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@@ -9,7 +9,7 @@ options(AMR_guideline = "CLSI")'><meta property="og:image" content="https://amr-
<a class="navbar-brand me-2" href="../index.html">AMR (for R)</a>
<small class="nav-text text-muted me-auto" data-bs-toggle="tooltip" data-bs-placement="bottom" title="">3.0.1.9040</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>