To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see Details."><metaproperty="og:image"content="https://msberends.github.io/AMR/logo.svg"><metaname="twitter:card"content="summary_large_image"><metaname="twitter:creator"content="@msberends"><metaname="twitter:site"content="@univgroningen"><!-- mathjax --><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js"integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k="crossorigin="anonymous"></script><scriptsrc="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js"integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA="crossorigin="anonymous"></script><!--[if lt IE 9]>
<p>Apply rules for clinical breakpoints and intrinsic resistance as defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST, <ahref="https://eucast.org"class="external-link">https://eucast.org</a>), see <em>Source</em>. Use <code>eucast_dosage()</code> to get a <ahref="https://rdrr.io/r/base/data.frame.html"class="external-link">data.frame</a> with advised dosages of a certain bug-drug combination, which is based on the <ahref="dosage.html">dosage</a> data set.</p>
<p>To improve the interpretation of the antibiogram before EUCAST rules are applied, some non-EUCAST rules can applied at default, see <em>Details</em>.</p>
info <spanclass="op">=</span><spanclass="fu"><ahref="https://rdrr.io/r/base/interactive.html"class="external-link">interactive</a></span><spanclass="op">(</span><spanclass="op">)</span>,
<li><p>EUCAST Expert Rules, Intrinsic Resistance and Exceptional Phenotypes Tables. Version 3.1, 2016. <ahref="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/Expert_rules_intrinsic_exceptional_V3.1.pdf"class="external-link">(link)</a></p></li>
<li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.2, 2020. <ahref="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2020/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.2_20200225.pdf"class="external-link">(link)</a></p></li>
<li><p>EUCAST Intrinsic Resistance and Unusual Phenotypes. Version 3.3, 2021. <ahref="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Expert_Rules/2021/Intrinsic_Resistance_and_Unusual_Phenotypes_Tables_v3.3_20211018.pdf"class="external-link">(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 9.0, 2019. <ahref="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_9.0_Breakpoint_Tables.xlsx"class="external-link">(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 10.0, 2020. <ahref="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_10.0_Breakpoint_Tables.xlsx"class="external-link">(link)</a></p></li>
<li><p>EUCAST Breakpoint tables for interpretation of MICs and zone diameters. Version 11.0, 2021. <ahref="https://www.eucast.org/fileadmin/src/media/PDFs/EUCAST_files/Breakpoint_tables/v_11.0_Breakpoint_Tables.xlsx"class="external-link">(link)</a></p></li>
</ul></div>
<divid="arguments">
<h2>Arguments</h2>
<dl><dt>x</dt>
<dd><p>data with antibiotic columns, such as <code>amox</code>, <code>AMX</code> and <code>AMC</code></p></dd>
<dt>col_mo</dt>
<dd><p>column name of the IDs of the microorganisms (see <code><ahref="as.mo.html">as.mo()</a></code>), defaults to the first column of class <code><ahref="as.mo.html">mo</a></code>. Values will be coerced using <code><ahref="as.mo.html">as.mo()</a></code>.</p></dd>
<dt>info</dt>
<dd><p>a <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a> to indicate whether progress should be printed to the console, defaults to only print while in interactive sessions</p></dd>
<dt>rules</dt>
<dd><p>a <ahref="https://rdrr.io/r/base/character.html"class="external-link">character</a> vector that specifies which rules should be applied. 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>. The default value can be set to another value, e.g. using <code>options(AMR_eucastrules = "all")</code>. If using <code>"custom"</code>, be sure to fill in argument <code>custom_rules</code> too. Custom rules can be created with <code><ahref="custom_eucast_rules.html">custom_eucast_rules()</a></code>.</p></dd>
<dt>verbose</dt>
<dd><p>a <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a> to turn Verbose mode on and off (default is off). In Verbose mode, the function does not apply rules to the data, but instead returns a data set in logbook form with extensive info about which rows and columns would be effected and in which way. Using Verbose mode takes a lot more time.</p></dd>
<dt>version_breakpoints</dt>
<dd><p>the version number to use for the EUCAST Clinical Breakpoints guideline. Can be either "11.0" or "10.0".</p></dd>
<dt>version_expertrules</dt>
<dd><p>the version number to use for the EUCAST Expert Rules and Intrinsic Resistance guideline. Can be either "3.3", "3.2" or "3.1".</p></dd>
<dd><p>a <ahref="https://rdrr.io/r/base/character.html"class="external-link">character</a> value that should be applied to cefotaxime, ceftriaxone and ceftazidime for AmpC de-repressed cephalosporin-resistant mutants, defaults to <code>NA</code>. Currently only works when <code>version_expertrules</code> is <code>3.2</code> and higher; these version of '<em>EUCAST Expert Rules on Enterobacterales</em>' state that results of cefotaxime, ceftriaxone and ceftazidime should be reported with a note, or results should be suppressed (emptied) for these three agents. A value of <code>NA</code> (the default) for this argument will remove results for these three agents, while e.g. a value of <code>"R"</code> will make the results for these agents resistant. Use <code>NULL</code> or <code>FALSE</code> to not alter results for these three agents of AmpC de-repressed cephalosporin-resistant mutants. Using <code>TRUE</code> is equal to using <code>"R"</code>. <br> For <em>EUCAST Expert Rules</em> v3.2, this rule applies to: <em>Citrobacter braakii</em>, <em>Citrobacter freundii</em>, <em>Citrobacter gillenii</em>, <em>Citrobacter murliniae</em>, <em>Citrobacter rodenticum</em>, <em>Citrobacter sedlakii</em>, <em>Citrobacter werkmanii</em>, <em>Citrobacter youngae</em>, <em>Enterobacter</em>, <em>Hafnia alvei</em>, <em>Klebsiella aerogenes</em>, <em>Morganella morganii</em>, <em>Providencia</em> and <em>Serratia</em>.</p></dd>
<dd><p>a <ahref="https://rdrr.io/r/base/logical.html"class="external-link">logical</a> to indicate whether only antibiotic columns must be detected that were transformed to class <code><rsi></code> (see <code><ahref="as.rsi.html">as.rsi()</a></code>) on beforehand (defaults to <code>FALSE</code>)</p></dd>
<dt>custom_rules</dt>
<dd><p>custom rules to apply, created with <code><ahref="custom_eucast_rules.html">custom_eucast_rules()</a></code></p></dd>
<dt>...</dt>
<dd><p>column name of an antibiotic, see section <em>Antibiotics</em> below</p></dd>
<dt>ab</dt>
<dd><p>any (vector of) text that can be coerced to a valid antibiotic code with <code><ahref="as.ab.html">as.ab()</a></code></p></dd>
<dt>administration</dt>
<dd><p>route of administration, either "im", "iv" or "oral"</p></dd>
</dl></div>
<divid="value">
<h2>Value</h2>
<p>The input of <code>x</code>, possibly with edited values of antibiotics. Or, if <code>verbose = TRUE</code>, a <ahref="https://rdrr.io/r/base/data.frame.html"class="external-link">data.frame</a> with all original and new values of the affected bug-drug combinations.</p>
</div>
<divid="details">
<h2>Details</h2>
<p><strong>Note:</strong> This function does not translate MIC values to RSI values. Use <code><ahref="as.rsi.html">as.rsi()</a></code> for that. <br><strong>Note:</strong> When ampicillin (AMP, J01CA01) is not available but amoxicillin (AMX, J01CA04) is, the latter will be used for all rules where there is a dependency on ampicillin. These drugs are interchangeable when it comes to expression of antimicrobial resistance. <br></p>
<p>The file containing all EUCAST rules is located here: <ahref="https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv"class="external-link">https://github.com/msberends/AMR/blob/main/data-raw/eucast_rules.tsv</a>. <strong>Note:</strong> Old taxonomic names are replaced with the current taxonomy where applicable. For example, <em>Ochrobactrum anthropi</em> was renamed to <em>Brucella anthropi</em> in 2020; the original EUCAST rules v3.1 and v3.2 did not yet contain this new taxonomic name. The file used as input for this <code>AMR</code> package contains the taxonomy updated until <ahref="catalogue_of_life.html">5 October 2021</a>.</p><divclass="section">
<p>Before further processing, two non-EUCAST rules about drug combinations can be applied to improve the efficacy of the EUCAST rules, and the reliability of your data (analysis). These rules are:</p><ol><li><p>A drug <strong>with</strong> enzyme inhibitor will be set to S if the same drug <strong>without</strong> enzyme inhibitor is S</p></li>
</ol><p>Important examples include amoxicillin and amoxicillin/clavulanic acid, and trimethoprim and trimethoprim/sulfamethoxazole. Needless to say, for these rules to work, both drugs must be available in the data set.</p>
<p>Since these rules are not officially approved by EUCAST, they are not applied at default. To use these rules, include <code>"other"</code> to the <code>rules</code> argument, or use <code>eucast_rules(..., rules = "all")</code>. You can also set the option <code>AMR_eucastrules</code>, i.e. run <code>options(AMR_eucastrules = "all")</code>.</p>
<p>To define antibiotics column names, leave as it is to determine it automatically with <code><ahref="guess_ab_col.html">guess_ab_col()</a></code> or input a text (case-insensitive), or use <code>NULL</code> to skip a column (e.g. <code>TIC = NULL</code> to skip ticarcillin). Manually defined but non-existing columns will be skipped with a warning.</p>
<p>The following antibiotics are eligible for the functions <code>eucast_rules()</code> and <code><ahref="mdro.html">mdro()</a></code>. These are shown below in the format 'name (<code>antimicrobial ID</code>, <ahref="https://www.whocc.no/atc/structure_and_principles/"class="external-link">ATC code</a>)', sorted alphabetically:</p>
The <ahref="lifecycle.html">lifecycle</a> of this function is <strong>stable</strong>. In a stable function, major changes are unlikely. This means that the unlying code will generally evolve by adding new arguments; removing arguments or changing the meaning of existing arguments will be avoided.</p>
<p>If the unlying code needs breaking changes, they will occur gradually. For example, an argument will be deprecated and first continue to work, but will emit a message informing you of the change. Next, typically after at least one newly released version on CRAN, the message will be transformed to an error.</p>
<p>All reference data sets (about microorganisms, antibiotics, R/SI interpretation, EUCAST rules, etc.) in this <code>AMR</code> package are publicly and freely available. We continually export our data sets to formats for use in R, SPSS, SAS, Stata and Excel. We also supply flat files that are machine-readable and suitable for input in any software program, such as laboratory information systems. Please find <ahref="https://msberends.github.io/AMR/articles/datasets.html">all download links on our website</a>, which is automatically updated with every code change.</p>
<p>On our website <ahref="https://msberends.github.io/AMR/">https://msberends.github.io/AMR/</a> you can find <ahref="https://msberends.github.io/AMR/articles/AMR.html">a comprehensive tutorial</a> about how to conduct AMR data analysis, the <ahref="https://msberends.github.io/AMR/reference/">complete documentation of all functions</a> and <ahref="https://msberends.github.io/AMR/articles/WHONET.html">an example analysis using WHONET data</a>.</p>
