href="../site.webmanifest"><script src="../deps/jquery-3.6.0/jquery-3.6.0.min.js"></script><meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no"><link href="../deps/bootstrap-5.3.1/bootstrap.min.css" rel="stylesheet"><script src="../deps/bootstrap-5.3.1/bootstrap.bundle.min.js"></script><link href="../deps/Lato-0.4.10/font.css" rel="stylesheet"><link href="../deps/Fira_Code-0.4.10/font.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/all.min.css" rel="stylesheet"><link href="../deps/font-awesome-6.5.2/css/v4-shims.min.css" rel="stylesheet"><script src="../deps/headroom-0.11.0/headroom.min.js"></script><script src="../deps/headroom-0.11.0/jQuery.headroom.min.js"></script><script src="../deps/bootstrap-toc-1.0.1/bootstrap-toc.min.js"></script><script src="../deps/clipboard.js-2.0.11/clipboard.min.js"></script><script src="../deps/search-1.0.0/autocomplete.jquery.min.js"></script><script src="../deps/search-1.0.0/fuse.min.js"></script><script src="../deps/search-1.0.0/mark.min.js"></script><!-- pkgdown --><script src="../pkgdown.js"></script><link href="../extra.css" rel="stylesheet"><script src="../extra.js"></script><meta property="og:title" content="Data Set with 6 050 Common Microorganism Codes — microorganisms.codes"><meta name="description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions."><meta property="og:description" content="A data set containing commonly used codes for microorganisms, from laboratory systems and WHONET. Define your own with set_mo_source(). They will all be searched when using as.mo() and consequently all the mo_* functions."><meta property="og:image" content="https://amr-for-r.org/logo.svg"><link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.css" integrity="sha384-nB0miv6/jRmo5UMMR1wu3Gz6NLsoTkbqJghGIsx//Rlm+ZU03BU6SQNC66uf4l5+" crossorigin="anonymous"><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/katex.min.js" integrity="sha384-7zkQWkzuo3B5mTepMUcHkMB5jZaolc2xDwL6VFqjFALcbeS9Ggm/Yr2r3Dy4lfFg" crossorigin="anonymous"></script><script defer src="https://cdn.jsdelivr.net/npm/katex@0.16.11/dist/contrib/auto-render.min.js" integrity="sha384-43gviWU0YVjaDtb/GhzOouOXtZMP/7XUzwPTstBeZFe/+rCMvRwr4yROQP43s0Xk" crossorigin="anonymous" onload="renderMathInElement(document.body);"></script></head><body>
    <a href="#main" class="visually-hidden-focusable">Skip to contents</a>


@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
@@ -44,7 +44,7 @@
 </nav><div class="container template-reference-topic">
 <div class="row">
  <main id="main" class="col-md-9"><div class="page-header">
-      <img src="../logo.svg" class="logo" alt=""><h1>Data Set with 6 036 Common Microorganism Codes</h1>
+      <img src="../logo.svg" class="logo" alt=""><h1>Data Set with 6 050 Common Microorganism Codes</h1>
      <small class="dont-index">Source: <a href="https://github.com/msberends/AMR/blob/main/R/data.R" class="external-link"><code>R/data.R</code></a></small>
      <div class="d-none name"><code>microorganisms.codes.Rd</code></div>
    </div>
@@ -60,7 +60,7 @@

    <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 6 036 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism. <em><strong>This is a unique identifier.</strong></em></p></li>
+    <p>A <a href="https://tibble.tidyverse.org/reference/tibble.html" class="external-link">tibble</a> with 6 050 observations and 2 variables:</p><ul><li><p><code>code</code><br> Commonly used code of a microorganism. <em><strong>This is a unique identifier.</strong></em></p></li>
 <li><p><code>mo</code><br> ID of the microorganism in the <a href="microorganisms.html">microorganisms</a> data set</p></li>
 </ul></div>
    <div class="section level2">
@@ -79,7 +79,7 @@
    <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">microorganisms.codes</span></span></span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 6,036 × 2</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># A tibble: 6,050 × 2</span></span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    code  mo               </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span>    <span style="color: #949494; font-style: italic;">&lt;chr&gt;</span> <span style="color: #949494; font-style: italic;">&lt;mo&gt;</span>             </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 1</span> 1011  <span style="color: #949494;">B_</span>GRAMP          </span>
@@ -92,7 +92,7 @@
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 8</span> 1100  <span style="color: #949494;">B_</span>STRPT          </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;"> 9</span> 1101  <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>VIRI     </span>
 <span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #BCBCBC;">10</span> 1102  <span style="color: #949494;">B_</span>STRPT<span style="color: #949494;">_</span>HAEM     </span>
-<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 6,026 more rows</span></span>
+<span class="r-out co"><span class="r-pr">#&gt;</span> <span style="color: #949494;"># ℹ 6,040 more rows</span></span>
 <span class="r-in"><span></span></span>
 <span class="r-in"><span><span class="co"># 'ECO' or 'eco' is the WHONET code for E. coli:</span></span></span>
 <span class="r-in"><span><span class="va">microorganisms.codes</span><span class="op">[</span><span class="va">microorganisms.codes</span><span class="op">$</span><span class="va">code</span> <span class="op">==</span> <span class="st">"ECO"</span>, <span class="op">]</span></span></span>
--- a/reference/microorganisms.codes.md
+++ b/reference/microorganisms.codes.md
@@ -1,4 +1,4 @@
-# Data Set with 6 036 Common Microorganism Codes
+# Data Set with 6 050 Common Microorganism Codes

 A data set containing commonly used codes for microorganisms, from
 laboratory systems and [WHONET](https://whonet.org). Define your own
@@ -17,7 +17,7 @@ microorganisms.codes
 ## Format

 A [tibble](https://tibble.tidyverse.org/reference/tibble.html) with 6
-036 observations and 2 variables:
+050 observations and 2 variables:

 - `code`  
  Commonly used code of a microorganism. ***This is a unique
@@ -53,7 +53,7 @@ repository](https://github.com/msberends/AMR/tree/main/data-raw/datasets).

 ``` r
 microorganisms.codes
-#> # A tibble: 6,036 × 2
+#> # A tibble: 6,050 × 2
 #>    code  mo               
 #>    <chr> <mo>             
 #>  1 1011  B_GRAMP          
@@ -66,7 +66,7 @@ microorganisms.codes
 #>  8 1100  B_STRPT          
 #>  9 1101  B_STRPT_VIRI     
 #> 10 1102  B_STRPT_HAEM     
-#> # ℹ 6,026 more rows
+#> # ℹ 6,040 more rows

 # 'ECO' or 'eco' is the WHONET code for E. coli:
 microorganisms.codes[microorganisms.codes$code == "ECO", ]
--- a/reference/microorganisms.groups.html
+++ b/reference/microorganisms.groups.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/microorganisms.html
+++ b/reference/microorganisms.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/mo_matching_score.html
+++ b/reference/mo_matching_score.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/mo_property.html
+++ b/reference/mo_property.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/mo_source.html
+++ b/reference/mo_source.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/pca.html
+++ b/reference/pca.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/plot-15.png
+++ b/reference/plot-15.png
--- a/reference/plot-17.png
+++ b/reference/plot-17.png
--- a/reference/plot-18.png
+++ b/reference/plot-18.png
--- a/reference/plot-2.png
+++ b/reference/plot-2.png
--- a/reference/plot-3.png
+++ b/reference/plot-3.png
--- a/reference/plot.html
+++ b/reference/plot.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
@@ -291,7 +291,7 @@ Especially the scale_*_mic() functions are relevant wrappers to plot MIC values
 <li><p><code>theme_sir()</code> is a <a href="https://ggplot2.tidyverse.org/reference/theme.html" class="external-link">ggplot2 theme</a> with minimal distraction.</p></li>
 <li><p><code>labels_sir_count()</code> print datalabels on the bars with percentage and number of isolates, using <code><a href="https://ggplot2.tidyverse.org/reference/geom_text.html" class="external-link">ggplot2::geom_text()</a></code>.</p></li>
 </ul><p>The interpretation of "I" will be named "Increased exposure" for all EUCAST guidelines since 2019, and will be named "Intermediate" in all other cases.</p>
-<p>For interpreting MIC values as well as disk diffusion diameters, the default guideline is EUCAST 2025, unless the package option <code><a href="AMR-options.html">AMR_guideline</a></code> is set. See <code><a href="as.sir.html">as.sir()</a></code> for more information.</p>
+<p>For interpreting MIC values as well as disk diffusion diameters, the default guideline is EUCAST 2026, unless the package option <code><a href="AMR-options.html">AMR_guideline</a></code> is set. See <code><a href="as.sir.html">as.sir()</a></code> for more information.</p>
 </div>

    </div>
--- a/reference/plot.md
+++ b/reference/plot.md
@@ -336,7 +336,7 @@ EUCAST guidelines since 2019, and will be named "Intermediate" in all
 other cases.

 For interpreting MIC values as well as disk diffusion diameters, the
-default guideline is EUCAST 2025, unless the package option
+default guideline is EUCAST 2026, unless the package option
 [`AMR_guideline`](https://amr-for-r.org/reference/AMR-options.md) is
 set. See [`as.sir()`](https://amr-for-r.org/reference/as.sir.md) for
 more information.
--- a/reference/proportion.html
+++ b/reference/proportion.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/random.html
+++ b/reference/random.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/resistance_predict.html
+++ b/reference/resistance_predict.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/skewness.html
+++ b/reference/skewness.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/top_n_microorganisms.html
+++ b/reference/top_n_microorganisms.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">
--- a/reference/translate.html
+++ b/reference/translate.html
@@ -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="">3.0.1.9040</small>
+    <small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9041</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">